Tue Dec 3 11:23:15 UTC 2024 I: starting to build gromacs/unstable/amd64 on jenkins on '2024-12-03 11:22' Tue Dec 3 11:23:15 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_34/38244/console.log Tue Dec 3 11:23:15 UTC 2024 I: Downloading source for unstable/gromacs=2024.4-1 --2024-12-03 11:23:15-- http://deb.debian.org/debian/pool/main/g/gromacs/gromacs_2024.4-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 3305 (3.2K) [text/prs.lines.tag] Saving to: ‘gromacs_2024.4-1.dsc’ 0K ... 100% 417M=0s 2024-12-03 11:23:16 (417 MB/s) - ‘gromacs_2024.4-1.dsc’ saved [3305/3305] Tue Dec 3 11:23:16 UTC 2024 I: gromacs_2024.4-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: gromacs Binary: gromacs, gromacs-data, libgromacs9, libgromacs-dev, libnblib-gmx0, libnblib-gmx-dev Architecture: any all Version: 2024.4-1 Maintainer: Debichem Team Uploaders: Nicholas Breen Homepage: https://www.gromacs.org/ Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/debichem-team/gromacs Vcs-Git: https://salsa.debian.org/debichem-team/gromacs.git Testsuite: autopkgtest Testsuite-Triggers: build-essential, mpi-default-bin, perl Build-Depends: architecture-is-64-bit, bash-completion, chrpath, cmake (>= 3.13), debhelper-compat (= 13), dh-python, libblas-dev, libboost-dev, libfftw3-dev, libhwloc-dev, liblapack-dev, libmuparser-dev (>= 2.3.4), lsb-release, mpi-default-bin, mpi-default-dev, pkgconf, python3-dev, python3-mpi4py, python3-networkx, python3-numpy, python3-pybind11, python3-pytest, zlib1g-dev Build-Depends-Indep: doxygen, furo, ghostscript, graphicsmagick, graphviz, mscgen, python3-pygments, python3-sphinx, python3-sphinx-argparse, python3-sphinx-copybutton, python3-sphinx-inline-tabs, python3-sphinxcontrib.autoprogram, python3-sphinxcontrib.plantuml, rdfind, symlinks, tex-gyre, texlive-fonts-recommended, texlive-latex-base, texlive-latex-extra Package-List: gromacs deb science optional arch=any gromacs-data deb science optional arch=all libgromacs-dev deb libdevel optional arch=any libgromacs9 deb libs optional arch=any libnblib-gmx-dev deb libdevel optional arch=any libnblib-gmx0 deb libs optional arch=any Checksums-Sha1: a390fa37578a2081c8becaf8241e3a00a0911b9d 32777006 gromacs_2024.4.orig-regressiontests.tar.gz 879ebba62023020fd3b53cfa60c89a8d942a8c68 42356162 gromacs_2024.4.orig.tar.gz 7d35d9269f64dff9b194865872f7dee5288ace37 38304 gromacs_2024.4-1.debian.tar.xz Checksums-Sha256: e24bb1588117055d5d94d14e8e47f759690b9903d93be9c1d5c599f8b977fd17 32777006 gromacs_2024.4.orig-regressiontests.tar.gz ac618ece2e58afa86b536c5a2c4fcb937f0760318f12d18f10346b6bdebd86a8 42356162 gromacs_2024.4.orig.tar.gz b3a36fcf8efced7bb90575d82a1088ee6bf3360ac5a03b196598492e95eea38e 38304 gromacs_2024.4-1.debian.tar.xz Files: d205b88092da42b04e112b636a7a7a77 32777006 gromacs_2024.4.orig-regressiontests.tar.gz 1ce06e1e330c7232e691c3cd7581aa75 42356162 gromacs_2024.4.orig.tar.gz 9e15b5de7b1061e142477c67ff73ebd9 38304 gromacs_2024.4-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEhD5fph5gYziYdtLl7kr9aexlEI8FAmclcwkSHG5icmVlbkBk ZWJpYW4ub3JnAAoJEO5K/WnsZRCP55IP/326BCeTnaL5Z2g6lHypZ4PgDKryY6d5 dzhgbYA9zL2OX2dQSnf1EoHfFWEHysdBMtpQ6azqjEav6rPpNmv6a8qEJsFTTsvx J3Djg/zAAqEiifHeo6mFTBfvXg+fm4vGS3AXTKB/H3dyzHXivAbhsnGXTRzVeNJG 2dwKwaLeDueDsFAh8t4Ptecl0rq08gc+R38oA/voak+3jAk9FySjcbFNk2i43qAl ELWX5tSmqKev8svaxDli8zS77I0FE1v6Oc0AdEEzryx6CNSghnadxZl45z72yZwq jX39aFVWyUKT3nmNYfk+HGglkd3Hi2LTq6AZ+gj+btNhIMUtVwMVfYcTrFIU0Xzx /a1n3UcxOjwl+T5sIApeF3+qqqVThkg0jr+Q6XC1mlO6vIXCFDU+Hb3/vNRBIJL9 zE0AvqNbKtDyvSaYt1HyiDJPafcdYgWOeOtWu2ZCJrX+13rSa01ZYPEGDNzaC+cx 8JBWkv2DW9MzOcGaij0nCan13xAx3EIW+qEw2s9JpgpBRkclkOmqp+IfymLkxVuc IMtYP0J5UxlI24KBqDVWk3X2dbq9k5myTsEKg5+y0qtsexqEfYfC5myEEyiPsC7O bX/N+o4Uzxh7z+bsaWS/zLNlEe9L/hh+AA44IS3RE8/0AD7HgT6IMSdEgyyB8Ezt Lq1V9aHEQ42r =35si -----END PGP SIGNATURE----- Tue Dec 3 11:23:16 UTC 2024 I: Checking whether the package is not for us Tue Dec 3 11:23:16 UTC 2024 I: Starting 1st build on remote node infom02-amd64.debian.net. Tue Dec 3 11:23:16 UTC 2024 I: Preparing to do remote build '1' on infom02-amd64.debian.net. Tue Dec 3 12:36:13 UTC 2024 I: Deleting $TMPDIR on infom02-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Jan 5 05:46:20 -12 2026 I: pbuilder-time-stamp: 1767635180 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [gromacs_2024.4-1.dsc] I: copying [./gromacs_2024.4.orig-regressiontests.tar.gz] I: copying [./gromacs_2024.4.orig.tar.gz] I: copying [./gromacs_2024.4-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Nov 2 00:32:09 2024 gpgv: using RSA key 843E5FA61E6063389876D2E5EE4AFD69EC65108F gpgv: issuer "nbreen@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./gromacs_2024.4-1.dsc: no acceptable signature found dpkg-source: info: extracting gromacs in gromacs-2024.4 dpkg-source: info: unpacking gromacs_2024.4.orig.tar.gz dpkg-source: info: unpacking gromacs_2024.4.orig-regressiontests.tar.gz dpkg-source: info: unpacking gromacs_2024.4-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying readme.patch dpkg-source: info: applying copyright-file.patch dpkg-source: info: applying disable-cpuinfotest.patch dpkg-source: info: applying mdrun-test-timeout.patch dpkg-source: info: applying manual-local-mathjax.patch dpkg-source: info: applying mpi-tests-localhost.patch dpkg-source: info: applying manual-image-conversion.patch dpkg-source: info: applying disable-gmxtimingtests.patch dpkg-source: info: applying script-shebang-line.patch dpkg-source: info: applying add-support-for-loong64.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3342599/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='03e5300fa8ee4f03bfceb967964a7552' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='3342599' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.lRBR3Ncd/pbuilderrc_spfZ --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.lRBR3Ncd/b1 --logfile b1/build.log gromacs_2024.4-1.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom02-amd64 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3342599/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: architecture-is-64-bit, bash-completion, chrpath, cmake (>= 3.13), debhelper-compat (= 13), dh-python, libblas-dev, libboost-dev, libfftw3-dev, libhwloc-dev, liblapack-dev, libmuparser-dev (>= 2.3.4), lsb-release, mpi-default-bin, mpi-default-dev, pkgconf, python3-dev, python3-mpi4py, python3-networkx, python3-numpy, python3-pybind11, python3-pytest, zlib1g-dev, doxygen, furo, ghostscript, graphicsmagick, graphviz, mscgen, python3-pygments, python3-sphinx, python3-sphinx-argparse, python3-sphinx-copybutton, python3-sphinx-inline-tabs, python3-sphinxcontrib.autoprogram, python3-sphinxcontrib.plantuml, rdfind, symlinks, tex-gyre, texlive-fonts-recommended, texlive-latex-base, texlive-latex-extra dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19968 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on architecture-is-64-bit; however: Package architecture-is-64-bit is not installed. pbuilder-satisfydepends-dummy depends on bash-completion; however: Package bash-completion is not installed. pbuilder-satisfydepends-dummy depends on chrpath; however: Package chrpath is not installed. pbuilder-satisfydepends-dummy depends on cmake (>= 3.13); however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on libblas-dev; however: Package libblas-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libfftw3-dev; however: Package libfftw3-dev is not installed. pbuilder-satisfydepends-dummy depends on libhwloc-dev; however: Package libhwloc-dev is not installed. pbuilder-satisfydepends-dummy depends on liblapack-dev; however: Package liblapack-dev is not installed. pbuilder-satisfydepends-dummy depends on libmuparser-dev (>= 2.3.4); however: Package libmuparser-dev is not installed. pbuilder-satisfydepends-dummy depends on lsb-release; however: Package lsb-release is not installed. pbuilder-satisfydepends-dummy depends on mpi-default-bin; however: Package mpi-default-bin is not installed. pbuilder-satisfydepends-dummy depends on mpi-default-dev; however: Package mpi-default-dev is not installed. pbuilder-satisfydepends-dummy depends on pkgconf; however: Package pkgconf is not installed. pbuilder-satisfydepends-dummy depends on python3-dev; however: Package python3-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-mpi4py; however: Package python3-mpi4py is not installed. pbuilder-satisfydepends-dummy depends on python3-networkx; however: Package python3-networkx is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-pybind11; however: Package python3-pybind11 is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on doxygen; however: Package doxygen is not installed. pbuilder-satisfydepends-dummy depends on furo; however: Package furo is not installed. pbuilder-satisfydepends-dummy depends on ghostscript; however: Package ghostscript is not installed. pbuilder-satisfydepends-dummy depends on graphicsmagick; however: Package graphicsmagick is not installed. pbuilder-satisfydepends-dummy depends on graphviz; however: Package graphviz is not installed. pbuilder-satisfydepends-dummy depends on mscgen; however: Package mscgen is not installed. pbuilder-satisfydepends-dummy depends on python3-pygments; however: Package python3-pygments is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-argparse; however: Package python3-sphinx-argparse is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-copybutton; however: Package python3-sphinx-copybutton is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-inline-tabs; however: Package python3-sphinx-inline-tabs is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinxcontrib.autoprogram; however: Package python3-sphinxcontrib.autoprogram is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinxcontrib.plantuml; however: Package python3-sphinxcontrib.plantuml is not installed. pbuilder-satisfydepends-dummy depends on rdfind; however: Package rdfind is not installed. pbuilder-satisfydepends-dummy depends on symlinks; however: Package symlinks is not installed. pbuilder-satisfydepends-dummy depends on tex-gyre; however: Package tex-gyre is not installed. pbuilder-satisfydepends-dummy depends on texlive-fonts-recommended; however: Package texlive-fonts-recommended is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-base; however: Package texlive-latex-base is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-extra; however: Package texlive-latex-extra is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: ant{a} ant-optional{a} architecture-properties{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bash-completion{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} chrpath{a} cmake{a} cmake-data{a} debhelper{a} default-jre-headless{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} doxygen{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-lmodern{a} fonts-urw-base35{a} furo{a} gettext{a} gettext-base{a} gfortran-14{a} gfortran-14-x86-64-linux-gnu{a} ghostscript{a} graphicsmagick{a} graphviz{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} java-common{a} java-wrappers{a} libabsl20230802{a} libamd-comgr2{a} libamdhip64-5{a} libann0{a} libaom3{a} libapache-pom-java{a} libarchive-zip-perl{a} libarchive13t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libavalon-framework-java{a} libavif16{a} libbatik-java{a} libbcpkix-java{a} libbcprov-java{a} libbcutil-java{a} libblas-dev{a} libblas3{a} libboost-dev{a} libboost1.83-dev{a} libbrotli1{a} libcairo2{a} libcbor0.10{a} libcdt5{a} libcgraph6{a} libclang-cpp19{a} libclang1-19{a} libcom-err2{a} libcommons-io-java{a} libcommons-logging-java{a} libcommons-parent-java{a} libcups2t64{a} libcurl4t64{a} libdatrie1{a} libdav1d7{a} libdbus-1-3{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm2{a} libedit2{a} libelf1t64{a} libevent-2.1-7t64{a} libevent-core-2.1-7t64{a} libevent-dev{a} libevent-extra-2.1-7t64{a} libevent-openssl-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libexpat1{a} libexpat1-dev{a} libfabric1{a} libfftw3-bin{a} libfftw3-dev{a} libfftw3-double3{a} libfftw3-long3{a} libfftw3-quad3{a} libfftw3-single3{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libfmt10{a} libfontbox-java{a} libfontbox2-java{a} libfontconfig1{a} libfontenc1{a} libfop-java{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgd3{a} libgfortran-14-dev{a} libgfortran5{a} libgif7{a} libglib2.0-0t64{a} libgraphicsmagick-q16-3t64{a} libgraphite2-3{a} libgs-common{a} libgs10{a} libgs10-common{a} libgssapi-krb5-2{a} libgts-0.7-5t64{a} libgvc6{a} libgvpr2{a} libharfbuzz0b{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libhsa-runtime64-1{a} libhsakmt1{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libhwy1t64{a} libibmad5{a} libibumad3{a} libibverbs-dev{a} libibverbs1{a} libice6{a} libicu72{a} libidn12{a} libijs-0.35{a} libimagequant0{a} libimath-3-1-29t64{a} libjakarta-servlet-api-java{a} libjaxp1.3-java{a} libjbig0{a} libjbig2dec0{a} libjlatexmath-java{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libjsoncpp26{a} libjxl0.9{a} libk5crypto3{a} libkeyutils1{a} libkpathsea6{a} libkrb5-3{a} libkrb5support0{a} liblab-gamut1{a} liblapack-dev{a} liblapack3{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} libllvm17t64{a} libllvm19{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmpfi0{a} libmunge2{a} libmuparser-dev{a} libmuparser2v5{a} libnghttp2-14{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnsl2{a} libnspr4{a} libnss3{a} libnuma-dev{a} libnuma1{a} libopenexr-3-1-30{a} libopenjp2-7{a} libopenmpi-dev{a} libopenmpi40{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libpathplan4{a} libpciaccess0{a} libpcsclite1{a} libpdfbox-java{a} libpipeline1{a} libpixman-1-0{a} libpkgconf3{a} libpmix-dev{a} libpmix2t64{a} libpng16-16t64{a} libpotrace0{a} libproc2-0{a} libpsl5t64{a} libpsm-infinipath1{a} libpsm2-2{a} libptexenc1{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libqdox-java{a} libraqm0{a} librav1e0.7{a} librdmacm1t64{a} libreadline8t64{a} librhash1{a} librhino-java{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsm6{a} libssh2-1t64{a} libsvtav1enc2{a} libsynctex2{a} libteckit0{a} libtexlua53-5{a} libthai-data{a} libthai0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libucx0{a} libuv1t64{a} libwebp7{a} libwebpmux3{a} libwmflite-0.2-7{a} libx11-6{a} libx11-data{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxi6{a} libxml-commons-external-java{a} libxml2{a} libxmlgraphics-commons-java{a} libxmu6{a} libxnvctrl0{a} libxpm4{a} libxrender1{a} libxt6t64{a} libyuv0{a} libz3-4{a} libzzip-0-13t64{a} lsb-release{a} m4{a} man-db{a} media-types{a} mpi-default-bin{a} mpi-default-dev{a} mscgen{a} netbase{a} ocl-icd-libopencl1{a} openjdk-21-jre-headless{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} openssl{a} pkgconf{a} pkgconf-bin{a} plantuml{a} po-debconf{a} poppler-data{a} preview-latex-style{a} procps{a} pybind11-dev{a} python-babel-localedata{a} python3{a} python3-alabaster{a} python3-autocommand{a} python3-babel{a} python3-bs4{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-defusedxml{a} python3-dev{a} python3-docutils{a} python3-idna{a} python3-imagesize{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-jinja2{a} python3-markupsafe{a} python3-minimal{a} python3-more-itertools{a} python3-mpi4py{a} python3-networkx{a} python3-numpy{a} python3-packaging{a} python3-pkg-resources{a} python3-pluggy{a} python3-pybind11{a} python3-pygments{a} python3-pytest{a} python3-requests{a} python3-roman{a} python3-setuptools{a} python3-six{a} python3-snowballstemmer{a} python3-soupsieve{a} python3-sphinx{a} python3-sphinx-argparse{a} python3-sphinx-copybutton{a} python3-sphinx-inline-tabs{a} python3-sphinxcontrib.autoprogram{a} python3-sphinxcontrib.plantuml{a} python3-typeguard{a} python3-typing-extensions{a} python3-urllib3{a} python3-zipp{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} rdfind{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-basic-ng{a} sphinx-common{a} symlinks{a} t1utils{a} tex-common{a} tex-gyre{a} texlive-base{a} texlive-binaries{a} texlive-fonts-recommended{a} texlive-latex-base{a} texlive-latex-extra{a} texlive-latex-recommended{a} texlive-pictures{a} tzdata{a} ucf{a} unzip{a} x11-common{a} xdg-utils{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl dbus default-jre dvisvgm fonts-droid-fallback fonts-liberation fonts-texgyre fonts-texgyre-math icc-profiles-free javascript-common krb5-locales libarchive-cpio-perl libasound2t64 libcoarrays-openmpi-dev libeigen3-dev libfile-mimeinfo-perl libglib2.0-data libgts-bin libheif-plugin-aomenc libheif-plugin-x265 libjson-xs-perl libldap-common libmail-sendmail-perl libnet-dbus-perl liboss4-salsa-asound2 libsasl2-modules libsaxon-java libspreadsheet-parseexcel-perl libx11-protocol-perl linux-sysctl-defaults lmodern lynx psmisc publicsuffix python3-gdal python3-lxml python3-matplotlib python3-pil python3-pydot python3-pygraphviz python3-scipy python3-yaml ruby shared-mime-info texlive-plain-generic tipa tk wget x11-utils x11-xserver-utils xauth xdg-user-dirs 0 packages upgraded, 369 newly installed, 0 to remove and 0 not upgraded. Need to get 468 MB of archives. After unpacking 1983 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 poppler-data all 0.4.12-1 [1601 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.7-3 [815 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.7-3 [2162 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.12.7-1 [26.8 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024b-3 [255 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2~rc1-1 [23.6 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 13 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.7-3 [1966 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.7-3 [671 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.12.7-1 [9712 B] Get: 23 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.12.7-1 [27.8 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31 [15.4 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-6 [879 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 bash-completion all 1:2.14.0-2 [310 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.3.2-2 [1382 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20240203 [158 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20240808-1 [93.9 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libcbor0.10 amd64 0.10.2-2 [28.3 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libfido2-1 amd64 1.15.0-1+b1 [78.7 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 openssh-client amd64 1:9.9p1-3 [991 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 ca-certificates-java all 20240118 [11.6 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 java-common all 0.76 [6776 B] Get: 47 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libnspr4 amd64 2:4.36-1 [110 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libnss3 amd64 2:3.106-1 [1392 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libpcsclite1 amd64 2.3.0-3 [55.8 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 openjdk-21-jre-headless amd64 21.0.5+11-1 [41.8 MB] Get: 53 http://deb.debian.org/debian unstable/main amd64 default-jre-headless amd64 2:1.21-76 [3192 B] Get: 54 http://deb.debian.org/debian unstable/main amd64 ant all 1.10.15-1 [2163 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 ant-optional all 1.10.15-1 [456 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 architecture-properties amd64 0.2.3 [2184 B] Get: 57 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 chrpath amd64 0.18-1 [13.5 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 cmake-data all 3.31.1-1 [2267 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.4-1.1 [349 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.11.0-1 [351 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 librhash1 amd64 1.4.5-1 [132 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.48.0-7 [148 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 cmake amd64 3.31.1-1 [11.9 MB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-8 [517 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 86 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 98 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 75.2.0-1 [213 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 75.2.0-1 [731 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20241024 [109 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libllvm19 amd64 1:19.1.4-1 [26.0 MB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libclang-cpp19 amd64 1:19.1.4-1 [13.2 MB] Get: 109 http://deb.debian.org/debian unstable/main amd64 libclang1-19 amd64 1:19.1.4-1 [7622 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libfmt10 amd64 10.1.1+ds1-4 [127 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 doxygen amd64 1.9.8+ds-2+b3 [5011 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.44-2 [280 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libfontenc1 amd64 1:1.1.8-1+b1 [23.3 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 119 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 fontconfig amd64 2.15.0-1.1+b1 [463 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 fonts-lmodern all 2.005-1 [4540 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 python3-soupsieve all 2.6-1 [38.3 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 python3-bs4 all 4.12.3-3 [133 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 python3-pygments all 2.18.0+dfsg-1 [836 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 python3-defusedxml all 0.7.1-2 [43.3 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 7.4.7-4 [158 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 sphinx-common all 7.4.7-4 [731 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 python-babel-localedata all 2.16.0-1 [5696 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 python3-babel all 2.16.0-1 [114 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 python3-roman all 4.2-1 [10.4 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get: 138 http://deb.debian.org/debian unstable/main amd64 python3-markupsafe amd64 2.1.5-1+b2 [13.9 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 python3-jinja2 all 3.1.3-1 [119 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 python3-certifi all 2024.8.30+dfsg-1 [9576 B] Get: 142 http://deb.debian.org/debian unstable/main amd64 python3-charset-normalizer amd64 3.4.0-1+b1 [140 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 python3-idna all 3.8-2 [41.6 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 python3-urllib3 all 2.2.3-3 [112 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 python3-sphinx all 7.4.7-4 [588 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 sphinx-basic-ng all 1.0.0~beta2-1 [13.0 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 furo all 2024.08.06+dfsg-1 [62.8 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-8 [836 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 libgfortran-14-dev amd64 14.2.0-8 [878 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 gfortran-14-x86-64-linux-gnu amd64 14.2.0-8 [11.7 MB] Get: 154 http://deb.debian.org/debian unstable/main amd64 gfortran-14 amd64 14.2.0-8 [12.2 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 libgs-common all 10.04.0~dfsg-2 [148 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 libgs10-common all 10.04.0~dfsg-2 [475 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 libavahi-common-data amd64 0.8-14 [112 kB] Get: 158 http://deb.debian.org/debian unstable/main amd64 libavahi-common3 amd64 0.8-14 [43.8 kB] Get: 159 http://deb.debian.org/debian unstable/main amd64 libdbus-1-3 amd64 1.14.10-6 [203 kB] Get: 160 http://deb.debian.org/debian unstable/main amd64 libavahi-client3 amd64 0.8-14 [47.9 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 libcups2t64 amd64 2.4.10-2 [251 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 libidn12 amd64 1.42-2+b1 [81.4 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 libijs-0.35 amd64 0.35-15.1+b2 [15.2 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 libjbig2dec0 amd64 0.20-1+b3 [65.1 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 libopenjp2-7 amd64 2.5.0-2+b4 [199 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 libpaper1 amd64 1.1.29+b2 [12.8 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 169 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 170 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.4.0-0.1+b1 [113 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.4.0-0.1+b1 [313 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get: 173 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 176 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 177 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 178 http://deb.debian.org/debian unstable/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get: 179 http://deb.debian.org/debian unstable/main amd64 libsm6 amd64 2:1.2.4-1 [35.2 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b1 [188 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 libgs10 amd64 10.04.0~dfsg-2 [2562 kB] Get: 182 http://deb.debian.org/debian unstable/main amd64 ghostscript amd64 10.04.0~dfsg-2 [50.6 kB] Get: 183 http://deb.debian.org/debian unstable/main amd64 libdav1d7 amd64 1.5.0-1+b1 [550 kB] Get: 184 http://deb.debian.org/debian unstable/main amd64 libheif-plugin-dav1d amd64 1.19.3-1 [11.2 kB] Get: 185 http://deb.debian.org/debian unstable/main amd64 libde265-0 amd64 1.0.15-1+b2 [189 kB] Get: 186 http://deb.debian.org/debian unstable/main amd64 libheif-plugin-libde265 amd64 1.19.3-1 [15.0 kB] Get: 187 http://deb.debian.org/debian unstable/main amd64 libheif1 amd64 1.19.3-1 [489 kB] Get: 188 http://deb.debian.org/debian unstable/main amd64 libgif7 amd64 5.2.2-1+b1 [44.2 kB] Get: 189 http://deb.debian.org/debian unstable/main amd64 libhwy1t64 amd64 1.2.0-2+b1 [676 kB] Get: 190 http://deb.debian.org/debian unstable/main amd64 libimath-3-1-29t64 amd64 3.1.12-1+b1 [42.0 kB] Get: 191 http://deb.debian.org/debian unstable/main amd64 libopenexr-3-1-30 amd64 3.1.5-5.1+b3 [934 kB] Get: 192 http://deb.debian.org/debian unstable/main amd64 libjxl0.9 amd64 0.9.2-10+b1 [1052 kB] Get: 193 http://deb.debian.org/debian unstable/main amd64 libwebpmux3 amd64 1.4.0-0.1+b1 [123 kB] Get: 194 http://deb.debian.org/debian unstable/main amd64 libwmflite-0.2-7 amd64 0.2.13-1.1+b3 [75.6 kB] Get: 195 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB] Get: 196 http://deb.debian.org/debian unstable/main amd64 libgraphicsmagick-q16-3t64 amd64 1.4+really1.3.45-1+b1 [1229 kB] Get: 197 http://deb.debian.org/debian unstable/main amd64 graphicsmagick amd64 1.4+really1.3.45-1+b1 [1080 kB] Get: 198 http://deb.debian.org/debian unstable/main amd64 libann0 amd64 1.1.2+doc-9+b1 [25.1 kB] Get: 199 http://deb.debian.org/debian unstable/main amd64 libcdt5 amd64 2.42.4-2+b1 [40.5 kB] Get: 200 http://deb.debian.org/debian unstable/main amd64 libcgraph6 amd64 2.42.4-2+b1 [64.2 kB] Get: 201 http://deb.debian.org/debian unstable/main amd64 libaom3 amd64 3.11.0-1 [1879 kB] Get: 202 http://deb.debian.org/debian unstable/main amd64 libabsl20230802 amd64 20230802.1-4 [464 kB] Get: 203 http://deb.debian.org/debian unstable/main amd64 libgav1-1 amd64 0.19.0-2+b2 [350 kB] Get: 204 http://deb.debian.org/debian unstable/main amd64 librav1e0.7 amd64 0.7.1-7+b2 [936 kB] Get: 205 http://deb.debian.org/debian unstable/main amd64 libsvtav1enc2 amd64 2.2.1+dfsg-2 [2173 kB] Get: 206 http://deb.debian.org/debian unstable/main amd64 libyuv0 amd64 0.0.1898.20241125-1 [172 kB] Get: 207 http://deb.debian.org/debian unstable/main amd64 libavif16 amd64 1.1.1-1 [117 kB] Get: 208 http://deb.debian.org/debian unstable/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get: 209 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.15-1 [71.8 kB] Get: 210 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.82.2-3 [1501 kB] Get: 211 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 212 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 10.0.1-1 [477 kB] Get: 213 http://deb.debian.org/debian unstable/main amd64 libraqm0 amd64 0.10.1-1+b2 [14.1 kB] Get: 214 http://deb.debian.org/debian unstable/main amd64 libxpm4 amd64 1:3.5.17-1+b2 [56.3 kB] Get: 215 http://deb.debian.org/debian unstable/main amd64 libgd3 amd64 2.3.3-12+b1 [126 kB] Get: 216 http://deb.debian.org/debian unstable/main amd64 libgts-0.7-5t64 amd64 0.7.6+darcs121130-5.2+b1 [160 kB] Get: 217 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 218 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 219 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 220 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b2 [27.8 kB] Get: 221 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get: 222 http://deb.debian.org/debian unstable/main amd64 libltdl7 amd64 2.4.7-8 [393 kB] Get: 223 http://deb.debian.org/debian unstable/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 224 http://deb.debian.org/debian unstable/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get: 225 http://deb.debian.org/debian unstable/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get: 226 http://deb.debian.org/debian unstable/main amd64 libpango-1.0-0 amd64 1.54.0+ds-3 [223 kB] Get: 227 http://deb.debian.org/debian unstable/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-3 [54.2 kB] Get: 228 http://deb.debian.org/debian unstable/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-3 [35.2 kB] Get: 229 http://deb.debian.org/debian unstable/main amd64 libpathplan4 amd64 2.42.4-2+b1 [42.8 kB] Get: 230 http://deb.debian.org/debian unstable/main amd64 libgvc6 amd64 2.42.4-2+b1 [685 kB] Get: 231 http://deb.debian.org/debian unstable/main amd64 libgvpr2 amd64 2.42.4-2+b1 [193 kB] Get: 232 http://deb.debian.org/debian unstable/main amd64 liblab-gamut1 amd64 2.42.4-2+b1 [198 kB] Get: 233 http://deb.debian.org/debian unstable/main amd64 libxmu6 amd64 2:1.1.3-3+b3 [58.8 kB] Get: 234 http://deb.debian.org/debian unstable/main amd64 libxaw7 amd64 2:1.0.16-1 [212 kB] Get: 235 http://deb.debian.org/debian unstable/main amd64 graphviz amd64 2.42.4-2+b1 [616 kB] Get: 236 http://deb.debian.org/debian unstable/main amd64 libnl-3-200 amd64 3.7.0-0.3+b1 [59.4 kB] Get: 237 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-200 amd64 3.7.0-0.3+b1 [182 kB] Get: 238 http://deb.debian.org/debian unstable/main amd64 libibverbs1 amd64 52.0-2+b1 [62.2 kB] Get: 239 http://deb.debian.org/debian unstable/main amd64 ibverbs-providers amd64 52.0-2+b1 [343 kB] Get: 240 http://deb.debian.org/debian unstable/main amd64 unzip amd64 6.0-28 [166 kB] Get: 241 http://deb.debian.org/debian unstable/main amd64 java-wrappers all 0.5 [8848 B] Get: 242 http://deb.debian.org/debian unstable/main amd64 libllvm17t64 amd64 1:17.0.6-18 [23.6 MB] Get: 243 http://deb.debian.org/debian unstable/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b2 [13.0 MB] Get: 244 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.123-1 [8084 B] Get: 245 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.123-1 [38.7 kB] Get: 246 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.123-1 [22.3 kB] Get: 247 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.18-1+b1 [22.3 kB] Get: 248 http://deb.debian.org/debian unstable/main amd64 libhsakmt1 amd64 6.1.2+ds-1 [59.8 kB] Get: 249 http://deb.debian.org/debian unstable/main amd64 libhsa-runtime64-1 amd64 6.1.2-2 [535 kB] Get: 250 http://deb.debian.org/debian unstable/main amd64 libamdhip64-5 amd64 5.7.1-5 [8877 kB] Get: 251 http://deb.debian.org/debian unstable/main amd64 libapache-pom-java all 33-2 [5852 B] Get: 252 http://deb.debian.org/debian unstable/main amd64 libavalon-framework-java all 4.2.0+ds-1 [70.8 kB] Get: 253 http://deb.debian.org/debian unstable/main amd64 libjaxp1.3-java all 1.3.05-6 [227 kB] Get: 254 http://deb.debian.org/debian unstable/main amd64 libxml-commons-external-java all 1.4.01-6 [240 kB] Get: 255 http://deb.debian.org/debian unstable/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 256 http://deb.debian.org/debian unstable/main amd64 libcommons-io-java all 2.17.0-1 [488 kB] Get: 257 http://deb.debian.org/debian unstable/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 258 http://deb.debian.org/debian unstable/main amd64 libxmlgraphics-commons-java all 2.10-2 [628 kB] Get: 259 http://deb.debian.org/debian unstable/main amd64 librhino-java all 1.7.15-1 [1382 kB] Get: 260 http://deb.debian.org/debian unstable/main amd64 libbatik-java all 1.18+dfsg-2 [3940 kB] Get: 261 http://deb.debian.org/debian unstable/main amd64 libbcprov-java all 1.77-1 [5300 kB] Get: 262 http://deb.debian.org/debian unstable/main amd64 libbcutil-java all 1.77-1 [593 kB] Get: 263 http://deb.debian.org/debian unstable/main amd64 libbcpkix-java all 1.77-1 [956 kB] Get: 264 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.0-4 [152 kB] Get: 265 http://deb.debian.org/debian unstable/main amd64 libblas-dev amd64 3.12.0-4 [161 kB] Get: 266 http://deb.debian.org/debian unstable/main amd64 libboost1.83-dev amd64 1.83.0-3.2+b2 [10.6 MB] Get: 267 http://deb.debian.org/debian unstable/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get: 268 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 269 http://deb.debian.org/debian unstable/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10+b1 [132 kB] Get: 270 http://deb.debian.org/debian unstable/main amd64 libevent-extra-2.1-7t64 amd64 2.1.12-stable-10+b1 [108 kB] Get: 271 http://deb.debian.org/debian unstable/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10+b1 [54.3 kB] Get: 272 http://deb.debian.org/debian unstable/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.12-stable-10+b1 [61.1 kB] Get: 273 http://deb.debian.org/debian unstable/main amd64 libevent-dev amd64 2.1.12-stable-10+b1 [305 kB] Get: 274 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB] Get: 275 http://deb.debian.org/debian unstable/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3 [170 kB] Get: 276 http://deb.debian.org/debian unstable/main amd64 libpsm2-2 amd64 11.2.185-2.1 [181 kB] Get: 277 http://deb.debian.org/debian unstable/main amd64 librdmacm1t64 amd64 52.0-2+b1 [70.4 kB] Get: 278 http://deb.debian.org/debian unstable/main amd64 libfabric1 amd64 1.17.0-3.1 [631 kB] Get: 279 http://deb.debian.org/debian unstable/main amd64 libfftw3-double3 amd64 3.3.10-2+b1 [781 kB] Get: 280 http://deb.debian.org/debian unstable/main amd64 libfftw3-long3 amd64 3.3.10-2+b1 [347 kB] Get: 281 http://deb.debian.org/debian unstable/main amd64 libfftw3-quad3 amd64 3.3.10-2+b1 [618 kB] Get: 282 http://deb.debian.org/debian unstable/main amd64 libfftw3-single3 amd64 3.3.10-2+b1 [809 kB] Get: 283 http://deb.debian.org/debian unstable/main amd64 libfftw3-bin amd64 3.3.10-2+b1 [51.3 kB] Get: 284 http://deb.debian.org/debian unstable/main amd64 libfftw3-dev amd64 3.3.10-2+b1 [2118 kB] Get: 285 http://deb.debian.org/debian unstable/main amd64 libfontbox-java all 1:1.8.16-5 [211 kB] Get: 286 http://deb.debian.org/debian unstable/main amd64 libfontbox2-java all 2.0.29-1 [1510 kB] Get: 287 http://deb.debian.org/debian unstable/main amd64 libqdox-java all 1.12.1-4 [173 kB] Get: 288 http://deb.debian.org/debian unstable/main amd64 libjakarta-servlet-api-java all 6.1.0-1 [376 kB] Get: 289 http://deb.debian.org/debian unstable/main amd64 libfop-java all 1:2.10+dfsg-1 [4588 kB] Get: 290 http://deb.debian.org/debian unstable/main amd64 libhwloc15 amd64 2.11.2-1 [164 kB] Get: 291 http://deb.debian.org/debian unstable/main amd64 libnuma-dev amd64 2.0.18-1+b1 [36.6 kB] Get: 292 http://deb.debian.org/debian unstable/main amd64 libltdl-dev amd64 2.4.7-8 [165 kB] Get: 293 http://deb.debian.org/debian unstable/main amd64 libhwloc-dev amd64 2.11.2-1 [254 kB] Get: 294 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b2 [51.9 kB] Get: 295 http://deb.debian.org/debian unstable/main amd64 libxnvctrl0 amd64 535.171.04-1+b1 [14.2 kB] Get: 296 http://deb.debian.org/debian unstable/main amd64 ocl-icd-libopencl1 amd64 2.3.2-1+b2 [40.2 kB] Get: 297 http://deb.debian.org/debian unstable/main amd64 libhwloc-plugins amd64 2.11.2-1 [18.1 kB] Get: 298 http://deb.debian.org/debian unstable/main amd64 libibumad3 amd64 52.0-2+b1 [28.2 kB] Get: 299 http://deb.debian.org/debian unstable/main amd64 libibmad5 amd64 52.0-2+b1 [43.4 kB] Get: 300 http://deb.debian.org/debian unstable/main amd64 libnl-3-dev amd64 3.7.0-0.3+b1 [100 kB] Get: 301 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-dev amd64 3.7.0-0.3+b1 [200 kB] Get: 302 http://deb.debian.org/debian unstable/main amd64 libibverbs-dev amd64 52.0-2+b1 [636 kB] Get: 303 http://deb.debian.org/debian unstable/main amd64 libjlatexmath-java all 1.0.7-3 [995 kB] Get: 304 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 305 http://deb.debian.org/debian unstable/main amd64 libkpathsea6 amd64 2024.20240313.70630+ds-5 [157 kB] Get: 306 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.0-4 [2450 kB] Get: 307 http://deb.debian.org/debian unstable/main amd64 liblapack-dev amd64 3.12.0-4 [4991 kB] Get: 308 http://deb.debian.org/debian unstable/main amd64 libmpfi0 amd64 1.5.4+ds-4 [35.5 kB] Get: 309 http://deb.debian.org/debian unstable/main amd64 libmunge2 amd64 0.5.15-4+b1 [20.0 kB] Get: 310 http://deb.debian.org/debian unstable/main amd64 libmuparser2v5 amd64 2.3.4-1+b1 [149 kB] Get: 311 http://deb.debian.org/debian unstable/main amd64 libmuparser-dev amd64 2.3.4-1+b1 [33.6 kB] Get: 312 http://deb.debian.org/debian unstable/main amd64 libpmix2t64 amd64 5.0.4-1 [661 kB] Get: 313 http://deb.debian.org/debian unstable/main amd64 libucx0 amd64 1.17.0+ds-3 [1130 kB] Get: 314 http://deb.debian.org/debian unstable/main amd64 libopenmpi40 amd64 5.0.6-3 [2360 kB] Get: 315 http://deb.debian.org/debian unstable/main amd64 openmpi-common all 5.0.6-3 [97.0 kB] Get: 316 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 317 http://deb.debian.org/debian unstable/main amd64 libpmix-dev amd64 5.0.4-1 [3972 kB] Get: 318 http://deb.debian.org/debian unstable/main amd64 openmpi-bin amd64 5.0.6-3 [188 kB] Get: 319 http://deb.debian.org/debian unstable/main amd64 libopenmpi-dev amd64 5.0.6-3 [1088 kB] Get: 320 http://deb.debian.org/debian unstable/main amd64 libpaper-utils amd64 1.1.29+b2 [9236 B] Get: 321 http://deb.debian.org/debian unstable/main amd64 libpdfbox-java all 1:1.8.16-5 [5527 kB] Get: 322 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 323 http://deb.debian.org/debian unstable/main amd64 libpotrace0 amd64 1.16-2+b2 [25.6 kB] Get: 324 http://deb.debian.org/debian unstable/main amd64 libptexenc1 amd64 2024.20240313.70630+ds-5 [49.1 kB] Get: 325 http://deb.debian.org/debian unstable/main amd64 libpython3.12t64 amd64 3.12.7-3 [2153 kB] Get: 326 http://deb.debian.org/debian unstable/main amd64 libpython3.12-dev amd64 3.12.7-3 [5124 kB] Get: 327 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.12.7-1 [9976 B] Get: 328 http://deb.debian.org/debian unstable/main amd64 libsynctex2 amd64 2024.20240313.70630+ds-5 [62.7 kB] Get: 329 http://deb.debian.org/debian unstable/main amd64 libteckit0 amd64 2.5.12+ds1-1+b1 [341 kB] Get: 330 http://deb.debian.org/debian unstable/main amd64 libtexlua53-5 amd64 2024.20240313.70630+ds-5 [114 kB] Get: 331 http://deb.debian.org/debian unstable/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB] Get: 332 http://deb.debian.org/debian unstable/main amd64 libzzip-0-13t64 amd64 0.13.72+dfsg.1-1.3 [56.2 kB] Get: 333 http://deb.debian.org/debian unstable/main amd64 lsb-release all 12.1-1 [5912 B] Get: 334 http://deb.debian.org/debian unstable/main amd64 mpi-default-bin amd64 1.17 [2372 B] Get: 335 http://deb.debian.org/debian unstable/main amd64 mpi-default-dev amd64 1.17 [3148 B] Get: 336 http://deb.debian.org/debian unstable/main amd64 mscgen amd64 0.20-16 [46.8 kB] Get: 337 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 338 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 339 http://deb.debian.org/debian unstable/main amd64 plantuml all 1:1.2020.2+ds-5 [8132 kB] Get: 340 http://deb.debian.org/debian unstable/main amd64 tex-common all 6.18 [32.5 kB] Get: 341 http://deb.debian.org/debian unstable/main amd64 preview-latex-style all 13.2-1 [350 kB] Get: 342 http://deb.debian.org/debian unstable/main amd64 pybind11-dev all 2.13.6-1 [204 kB] Get: 343 http://deb.debian.org/debian unstable/main amd64 python3.12-dev amd64 3.12.7-3 [505 kB] Get: 344 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.12.7-1 [26.1 kB] Get: 345 http://deb.debian.org/debian unstable/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 346 http://deb.debian.org/debian unstable/main amd64 python3-mpi4py amd64 4.0.1-6+b1 [1000 kB] Get: 347 http://deb.debian.org/debian unstable/main amd64 python3-networkx all 3.2.1-5 [13.0 MB] Get: 348 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:1.26.4+ds-12 [4738 kB] Get: 349 http://deb.debian.org/debian unstable/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 350 http://deb.debian.org/debian unstable/main amd64 python3-pybind11 all 2.13.6-1 [215 kB] Get: 351 http://deb.debian.org/debian unstable/main amd64 python3-pytest all 8.3.3-1 [249 kB] Get: 352 http://deb.debian.org/debian unstable/main amd64 python3-six all 1.16.0-7 [16.4 kB] Get: 353 http://deb.debian.org/debian unstable/main amd64 python3-sphinx-argparse all 0.5.2-1 [59.6 kB] Get: 354 http://deb.debian.org/debian unstable/main amd64 python3-sphinx-copybutton all 0.5.2-2 [17.9 kB] Get: 355 http://deb.debian.org/debian unstable/main amd64 python3-sphinx-inline-tabs all 2023.4.21-1 [35.9 kB] Get: 356 http://deb.debian.org/debian unstable/main amd64 python3-sphinxcontrib.autoprogram all 0.1.9-1 [10.6 kB] Get: 357 http://deb.debian.org/debian unstable/main amd64 python3-sphinxcontrib.plantuml all 0.5-8 [7992 B] Get: 358 http://deb.debian.org/debian unstable/main amd64 rdfind amd64 1.6.0-1+b1 [44.7 kB] Get: 359 http://deb.debian.org/debian unstable/main amd64 symlinks amd64 1.4-4 [11.3 kB] Get: 360 http://deb.debian.org/debian unstable/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get: 361 http://deb.debian.org/debian unstable/main amd64 tex-gyre all 20180621-6 [6209 kB] Get: 362 http://deb.debian.org/debian unstable/main amd64 texlive-binaries amd64 2024.20240313.70630+ds-5 [8492 kB] Get: 363 http://deb.debian.org/debian unstable/main amd64 xdg-utils all 1.2.1-2 [75.8 kB] Get: 364 http://deb.debian.org/debian unstable/main amd64 texlive-base all 2024.20241115-1 [22.7 MB] Get: 365 http://deb.debian.org/debian unstable/main amd64 texlive-fonts-recommended all 2024.20241115-1 [4991 kB] Get: 366 http://deb.debian.org/debian unstable/main amd64 texlive-latex-base all 2024.20241115-1 [1278 kB] Get: 367 http://deb.debian.org/debian unstable/main amd64 texlive-latex-recommended all 2024.20241115-1 [8757 kB] Get: 368 http://deb.debian.org/debian unstable/main amd64 texlive-pictures all 2024.20241115-1 [17.0 MB] Get: 369 http://deb.debian.org/debian unstable/main amd64 texlive-latex-extra all 2024.20241115-1 [24.6 MB] Fetched 468 MB in 6s (80.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package poppler-data. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19968 files and directories currently installed.) Preparing to unpack .../poppler-data_0.4.12-1_all.deb ... Unpacking poppler-data (0.4.12-1) ... Selecting previously unselected package libpython3.12-minimal:amd64. Preparing to unpack .../libpython3.12-minimal_3.12.7-3_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.7-3) ... Selecting previously unselected package libexpat1:amd64. 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Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-3_all.deb ... Unpacking tzdata (2024b-3) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../05-libcom-err2_1.47.2~rc1-1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.2~rc1-1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../07-libkeyutils1_1.6.3-4_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:amd64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../14-libreadline8t64_8.2-5_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.7-3_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.7-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.7-3_amd64.deb ... Unpacking python3.12 (3.12.7-3) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../17-libpython3-stdlib_3.12.7-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.7-1) ... Setting up python3-minimal (3.12.7-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21883 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.7-1_amd64.deb ... Unpacking python3 (3.12.7-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../002-libproc2-0_2%3a4.0.4-6_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-6) ... Selecting previously unselected package procps. Preparing to unpack .../003-procps_2%3a4.0.4-6_amd64.deb ... Unpacking procps (2:4.0.4-6) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../004-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package bash-completion. Preparing to unpack .../005-bash-completion_1%3a2.14.0-2_all.deb ... Unpacking bash-completion (1:2.14.0-2) ... Selecting previously unselected package openssl. Preparing to unpack .../006-openssl_3.3.2-2_amd64.deb ... Unpacking openssl (3.3.2-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../007-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../008-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../009-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../010-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../011-gettext-base_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../012-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../013-groff-base_1.23.0-5_amd64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../014-bsdextrautils_2.40.2-11_amd64.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:amd64. 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Preparing to unpack .../021-ucf_3.0043+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0043+nmu1) ... Selecting previously unselected package ca-certificates-java. Preparing to unpack .../022-ca-certificates-java_20240118_all.deb ... Unpacking ca-certificates-java (20240118) ... Selecting previously unselected package java-common. Preparing to unpack .../023-java-common_0.76_all.deb ... Unpacking java-common (0.76) ... Selecting previously unselected package liblcms2-2:amd64. Preparing to unpack .../024-liblcms2-2_2.16-2_amd64.deb ... Unpacking liblcms2-2:amd64 (2.16-2) ... Selecting previously unselected package libjpeg62-turbo:amd64. Preparing to unpack .../025-libjpeg62-turbo_1%3a2.1.5-3+b1_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Selecting previously unselected package libnspr4:amd64. Preparing to unpack .../026-libnspr4_2%3a4.36-1_amd64.deb ... Unpacking libnspr4:amd64 (2:4.36-1) ... Selecting previously unselected package libnss3:amd64. Preparing to unpack .../027-libnss3_2%3a3.106-1_amd64.deb ... Unpacking libnss3:amd64 (2:3.106-1) ... Selecting previously unselected package libpcsclite1:amd64. Preparing to unpack .../028-libpcsclite1_2.3.0-3_amd64.deb ... Unpacking libpcsclite1:amd64 (2.3.0-3) ... Selecting previously unselected package openjdk-21-jre-headless:amd64. Preparing to unpack .../029-openjdk-21-jre-headless_21.0.5+11-1_amd64.deb ... Unpacking openjdk-21-jre-headless:amd64 (21.0.5+11-1) ... Selecting previously unselected package default-jre-headless. Preparing to unpack .../030-default-jre-headless_2%3a1.21-76_amd64.deb ... Unpacking default-jre-headless (2:1.21-76) ... Selecting previously unselected package ant. Preparing to unpack .../031-ant_1.10.15-1_all.deb ... Unpacking ant (1.10.15-1) ... Selecting previously unselected package ant-optional. Preparing to unpack .../032-ant-optional_1.10.15-1_all.deb ... Unpacking ant-optional (1.10.15-1) ... Selecting previously unselected package architecture-properties:amd64. Preparing to unpack .../033-architecture-properties_0.2.3_amd64.deb ... Unpacking architecture-properties:amd64 (0.2.3) ... Selecting previously unselected package m4. Preparing to unpack .../034-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../035-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../036-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../037-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../038-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package chrpath. Preparing to unpack .../039-chrpath_0.18-1_amd64.deb ... Unpacking chrpath (0.18-1) ... Selecting previously unselected package cmake-data. Preparing to unpack .../040-cmake-data_3.31.1-1_all.deb ... Unpacking cmake-data (3.31.1-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../041-libicu72_72.1-5+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-5+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../042-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package libarchive13t64:amd64. Preparing to unpack .../043-libarchive13t64_3.7.4-1.1_amd64.deb ... Unpacking libarchive13t64:amd64 (3.7.4-1.1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../044-libbrotli1_1.1.0-2+b6_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b6) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../045-libsasl2-modules-db_2.1.28+dfsg1-8_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../046-libsasl2-2_2.1.28+dfsg1-8_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Selecting previously unselected package libldap-2.5-0:amd64. Preparing to unpack .../047-libldap-2.5-0_2.5.18+dfsg-3+b1_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../048-libnghttp2-14_1.64.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.64.0-1) ... Selecting previously unselected package libpsl5t64:amd64. Preparing to unpack .../049-libpsl5t64_0.21.2-1.1+b1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:amd64. 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Setting up libhwloc15:amd64 (2.11.2-1) ... Setting up libimath-3-1-29t64:amd64 (3.1.12-1+b1) ... Setting up libidn12:amd64 (1.42-2+b1) ... Setting up autopoint (0.22.5-2) ... Setting up libmpfi0:amd64 (1.5.4+ds-4) ... Setting up libpcsclite1:amd64 (2.3.0-3) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libltdl7:amd64 (2.4.7-8) ... Setting up libfftw3-double3:amd64 (3.3.10-2+b1) ... Setting up libkpathsea6:amd64 (2024.20240313.70630+ds-5) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Setting up libgfortran5:amd64 (14.2.0-8) ... Setting up autoconf (2.72-3) ... Setting up libwebp7:amd64 (1.4.0-0.1+b1) ... Setting up libgif7:amd64 (5.2.2-1+b1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libnuma1:amd64 (2.0.18-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up libdav1d7:amd64 (1.5.0-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up ocl-icd-libopencl1:amd64 (2.3.2-1+b2) ... Setting up libtiff6:amd64 (4.5.1+git230720-5) ... Setting up librav1e0.7:amd64 (0.7.1-7+b2) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libxml-commons-external-java (1.4.01-6) ... Setting up procps (2:4.0.4-6) ... Setting up libjson-perl (4.10000-1) ... Setting up libnl-3-200:amd64 (3.7.0-0.3+b1) ... Setting up libpsm2-2 (11.2.185-2.1) ... Setting up libavalon-framework-java (4.2.0+ds-1) ... Setting up openmpi-common (5.0.6-3) ... Setting up fonts-lmodern (2.005-1) ... Setting up libopenjp2-7:amd64 (2.5.0-2+b4) ... Setting up libx11-6:amd64 (2:1.8.10-2) ... Setting up libthai-data (0.1.29-2) ... Setting up netbase (6.4) ... Setting up libabsl20230802:amd64 (20230802.1-4) ... Setting up libgts-0.7-5t64:amd64 (0.7.6+darcs121130-5.2+b1) ... Setting up sgml-base (1.31) ... Setting up cmake-data (3.31.1-1) ... Setting up librhash1:amd64 (1.4.5-1) ... Setting up libcdt5:amd64 (2.42.4-2+b1) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libcgraph6:amd64 (2.42.4-2+b1) ... Setting up libboost-dev:amd64 (1.83.0.2+b2) ... Setting up libjlatexmath-java (1.0.7-3) ... Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libmuparser2v5:amd64 (2.3.4-1+b1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up lsb-release (12.1-1) ... Setting up libjaxp1.3-java (1.3.05-6) ... Setting up libfido2-1:amd64 (1.15.0-1+b1) ... Setting up libde265-0:amd64 (1.0.15-1+b2) ... Setting up libbcpkix-java (1.77-1) ... Setting up openssl (3.3.2-2) ... Setting up libwebpmux3:amd64 (1.4.0-0.1+b1) ... Setting up libdrm-common (2.4.123-1) ... Setting up libyuv0:amd64 (0.0.1898.20241125-1) ... Setting up readline-common (8.2-5) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up xdg-utils (1.2.1-2) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libfmt10:amd64 (10.1.1+ds1-4) ... Setting up chrpath (0.18-1) ... Setting up libblas-dev:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode Setting up libsynctex2:amd64 (2024.20240313.70630+ds-5) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libpotrace0:amd64 (1.16-2+b2) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libgfortran-14-dev:amd64 (14.2.0-8) ... Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libmuparser-dev:amd64 (2.3.4-1+b1) ... Setting up libllvm19:amd64 (1:19.1.4-1) ... Setting up libice6:amd64 (2:1.1.1-1) ... Setting up liblapack3:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up java-wrappers (0.5) ... Setting up libclang1-19 (1:19.1.4-1) ... Setting up libpdfbox-java (1:1.8.16-5) ... Setting up libxpm4:amd64 (1:3.5.17-1+b2) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b2) ... Setting up libtool (2.4.7-8) ... Setting up libfftw3-bin (3.3.10-2+b1) ... Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libevent-openssl-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:amd64 (0.8-14) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libxext6:amd64 (2:1.3.4-1+b2) ... Setting up libnss3:amd64 (2:3.106-1) ... Setting up libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ... Setting up gfortran-14-x86-64-linux-gnu (14.2.0-8) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:amd64 (2.0.18-1+b1) ... Setting up libnl-route-3-200:amd64 (3.7.0-0.3+b1) ... Setting up libxnvctrl0:amd64 (535.171.04-1+b1) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:amd64 (2.4.7-8) ... Setting up libthai0:amd64 (0.1.29-2+b1) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libptexenc1:amd64 (2024.20240313.70630+ds-5) ... Setting up libllvm17t64:amd64 (1:17.0.6-18) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libopenexr-3-1-30:amd64 (3.1.5-5.1+b3) ... Setting up liblapack-dev:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libgav1-1:amd64 (0.19.0-2+b2) ... Setting up ucf (3.0043+nmu1) ... Setting up libjs-sphinxdoc (7.4.7-4) ... Setting up libevent-extra-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libgvpr2:amd64 (2.42.4-2+b1) ... Setting up libdrm2:amd64 (2.4.123-1) ... Setting up libnl-3-dev:amd64 (3.7.0-0.3+b1) ... Setting up groff-base (1.23.0-5) ... Setting up xml-core (0.19) ... Setting up libharfbuzz0b:amd64 (10.0.1-1) ... Setting up libhwloc-dev:amd64 (2.11.2-1) ... Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b2) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up gfortran-14 (14.2.0-8) ... Setting up libsm6:amd64 (2:1.2.4-1) ... Setting up libarchive13t64:amd64 (3.7.4-1.1) ... Setting up libfftw3-dev:amd64 (3.3.10-2+b1) ... Setting up libavahi-client3:amd64 (0.8-14) ... Setting up libclang-cpp19 (1:19.1.4-1) ... Setting up libdrm-amdgpu1:amd64 (2.4.123-1) ... Setting up libpaper1:amd64 (1.1.29+b2) ... Creating config file /etc/papersize with new version Setting up libibverbs1:amd64 (52.0-2+b1) ... Setting up libavif16:amd64 (1.1.1-1) ... Setting up openjdk-21-jre-headless:amd64 (21.0.5+11-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libxi6:amd64 (2:1.8.2-1) ... Setting up libcurl4t64:amd64 (8.11.0-1) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up ibverbs-providers:amd64 (52.0-2+b1) ... Setting up libcommons-io-java (2.17.0-1) ... Setting up openssh-client (1:9.9p1-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libjxl0.9:amd64 (0.9.2-10+b1) ... Setting up libxmlgraphics-commons-java (2.10-2) ... Setting up libpaper-utils (1.1.29+b2) ... Setting up xfonts-utils (1:7.7+7) ... Setting up libhwloc-plugins:amd64 (2.11.2-1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up tex-common (6.18) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libnl-route-3-dev:amd64 (3.7.0-0.3+b1) ... Setting up doxygen (1.9.8+ds-2+b3) ... Setting up libraqm0:amd64 (0.10.1-1+b2) ... Setting up sphinx-common (7.4.7-4) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2+b1) ... Setting up libevent-dev (2.1.12-stable-10+b1) ... Setting up libpmix2t64:amd64 (5.0.4-1) ... Setting up libnsl2:amd64 (1.3.0-3+b3) ... Setting up cmake (3.31.1-1) ... Setting up librdmacm1t64:amd64 (52.0-2+b1) ... Setting up libcups2t64:amd64 (2.4.10-2) ... Setting up tex-gyre (20180621-6) ... Setting up libhsakmt1:amd64 (6.1.2+ds-1) ... Setting up libfabric1:amd64 (1.17.0-3.1) ... Setting up libxmu6:amd64 (2:1.1.3-3+b3) ... Setting up libpython3.12-stdlib:amd64 (3.12.7-3) ... Setting up libbatik-java (1.18+dfsg-2) ... Setting up preview-latex-style (13.2-1) ... Setting up python3.12 (3.12.7-3) ... Setting up debhelper (13.20) ... Setting up libxaw7:amd64 (2:1.0.16-1) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up libibverbs-dev:amd64 (52.0-2+b1) ... Setting up libpython3.12t64:amd64 (3.12.7-3) ... Setting up libhsa-runtime64-1:amd64 (6.1.2-2) ... Setting up libpython3-stdlib:amd64 (3.12.7-1) ... Setting up libgs10-common (10.04.0~dfsg-2) ... Setting up fontconfig-config (2.15.0-1.1+b1) ... Setting up python3 (3.12.7-1) ... Setting up libpython3.12-dev:amd64 (3.12.7-3) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-markupsafe (2.1.5-1+b2) ... Setting up python3-six (1.16.0-7) ... Setting up python3-roman (4.2-1) ... Setting up python3-jinja2 (3.1.3-1) ... Setting up python3-packaging (24.2-1) ... Setting up libamdhip64-5 (5.7.1-5) ... Setting up python3-certifi (2024.8.30+dfsg-1) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up python3-idna (3.8-2) ... Setting up python3.12-dev (3.12.7-3) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-urllib3 (2.2.3-3) ... Setting up python3-pluggy (1.5.0-1) ... Setting up libfontconfig1:amd64 (2.15.0-1.1+b1) ... Setting up python3-soupsieve (2.6-1) ... Setting up python3-imagesize (1.4.1-1) ... Setting up libgs10:amd64 (10.04.0~dfsg-2) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up fontconfig (2.15.0-1.1+b1) ... Regenerating fonts cache... done. Setting up libucx0:amd64 (1.17.0+ds-3) ... Setting up libpython3-dev:amd64 (3.12.7-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-defusedxml (0.7.1-2) ... Setting up python3-charset-normalizer (3.4.0-1+b1) ... Setting up python3-pytest (8.3.3-1) ... Setting up python3-alabaster (0.7.16-0.1) ... Setting up libpango-1.0-0:amd64 (1.54.0+ds-3) ... Setting up python3-typeguard (4.4.1-1) ... Setting up ghostscript (10.04.0~dfsg-2) ... Setting up pybind11-dev (2.13.6-1) ... Setting up libcairo2:amd64 (1.18.2-2) ... Setting up python3-bs4 (4.12.3-3) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-dev (3.12.7-1) ... Setting up texlive-binaries (2024.20240313.70630+ds-5) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up libpangoft2-1.0-0:amd64 (1.54.0+ds-3) ... Setting up texlive-base (2024.20241115-1) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex Setting up python3-pybind11 (2.13.6-1) ... Setting up libpangocairo-1.0-0:amd64 (1.54.0+ds-3) ... Setting up python3-pkg-resources (75.2.0-1) ... Setting up libopenmpi40:amd64 (5.0.6-3) ... Setting up python3-setuptools (75.2.0-1) ... Setting up python3-babel (2.16.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-networkx (3.2.1-5) ... Setting up python3-pygments (2.18.0+dfsg-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up texlive-latex-base (2024.20241115-1) ... Setting up texlive-latex-recommended (2024.20241115-1) ... Setting up python3-requests (2.32.3+dfsg-1) ... Setting up python3-numpy (1:1.26.4+ds-12) ... Setting up texlive-pictures (2024.20241115-1) ... Setting up texlive-fonts-recommended (2024.20241115-1) ... Setting up openmpi-bin (5.0.6-3) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/mpiexec.1.gz because associated file /usr/share/man/man1/mpiexec.openmpi.1.gz (of link group mpirun) doesn't exist update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up dh-python (6.20241024) ... Setting up mpi-default-bin (1.17) ... Setting up texlive-latex-extra (2024.20241115-1) ... Setting up python3-mpi4py (4.0.1-6+b1) ... Setting up libheif-plugin-dav1d:amd64 (1.19.3-1) ... Setting up libheif-plugin-libde265:amd64 (1.19.3-1) ... Setting up libheif1:amd64 (1.19.3-1) ... Setting up libgd3:amd64 (2.3.3-12+b1) ... Setting up libgvc6 (2.42.4-2+b1) ... Setting up graphviz (2.42.4-2+b1) ... Setting up libgraphicsmagick-q16-3t64 (1.4+really1.3.45-1+b1) ... Setting up mscgen (0.20-16) ... Setting up graphicsmagick (1.4+really1.3.45-1+b1) ... Processing triggers for libc-bin (2.40-4) ... Processing triggers for ca-certificates-java (20240118) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:BJCA_Global_Root_CA1.pem Adding debian:BJCA_Global_Root_CA2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:CommScope_Public_Trust_ECC_Root-01.pem Adding debian:CommScope_Public_Trust_ECC_Root-02.pem Adding debian:CommScope_Public_Trust_RSA_Root-01.pem Adding debian:CommScope_Public_Trust_RSA_Root-02.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustAsia_Global_Root_CA_G3.pem Adding debian:TrustAsia_Global_Root_CA_G4.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up ant (1.10.15-1) ... Setting up default-jre-headless (2:1.21-76) ... Setting up ant-optional (1.10.15-1) ... Setting up libfop-java (1:2.10+dfsg-1) ... Setting up plantuml (1:1.2020.2+ds-5) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.21.2+dfsg-2) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up python3-sphinx (7.4.7-4) ... Setting up libpmix-dev:amd64 (5.0.4-1) ... Setting up python3-sphinx-copybutton (0.5.2-2) ... Setting up python3-sphinxcontrib.plantuml (0.5-8) ... Setting up python3-sphinx-argparse (0.5.2-1) ... Setting up sphinx-basic-ng (1.0.0~beta2-1) ... Setting up python3-sphinx-inline-tabs (2023.4.21-1) ... Setting up python3-sphinxcontrib.autoprogram (0.1.9-1) ... Setting up libopenmpi-dev:amd64 (5.0.6-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode Setting up furo (2024.08.06+dfsg-1) ... Setting up mpi-default-dev (1.17) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for tex-common (6.18) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. Processing triggers for ca-certificates-java (20240118) ... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/gromacs-2024.4/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../gromacs_2024.4-1_source.changes dpkg-buildpackage: info: source package gromacs dpkg-buildpackage: info: source version 2024.4-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nicholas Breen dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh_testdir dh_testroot dh_clean build-basic build-mpi build-manual build/ py3clean admin docs debian/rules binary dh_testdir (mkdir -p build/basic; cd build/basic; cmake \ /build/reproducible-path/gromacs-2024.4 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-2024.4-1" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMX_SIMD=SSE4.1 -DGMX_MPI=OFF -DGMX_INSTALL_LEGACY_API=ON) -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.12.7", minimum required is "3.7") found components: Interpreter Development Development.Module Development.Embed -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Using default binary suffix: "" -- Using default library suffix: "" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable version "2.11.0", minimum required is "1.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1") -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so - found -- Performing Test C_msse4_1_FLAG_ACCEPTED -- Performing Test C_msse4_1_FLAG_ACCEPTED - Success -- Performing Test C_msse4_1_COMPILE_WORKS -- Performing Test C_msse4_1_COMPILE_WORKS - Success -- Performing Test CXX_msse4_1_FLAG_ACCEPTED -- Performing Test CXX_msse4_1_FLAG_ACCEPTED - Success -- Performing Test CXX_msse4_1_COMPILE_WORKS -- Performing Test CXX_msse4_1_COMPILE_WORKS - Success -- Enabling SSE4.1 SIMD instructions using CXX flags: -msse4.1 -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - AMD -- Detected build CPU brand - AMD EPYC-Rome Processor -- Detected build CPU family - 23 -- Detected build CPU model - 49 -- Detected build CPU stepping - 0 -- Detected build CPU features - aes amd apic avx avx2 clfsh cmov cx8 cx16 f16c fma lahf misalignsse mmx msr pclmuldq pdpe1gb popcnt pse rdrnd rdtscp sha sse2 sse3 sse4a sse4.1 sse4.2 ssse3 x2apic -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3f' -- Found fftw3f, version 3.3.10 -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/x86_64-linux-gnu/liblapack.so;/usr/lib/x86_64-linux-gnu/libblas.so -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed CMake Deprecation Warning at src/external/googletest/CMakeLists.txt:4 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. CMake Deprecation Warning at src/external/googletest/googlemock/CMakeLists.txt:39 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. CMake Deprecation Warning at src/external/googletest/googletest/CMakeLists.txt:49 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Found Python: /usr/bin/python3 (found version "3.12.7") found components: Interpreter -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test HAS_WARNING_NO_ARRAY_BOUNDS -- Performing Test HAS_WARNING_NO_ARRAY_BOUNDS - Success -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "7.4.7", minimum required is "4.0.0") found components: pygments -- Configuring done (19.7s) -- Generating done (0.8s) -- Build files have been written to: /build/reproducible-path/gromacs-2024.4/build/basic (mkdir -p build/basic-dp; cd build/basic-dp; cmake \ /build/reproducible-path/gromacs-2024.4 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-2024.4-1" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMX_SIMD=SSE4.1 -DGMX_MPI=OFF -DGMX_DOUBLE=ON) -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.12.7", minimum required is "3.7") found components: Interpreter Development Development.Module Development.Embed -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Using default binary suffix: "_d" -- Using default library suffix: "_d" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable version "2.11.0", minimum required is "1.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1") -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so - found -- Performing Test C_msse4_1_FLAG_ACCEPTED -- Performing Test C_msse4_1_FLAG_ACCEPTED - Success -- Performing Test C_msse4_1_COMPILE_WORKS -- Performing Test C_msse4_1_COMPILE_WORKS - Success -- Performing Test CXX_msse4_1_FLAG_ACCEPTED -- Performing Test CXX_msse4_1_FLAG_ACCEPTED - Success -- Performing Test CXX_msse4_1_COMPILE_WORKS -- Performing Test CXX_msse4_1_COMPILE_WORKS - Success -- Enabling SSE4.1 SIMD instructions using CXX flags: -msse4.1 -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - AMD -- Detected build CPU brand - AMD EPYC-Rome Processor -- Detected build CPU family - 23 -- Detected build CPU model - 49 -- Detected build CPU stepping - 0 -- Detected build CPU features - aes amd apic avx avx2 clfsh cmov cx8 cx16 f16c fma lahf misalignsse mmx msr pclmuldq pdpe1gb popcnt pse rdrnd rdtscp sha sse2 sse3 sse4a sse4.1 sse4.2 ssse3 x2apic -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3' -- Found fftw3, version 3.3.10 -- Looking for fftw_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/x86_64-linux-gnu/liblapack.so;/usr/lib/x86_64-linux-gnu/libblas.so -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed CMake Deprecation Warning at src/external/googletest/CMakeLists.txt:4 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. CMake Deprecation Warning at src/external/googletest/googlemock/CMakeLists.txt:39 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. CMake Deprecation Warning at src/external/googletest/googletest/CMakeLists.txt:49 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Found Python: /usr/bin/python3 (found version "3.12.7") found components: Interpreter -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test HAS_WARNING_NO_ARRAY_BOUNDS -- Performing Test HAS_WARNING_NO_ARRAY_BOUNDS - Success -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "7.4.7", minimum required is "4.0.0") found components: pygments -- Configuring done (21.0s) -- Generating done (0.6s) -- Build files have been written to: /build/reproducible-path/gromacs-2024.4/build/basic-dp (mkdir -p build/mpi; cd build/mpi; CC=/usr/bin/mpicc CXX=/usr/bin/mpicxx cmake \ /build/reproducible-path/gromacs-2024.4 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-2024.4-1" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMX_SIMD=SSE4.1 -DGMX_MPI=ON -DMPIEXEC="/usr/bin/mpiexec" -DGMXAPI=ON -DGMX_PYTHON_PACKAGE=ON) -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/mpicc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/mpicxx - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.12.7", minimum required is "3.7") found components: Interpreter Development Development.Module Development.Embed -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Found MPI_CXX: /usr/bin/mpicxx (found version "3.1") -- Found MPI: TRUE (found version "3.1") found components: CXX -- GROMACS library will use OpenMPI 5.0.6 -- Using default binary suffix: "_mpi" -- Using default library suffix: "_mpi" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable version "2.11.0", minimum required is "1.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1") -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so - found -- Performing Test C_msse4_1_FLAG_ACCEPTED -- Performing Test C_msse4_1_FLAG_ACCEPTED - Success -- Performing Test C_msse4_1_COMPILE_WORKS -- Performing Test C_msse4_1_COMPILE_WORKS - Success -- Performing Test CXX_msse4_1_FLAG_ACCEPTED -- Performing Test CXX_msse4_1_FLAG_ACCEPTED - Success -- Performing Test CXX_msse4_1_COMPILE_WORKS -- Performing Test CXX_msse4_1_COMPILE_WORKS - Success -- Enabling SSE4.1 SIMD instructions using CXX flags: -msse4.1 -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - AMD -- Detected build CPU brand - AMD EPYC-Rome Processor -- Detected build CPU family - 23 -- Detected build CPU model - 49 -- Detected build CPU stepping - 0 -- Detected build CPU features - aes amd apic avx avx2 clfsh cmov cx8 cx16 f16c fma lahf misalignsse mmx msr pclmuldq pdpe1gb popcnt pse rdrnd rdtscp sha sse2 sse3 sse4a sse4.1 sse4.2 ssse3 x2apic -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3f' -- Found fftw3f, version 3.3.10 -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/x86_64-linux-gnu/liblapack.so;/usr/lib/x86_64-linux-gnu/libblas.so -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed CMake Deprecation Warning at src/external/googletest/CMakeLists.txt:4 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. CMake Deprecation Warning at src/external/googletest/googlemock/CMakeLists.txt:39 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. CMake Deprecation Warning at src/external/googletest/googletest/CMakeLists.txt:49 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Found Python: /usr/bin/python3 (found version "3.12.7") found components: Interpreter -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test HAS_WARNING_NO_ARRAY_BOUNDS -- Performing Test HAS_WARNING_NO_ARRAY_BOUNDS - Success -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Performing Test HAS_FLTO -- Performing Test HAS_FLTO - Success -- Configuring Python package for gmxapi version 0.4.0 -- Using /build/reproducible-path/gromacs-2024.4/build/mpi/bin/gmx_mpi from build tree. -- Found pybind11: /usr/include (found version "2.13.6") -- Found Python interpreter: /usr/bin/python3 -- Python site-packages directory is /usr/lib/python./site-packages -- Found Doxygen: /usr/bin/doxygen (found version "1.9.8") found components: doxygen dot -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "7.4.7", minimum required is "4.0.0") found components: pygments -- Configuring done (30.8s) -- Generating done (0.8s) -- Build files have been written to: /build/reproducible-path/gromacs-2024.4/build/mpi (mkdir -p build/mpi-dp; cd build/mpi-dp; CC=/usr/bin/mpicc CXX=/usr/bin/mpicxx cmake \ /build/reproducible-path/gromacs-2024.4 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-2024.4-1" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMX_SIMD=SSE4.1 -DGMX_MPI=ON -DMPIEXEC="/usr/bin/mpiexec" -DGMX_DOUBLE=ON) -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/mpicc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/mpicxx - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.12.7", minimum required is "3.7") found components: Interpreter Development Development.Module Development.Embed -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Found MPI_CXX: /usr/bin/mpicxx (found version "3.1") -- Found MPI: TRUE (found version "3.1") found components: CXX -- GROMACS library will use OpenMPI 5.0.6 -- Using default binary suffix: "_mpi_d" -- Using default library suffix: "_mpi_d" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable version "2.11.0", minimum required is "1.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1") -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so - found -- Performing Test C_msse4_1_FLAG_ACCEPTED -- Performing Test C_msse4_1_FLAG_ACCEPTED - Success -- Performing Test C_msse4_1_COMPILE_WORKS -- Performing Test C_msse4_1_COMPILE_WORKS - Success -- Performing Test CXX_msse4_1_FLAG_ACCEPTED -- Performing Test CXX_msse4_1_FLAG_ACCEPTED - Success -- Performing Test CXX_msse4_1_COMPILE_WORKS -- Performing Test CXX_msse4_1_COMPILE_WORKS - Success -- Enabling SSE4.1 SIMD instructions using CXX flags: -msse4.1 -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - AMD -- Detected build CPU brand - AMD EPYC-Rome Processor -- Detected build CPU family - 23 -- Detected build CPU model - 49 -- Detected build CPU stepping - 0 -- Detected build CPU features - aes amd apic avx avx2 clfsh cmov cx8 cx16 f16c fma lahf misalignsse mmx msr pclmuldq pdpe1gb popcnt pse rdrnd rdtscp sha sse2 sse3 sse4a sse4.1 sse4.2 ssse3 x2apic -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3' -- Found fftw3, version 3.3.10 -- Looking for fftw_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/x86_64-linux-gnu/liblapack.so;/usr/lib/x86_64-linux-gnu/libblas.so -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed CMake Deprecation Warning at src/external/googletest/CMakeLists.txt:4 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. CMake Deprecation Warning at src/external/googletest/googlemock/CMakeLists.txt:39 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. CMake Deprecation Warning at src/external/googletest/googletest/CMakeLists.txt:49 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Found Python: /usr/bin/python3 (found version "3.12.7") found components: Interpreter -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test HAS_WARNING_NO_ARRAY_BOUNDS -- Performing Test HAS_WARNING_NO_ARRAY_BOUNDS - Success -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "7.4.7", minimum required is "4.0.0") found components: pygments -- Configuring done (30.3s) -- Generating done (1.4s) -- Build files have been written to: /build/reproducible-path/gromacs-2024.4/build/mpi-dp touch configure-stamp dh_testdir /usr/bin/make -j12 -C build/basic make[1]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/cmake -S/build/reproducible-path/gromacs-2024.4 -B/build/reproducible-path/gromacs-2024.4/build/basic --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2024.4/build/basic/CMakeFiles /build/reproducible-path/gromacs-2024.4/build/basic//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/selection /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/selection /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/options /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/parser.cpp.o -MF CMakeFiles/scanner.dir/parser.cpp.o.d -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/parser.cpp /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2024.4-Debian_2024.4_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2024.4 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2024.4/build/basic/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2024.4/build/basic/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2024.4-1 -P /build/reproducible-path/gromacs-2024.4/cmake/gmxGenerateVersionInfoWithoutGit.cmake cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c 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directory '/build/reproducible-path/gromacs-2024.4/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/programs /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/errhandler.cpp /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/bwlzh.c make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -MF CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o.d -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/lmfit/lmmin.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -c 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractoption.cpp.o -MF CMakeFiles/options.dir/abstractoption.cpp.o.d -o CMakeFiles/options.dir/abstractoption.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/abstractoption.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/energyanalysis && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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'/build/reproducible-path/gromacs-2024.4/build/basic' make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -MF CMakeFiles/linearalgebra.dir/eigensolver.cpp.o.d -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/eigensolver.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 1%] Built target release-version-info /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractsection.cpp.o -MF CMakeFiles/options.dir/abstractsection.cpp.o.d -o CMakeFiles/options.dir/abstractsection.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/abstractsection.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o -MF CMakeFiles/gmx_objlib.dir/gmx.cpp.o.d -o CMakeFiles/gmx_objlib.dir/gmx.cpp.o -c 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/lock.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/p2p_protocol.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/include 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-I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/p2p_wait.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include 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-I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/behaviorcollection.cpp.o -MF CMakeFiles/options.dir/behaviorcollection.cpp.o.d -o CMakeFiles/options.dir/behaviorcollection.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/behaviorcollection.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/collective.cpp [ 3%] Built target gmx_objlib cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o -MF CMakeFiles/linearalgebra.dir/matrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/matrix.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 3%] Built target lmfit_objlib cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvar_neuralnetworkcompute.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/huffmem.c [ 3%] Built target energyanalysis cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvaratoms.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/nonbonded_bench.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/profile.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarbias.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/comm.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/lz77.c cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoption.cpp.o -MF CMakeFiles/options.dir/filenameoption.cpp.o.d -o CMakeFiles/options.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/filenameoption.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast 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-fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/reduce.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/mtf.c cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/event.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT 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src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/topology.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 3%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/options.cpp.o -MF CMakeFiles/options.dir/options.cpp.o.d -o CMakeFiles/options.dir/options.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/options.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/list.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/type.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG 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-I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsassigner.cpp.o -MF CMakeFiles/options.dir/optionsassigner.cpp.o.d -o CMakeFiles/options.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionsassigner.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/xtc2.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 3%] Built target linearalgebra cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/scan.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/numa_malloc.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/once.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/xtc3.c cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/lib/tng_io.c cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/lib/md5.c cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarbias_histogram.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsection.cpp.o -MF CMakeFiles/options.dir/optionsection.cpp.o.d -o CMakeFiles/options.dir/optionsection.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionsection.cpp /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pulling /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/output.cpp.o -MF CMakeFiles/pulling.dir/output.cpp.o.d -o CMakeFiles/pulling.dir/output.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/output.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsvisitor.cpp.o -MF CMakeFiles/options.dir/optionsvisitor.cpp.o.d -o CMakeFiles/options.dir/optionsvisitor.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionsvisitor.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 7%] Built target thread_mpi cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarbias_histogram_reweight_amd.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarbias_meta.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarbias_restraint.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/timeunitmanager.cpp.o -MF CMakeFiles/options.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/treesupport.cpp.o -MF CMakeFiles/options.dir/treesupport.cpp.o.d -o CMakeFiles/options.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/treesupport.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull.cpp.o -MF CMakeFiles/pulling.dir/pull.cpp.o.d -o CMakeFiles/pulling.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/pull.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull_rotation.cpp.o -MF CMakeFiles/pulling.dir/pull_rotation.cpp.o.d -o CMakeFiles/pulling.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/pull_rotation.cpp cd 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src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullutil.cpp.o -MF CMakeFiles/pulling.dir/pullutil.cpp.o.d -o CMakeFiles/pulling.dir/pullutil.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/pullutil.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY 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-DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -MF CMakeFiles/pulling.dir/transformationcoordinate.cpp.o.d -o CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/transformationcoordinate.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_alchlambda.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 9%] Built target options cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_angles.cpp cd 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/build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_coordnums.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_distances.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection 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CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_neuralnetwork.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 11%] Built target tng_io_obj cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_protein.cpp cd 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/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -MF CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/checkpointhelper.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG 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/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/reportgpuusage.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o.d -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/computeglobalselement.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/constraintelement.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/topologyholder.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -MF CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/trajectoryelement.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 18%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2024.4/build/basic/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2024.4/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/errorformat.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -MF CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/exceptions.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/fatalerror.cpp In file included from /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/binaryinformation.cpp:87: /build/reproducible-path/gromacs-2024.4/build/basic/src/include/buildinfo.h:73:9: warning: "HWLOC_VERSION" redefined 73 | #define HWLOC_VERSION "2.11.0" | ^~~~~~~~~~~~~ In file included from /usr/include/hwloc.h:56, from /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/binaryinformation.cpp:62: /usr/include/x86_64-linux-gnu/hwloc/autogen/config.h:15:9: note: this is the location of the previous definition 15 | #define HWLOC_VERSION "2.11.2" | ^~~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include 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-DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -MF CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/inmemoryserializer.cpp cc1plus: note: unrecognized command-line option '-Wno-cast-function-type-strict' may have been intended to silence earlier diagnostics cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/mpiinfo.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -MF CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/niceheader.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/path.cpp.o -MF CMakeFiles/libgromacs.dir/utility/path.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/path.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/path.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/physicalnodecommunicator.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -MF CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -MF CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/smalloc.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -MF CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -MF CMakeFiles/libgromacs.dir/utility/strdb.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -MF CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -MF CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/txtdump.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include 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-DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include 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-msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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-DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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-DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include 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-msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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-I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/atomdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlist.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlist_tuning.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlistparams.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlistset.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistwork.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistwork.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistwork.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlistwork.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairsearch.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/prunekerneldispatch.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/simd_prune_kernel.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/simd_prune_kernel.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/simd_prune_kernel.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_prune_kernel.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/cmdlinehelpcontext.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/cmdlinehelpmodule.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o.d -o 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/neldermead.cpp.o -MF CMakeFiles/libgromacs.dir/math/neldermead.cpp.o.d -o CMakeFiles/libgromacs.dir/math/neldermead.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/nrjac.cpp.o -MF CMakeFiles/libgromacs.dir/math/nrjac.cpp.o.d -o CMakeFiles/libgromacs.dir/math/nrjac.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/optimization.cpp.o -MF CMakeFiles/libgromacs.dir/math/optimization.cpp.o.d -o CMakeFiles/libgromacs.dir/math/optimization.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/utilities.cpp.o -MF CMakeFiles/libgromacs.dir/math/utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -MF CMakeFiles/libgromacs.dir/math/veccompare.cpp.o.d -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -MF CMakeFiles/libgromacs.dir/math/vecdump.cpp.o.d -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/vecdump.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c 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/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/interaction_const.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/multipletimestepping.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/observableshistory.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/observablesreducer.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/state.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/threaded_force_buffer.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/helpformat.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/helpmanager.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/helptopic.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/random/seed.cpp.o -MF CMakeFiles/libgromacs.dir/random/seed.cpp.o.d -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -MF CMakeFiles/libgromacs.dir/restraint/manager.cpp.o.d -o 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -MF CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/restraintmdmodule.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -MF CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -MF CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -MF CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -MF CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -MF CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/idef.cpp.o -MF CMakeFiles/libgromacs.dir/topology/idef.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -MF CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/ifunc.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/index.cpp.o -MF CMakeFiles/libgromacs.dir/topology/index.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/index.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -MF CMakeFiles/libgromacs.dir/topology/invblock.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/invblock.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o -MF CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/mtop_atomloops.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -MF CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/mtop_util.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -MF CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/residuetypes.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -MF CMakeFiles/libgromacs.dir/topology/symtab.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -MF CMakeFiles/libgromacs.dir/topology/topsort.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -MF CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c 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cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -MF CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o.d -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/imd/imdsocket.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o -MF CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/communicator_stub.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -MF CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/utilities.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/angle_correction.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/binsearch.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/eigio.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_cluster.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_clustsize.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_confrms.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_covar.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_current.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_density.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_densmap.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_h2order.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_hbond.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_helix.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_helixorient.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_rama.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_rms.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_rmsdist.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_rmsf.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_vanhove.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_velacc.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wheel.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/fflibutil.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -MF 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CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/genconf.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/genhydro.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/genion.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o.d -o 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o.d -o 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constraint_gpu_helpers.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constraint_gpu_helpers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constraint_gpu_helpers.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl_stubs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl_stubs.cpp.o.d -o 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/lincs.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/mdatoms.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/mdgraph_gpu_impl.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/mdoutf.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/membed.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/sighandler.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/sim_util.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/simulationsignal.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/splitter.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o.d -o 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/updategroups.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/vcm.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/electricfield.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/awh.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/bias.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/biasgrid.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/biasparams.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/biassharing.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/biasstate.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o.d -o 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/listed_forces_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/listed_forces_gpu_impl.cpp.o.d -o 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -MF CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/calcgrid.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/fft.cpp 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CMakeFiles/libgromacs.dir/gpu_utils/pmalloc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/pmalloc.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -MF 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-DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacysimulator.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/threadaffinity.cpp cd 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/confio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/espio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/filetypes.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/groio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/matio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/matio.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/md5.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/md5.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/mrcdensitymap.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/mrcdensitymapheader.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/oenv.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/xtcio.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/xvgr.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -MF CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/centerofmass.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -MF CMakeFiles/libgromacs.dir/selection/compiler.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/compiler.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -MF CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/indexutil.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -MF CMakeFiles/libgromacs.dir/selection/mempool.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/mempool.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -MF CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -MF CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -MF CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -MF CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o.d -o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/gmxcalculatorcpu.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/integrator.cpp.o -MF CMakeFiles/nblib.dir/integrator.cpp.o.d -o CMakeFiles/nblib.dir/integrator.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/integrator.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/gmx.dir/link.d CMakeFiles/gmx_objlib.dir/gmx.cpp.o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../bin/gmx ../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 92%] Built target gmx cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/interactions.cpp.o -MF CMakeFiles/nblib.dir/interactions.cpp.o.d -o CMakeFiles/nblib.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/interactions.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/session.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/session.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/session.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/session.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/status.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/status.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/status.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/status.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/system.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/system.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/system.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/system.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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-I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/molecules.cpp.o -MF CMakeFiles/nblib.dir/molecules.cpp.o.d -o CMakeFiles/nblib.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/molecules.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/version.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/version.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/version.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/version.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/particletype.cpp.o -MF CMakeFiles/nblib.dir/particletype.cpp.o.d -o CMakeFiles/nblib.dir/particletype.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/particletype.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/template.dir/link.d CMakeFiles/template.dir/template.cpp.o -o ../../bin/template ../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 94%] Built target template cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/simulationstate.cpp.o -MF CMakeFiles/nblib.dir/simulationstate.cpp.o.d -o CMakeFiles/nblib.dir/simulationstate.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/simulationstate.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/tpr.cpp.o -MF CMakeFiles/nblib.dir/tpr.cpp.o.d -o CMakeFiles/nblib.dir/tpr.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tpr.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/virials.cpp.o -MF CMakeFiles/nblib.dir/virials.cpp.o.d -o CMakeFiles/nblib.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/virials.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tpr.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include 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CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/calculator.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/transformations.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/conversions.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/convertGmxToNblib.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/util/setup.cpp.o -MF CMakeFiles/nblib.dir/util/setup.cpp.o.d -o CMakeFiles/nblib.dir/util/setup.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/util/setup.cpp cd 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CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o ../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a cd /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgmxapi.so.0.4.0 ../../lib/libgmxapi.so.0 ../../lib/libgmxapi.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 96%] Built target gmxapi cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file,CMakeFiles/nblib.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libnblib_gmx.so.0 -o ../../lib/libnblib_gmx.so.0.1.0 CMakeFiles/nblib.dir/box.cpp.o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o CMakeFiles/nblib.dir/integrator.cpp.o CMakeFiles/nblib.dir/interactions.cpp.o CMakeFiles/nblib.dir/molecules.cpp.o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o CMakeFiles/nblib.dir/particlesequencer.cpp.o CMakeFiles/nblib.dir/particletype.cpp.o CMakeFiles/nblib.dir/simulationstate.cpp.o CMakeFiles/nblib.dir/topologyhelpers.cpp.o CMakeFiles/nblib.dir/topology.cpp.o CMakeFiles/nblib.dir/tpr.cpp.o CMakeFiles/nblib.dir/virials.cpp.o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o CMakeFiles/nblib.dir/util/setup.cpp.o -lm ../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib && /usr/bin/cmake -E cmake_symlink_library ../../lib/libnblib_gmx.so.0.1.0 ../../lib/libnblib_gmx.so.0 ../../lib/libnblib_gmx.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 98%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/basic 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src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build cd /build/reproducible-path/gromacs-2024.4 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2024.4-Debian_2024.4_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2024.4 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2024.4/build/basic-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2024.4/build/basic-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2024.4-1 -P /build/reproducible-path/gromacs-2024.4/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD 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-std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/errhandler.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/include 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-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/bwlzh.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 0%] Built target release-version-info cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -MF CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o.d -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/alltoall.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/p2p_protocol.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/bwt.c cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/scanner.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 0%] Built target gmx_objlib cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvar_neuralnetworkcompute.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/coder.c cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/barrier.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/p2p_send_recv.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/bcast.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/p2p_wait.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractsection.cpp.o -MF CMakeFiles/options.dir/abstractsection.cpp.o.d -o CMakeFiles/options.dir/abstractsection.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/abstractsection.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 0%] Built target lmfit_objlib cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvaratoms.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/dict.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 0%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o -MF CMakeFiles/linearalgebra.dir/matrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/matrix.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/fixpoint.c [ 0%] Built target energyanalysis cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/rle.c cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/group.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/tng_compress.c cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/tmpi_init.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/topology.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/list.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/type.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarbias_histogram.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/sparsematrix.cpp [ 0%] Built target scanner cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/scan.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/numa_malloc.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/vals16.c cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarbias_histogram_reweight_amd.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/once.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/warnmalloc.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 0%] Built target linearalgebra cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/widemuldiv.c cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/xtc2.c cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarbias_meta.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/options.cpp.o -MF CMakeFiles/options.dir/options.cpp.o.d -o CMakeFiles/options.dir/options.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/options.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/xtc3.c cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarbias_restraint.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/lib/tng_io.c /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pulling /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/output.cpp.o -MF CMakeFiles/pulling.dir/output.cpp.o.d -o CMakeFiles/pulling.dir/output.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/output.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsassigner.cpp.o -MF CMakeFiles/options.dir/optionsassigner.cpp.o.d -o CMakeFiles/options.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionsassigner.cpp [ 3%] Built target thread_mpi cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/lib/md5.c cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_alchlambda.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsection.cpp.o -MF CMakeFiles/options.dir/optionsection.cpp.o.d -o CMakeFiles/options.dir/optionsection.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionsection.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_angles.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsvisitor.cpp.o -MF CMakeFiles/options.dir/optionsvisitor.cpp.o.d -o CMakeFiles/options.dir/optionsvisitor.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionsvisitor.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_apath.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_combination.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/timeunitmanager.cpp.o -MF CMakeFiles/options.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull.cpp.o -MF CMakeFiles/pulling.dir/pull.cpp.o.d -o CMakeFiles/pulling.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/pull.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_distances.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/treesupport.cpp.o -MF CMakeFiles/options.dir/treesupport.cpp.o.d -o CMakeFiles/options.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/treesupport.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_gpath.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_neuralnetwork.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_protein.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull_rotation.cpp.o -MF CMakeFiles/pulling.dir/pull_rotation.cpp.o.d -o CMakeFiles/pulling.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/pull_rotation.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_rotations.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_volmaps.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvardeps.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 5%] Built target tng_io_obj cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvargrid.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarmodule.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 7%] Built target options cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 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/build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarparse.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarproxy.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullutil.cpp.o -MF CMakeFiles/pulling.dir/pullutil.cpp.o.d -o CMakeFiles/pulling.dir/pullutil.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/pullutil.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarproxy_io.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT 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/build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarproxy_volmaps.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvars_memstream.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat 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CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarscript_commands.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarscript_commands_bias.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarscript_commands_colvar.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 9%] Built target pulling cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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/build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarvalue.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/nr_jacobi.cpp /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/decidegpuusage.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include 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-DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/reportgpuusage.cpp /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator 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/build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/andersentemperaturecoupling.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/resourcedivision.cpp.o -MF CMakeFiles/taskassignment.dir/resourcedivision.cpp.o.d -o CMakeFiles/taskassignment.dir/resourcedivision.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/resourcedivision.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/taskassignment.cpp.o -MF CMakeFiles/taskassignment.dir/taskassignment.cpp.o.d -o CMakeFiles/taskassignment.dir/taskassignment.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/taskassignment.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include 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-std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o -MF CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o.d -o CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/freeenergyperturbationdata.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 9%] Built target taskassignment cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/mttk.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 13%] Built target colvars_objlib cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -MF CMakeFiles/modularsimulator.dir/topologyholder.cpp.o.d -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/topologyholder.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 15%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2024.4/build/basic-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2024.4/cmake/gmxConfigureVersionInfo.cmake cd 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/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/any.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -MF CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/basenetwork.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/baseversion.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -MF CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/binaryinformation.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/booltype.cpp.o -MF CMakeFiles/libgromacs.dir/utility/booltype.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/booltype.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/booltype.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/compare.cpp.o -MF CMakeFiles/libgromacs.dir/utility/compare.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/compare.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -MF CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/coolstuff.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/cstringutil.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -MF CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/datafilefinder.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/directoryenumerator.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/errorcodes.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/errorformat.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -MF CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/exceptions.cpp In file included from /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/binaryinformation.cpp:87: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include/buildinfo.h:73:9: warning: "HWLOC_VERSION" redefined 73 | #define HWLOC_VERSION "2.11.0" | ^~~~~~~~~~~~~ In file included from /usr/include/hwloc.h:56, from /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/binaryinformation.cpp:62: /usr/include/x86_64-linux-gnu/hwloc/autogen/config.h:15:9: note: this is the location of the previous definition 15 | #define HWLOC_VERSION "2.11.2" | ^~~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/fatalerror.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -MF CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/inmemoryserializer.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -MF CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/int64_to_int.cpp cc1plus: note: unrecognized command-line option '-Wno-cast-function-type-strict' may have been intended to silence earlier diagnostics cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/keyvaluetree.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -MF 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-Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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-I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include 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-funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/atomdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/exclusionchecker.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/exclusionchecker.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/exclusionchecker.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/freeenergydispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/freeenergydispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/freeenergydispatch.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/freeenergydispatch.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/grid.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/gridset.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernel_common.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kerneldispatch.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include 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-O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_geometry.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c 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/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/domdec_specatomcomm.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/domdec_vsite.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dump.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/dump.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/ga2la.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/gpuhaloexchange_impl.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/localatomset.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/localatomsetdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/localatomsetmanager.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localtopology.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localtopology.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localtopology.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/localtopology.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localtopologychecker.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localtopologychecker.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localtopologychecker.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/localtopologychecker.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/makebondedlinks.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/makebondedlinks.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/makebondedlinks.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/makebondedlinks.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/mdsetup.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/nsgrid.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/partition.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/partition.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/utility.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/utility.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -MF CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o.d -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/3dtransforms.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -MF CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o.d -o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/coordinatetransformation.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -MF CMakeFiles/libgromacs.dir/math/densityfit.cpp.o.d -o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/densityfit.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -MF CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o.d -o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/densityfittingforce.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -MF CMakeFiles/libgromacs.dir/math/do_fit.cpp.o.d -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/do_fit.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -MF CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o.d -o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/exponentialmovingaverage.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/functions.cpp.o -MF CMakeFiles/libgromacs.dir/math/functions.cpp.o.d -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/functions.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -MF CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o.d -o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/gausstransform.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -MF CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o.d -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/invertmatrix.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/matrix.cpp.o -MF CMakeFiles/libgromacs.dir/math/matrix.cpp.o.d -o CMakeFiles/libgromacs.dir/math/matrix.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/matrix.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/neldermead.cpp.o -MF CMakeFiles/libgromacs.dir/math/neldermead.cpp.o.d -o CMakeFiles/libgromacs.dir/math/neldermead.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/nrjac.cpp.o -MF CMakeFiles/libgromacs.dir/math/nrjac.cpp.o.d -o CMakeFiles/libgromacs.dir/math/nrjac.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/optimization.cpp.o -MF CMakeFiles/libgromacs.dir/math/optimization.cpp.o.d -o CMakeFiles/libgromacs.dir/math/optimization.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/optimization.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/utilities.cpp.o -MF CMakeFiles/libgromacs.dir/math/utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/utilities.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -MF CMakeFiles/libgromacs.dir/math/veccompare.cpp.o.d -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -MF CMakeFiles/libgromacs.dir/math/vecdump.cpp.o.d -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/commrec.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/df_history.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/energyhistory.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/forcebuffers.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/group.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/iforceprovider.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/inputrec.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/interaction_const.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/md_enums.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/state.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/helpformat.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/helpmanager.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/boxutilities.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/com.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/mshift.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/pbc.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/random/seed.cpp.o -MF CMakeFiles/libgromacs.dir/random/seed.cpp.o.d -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -MF CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -MF CMakeFiles/libgromacs.dir/restraint/manager.cpp.o.d -o 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -MF CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -MF CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/tables/splineutil.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -MF CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/timing/cyclecounter.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -MF CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/timing/wallcycle.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -MF CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/timing/walltime_accounting.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/atomprop.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atoms.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/atoms.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/atomsbuilder.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/block.cpp.o -MF CMakeFiles/libgromacs.dir/topology/block.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/block.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -MF CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/exclusionblocks.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -MF CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/idef.cpp.o -MF CMakeFiles/libgromacs.dir/topology/idef.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/idef.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -MF CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/ifunc.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/index.cpp.o -MF CMakeFiles/libgromacs.dir/topology/index.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/index.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -MF CMakeFiles/libgromacs.dir/topology/invblock.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o -MF CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -MF CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -MF CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/residuetypes.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -MF CMakeFiles/libgromacs.dir/topology/symtab.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/symtab.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/topology.cpp.o -MF CMakeFiles/libgromacs.dir/topology/topology.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/topology.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -MF CMakeFiles/libgromacs.dir/topology/topsort.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/topsort.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -MF CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/energyframe.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -MF CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/trajectoryframe.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -MF CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o.d -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/swap/swapcoords.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -MF CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o.d -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/edsam.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/imd/imd.cpp.o -MF CMakeFiles/libgromacs.dir/imd/imd.cpp.o.d -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/imd/imd.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -MF CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o.d -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/imd/imdsocket.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o -MF CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -MF CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/dens_filter.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/dlist.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/eigio.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/fitahx.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_anaeig.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_analyze.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_angle.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_confrms.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_dipoles.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_disre.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_dos.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_dyecoupl.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_nmeig.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_nmens.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_nmr.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_nmtraj.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_sham.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_sorient.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_spatial.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/nsfactor.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/powerspect.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/pp2shift.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/princ.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/sfactor.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/thermochemistry.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/add_par.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/calch.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/convparm.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/gen_maxwell_velocities.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2top.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pgutil.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/readir.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/readpull.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/readrot.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/resall.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/solvate.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/specbond.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/ter_db.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/topshake.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/toputil.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/vsite_parm.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/x2top.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/xlate.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/autocorr.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/abstractdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/analysisdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/arraydata.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/dataframe.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/datamodule.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/datamodulemanager.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/dataproxy.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/modules/scattering-debye.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && 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-DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o -MF CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/tools/trjcat.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -MF CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/tools/trjconv.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -MF CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/tools/tune_pme.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/conformation_utilities.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/network.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nrnb.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/calcmu.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/calcvir.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constraint_gpu_helpers.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constraint_gpu_helpers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constraint_gpu_helpers.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/constraintrange.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/dispersioncorrection.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/ebin.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/enerdata_utils.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/energydrifttracker.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/energyoutput.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/expanded.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/expanded_internal.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/force.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/force.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/forcerec.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl_stubs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl_stubs.cpp.o.d -o 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/md_support.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/mdatoms.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/mdebin_bar.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/mdgraph_gpu_impl.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/mdoutf.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/membed.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/perf_est.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/rbin.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/settle.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/sim_util.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/simulationsignal.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tgroup.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update_constrain_gpu_impl_stubs.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update_vv.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/updategroups.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/updategroupscog.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/vcm.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/vsite.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/wall.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/wholemoleculetransform.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/electricfield.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o.d -o 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o -MF 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/densityfitting/densityfittingoutputprovider.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/qmmm/qmmm.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceprovider_stub.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceprovider_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceprovider_stub.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/qmmm/qmmmforceprovider_stub.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsMDModule.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsMDModule.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsMDModule.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/colvarsMDModule.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/listed_forces_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/listed_forces_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/listed_forces_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_impl.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_internal.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_comm_gpu_impl.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_force_sender_gpu_impl.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/pmalloc.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/pmalloc.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/pmalloc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/pmalloc.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/cpuinfo.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/detecthardware.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o.d -o 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/device_management.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/mimic.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/minimize.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/replicaexchange.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/rerun.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/runner.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/shellfc.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationcontext.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinput.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinputhandle.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/tpi.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/freeenergy.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/handlerestart.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/logging.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o.d 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/printtime.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -MF CMakeFiles/libgromacs.dir/selection/compiler.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/compiler.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -MF CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -MF CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/indexutil.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -MF CMakeFiles/libgromacs.dir/selection/mempool.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/mempool.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -MF CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/nbsearch.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/params.cpp.o -MF CMakeFiles/libgromacs.dir/selection/params.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/params.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/params.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -MF CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/parsetree.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -MF CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/position.cpp.o -MF CMakeFiles/libgromacs.dir/selection/position.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/position.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -MF CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/selection.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/selectionoption.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o.d -o 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -MF CMakeFiles/libgromacs.dir/selection/symrec.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/symrec.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file,CMakeFiles/libgromacs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgromacs_d.so.9 -o ../../lib/libgromacs_d.so.9.0.0 @CMakeFiles/libgromacs.dir/objects1.rsp /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so -lm /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 -lmuparser cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs_d.so.9.0.0 ../../lib/libgromacs_d.so.9 ../../lib/libgromacs_d.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 92%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/gmxapi /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/resourceassignment.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/box.cpp.o -MF CMakeFiles/nblib.dir/box.cpp.o.d -o CMakeFiles/nblib.dir/box.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/box.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/context.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/context.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/context.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/context.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -MF CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o.d -o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/gmxcalculatorcpu.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/exceptions.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/integrator.cpp.o -MF CMakeFiles/nblib.dir/integrator.cpp.o.d -o CMakeFiles/nblib.dir/integrator.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/integrator.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/gmxapi.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/md.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/md.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/md.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/md.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/interactions.cpp.o -MF CMakeFiles/nblib.dir/interactions.cpp.o.d -o CMakeFiles/nblib.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/interactions.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/mdmodule.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/molecules.cpp.o -MF CMakeFiles/nblib.dir/molecules.cpp.o.d -o CMakeFiles/nblib.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/molecules.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/mdsignals.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/gmx.dir/link.d CMakeFiles/gmx_objlib.dir/gmx.cpp.o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../bin/gmx_d ../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/session.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/session.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/session.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/session.cpp [ 94%] Built target gmx cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/status.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/status.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/status.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/status.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/system.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/system.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/system.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/system.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/version.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/version.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/version.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/version.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -MF CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o.d -o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/nbnxmsetuphelpers.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/workflow.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tpr.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/particlesequencer.cpp.o -MF CMakeFiles/nblib.dir/particlesequencer.cpp.o.d -o CMakeFiles/nblib.dir/particlesequencer.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/particlesequencer.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/particletype.cpp.o -MF CMakeFiles/nblib.dir/particletype.cpp.o.d -o CMakeFiles/nblib.dir/particletype.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/particletype.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/simulationstate.cpp.o -MF CMakeFiles/nblib.dir/simulationstate.cpp.o.d -o CMakeFiles/nblib.dir/simulationstate.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/simulationstate.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include 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CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o CMakeFiles/gmxapi.dir/cpp/md.cpp.o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o CMakeFiles/gmxapi.dir/cpp/session.cpp.o CMakeFiles/gmxapi.dir/cpp/status.cpp.o CMakeFiles/gmxapi.dir/cpp/system.cpp.o CMakeFiles/gmxapi.dir/cpp/version.cpp.o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o ../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgmxapi_d.so.0.4.0 ../../lib/libgmxapi_d.so.0 ../../lib/libgmxapi_d.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 96%] Built target gmxapi cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file,CMakeFiles/nblib.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libnblib_gmx.so.0 -o ../../lib/libnblib_gmx.so.0.1.0 CMakeFiles/nblib.dir/box.cpp.o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o CMakeFiles/nblib.dir/integrator.cpp.o CMakeFiles/nblib.dir/interactions.cpp.o CMakeFiles/nblib.dir/molecules.cpp.o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o CMakeFiles/nblib.dir/particlesequencer.cpp.o CMakeFiles/nblib.dir/particletype.cpp.o CMakeFiles/nblib.dir/simulationstate.cpp.o CMakeFiles/nblib.dir/topologyhelpers.cpp.o CMakeFiles/nblib.dir/topology.cpp.o CMakeFiles/nblib.dir/tpr.cpp.o CMakeFiles/nblib.dir/virials.cpp.o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o 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-I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -MF CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o.d -o CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/samples/argon-forces-integration.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/methane-water-integration.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong 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/usr/bin/cmake -S/build/reproducible-path/gromacs-2024.4 -B/build/reproducible-path/gromacs-2024.4/build/basic --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 tests make[2]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/cmake -S/build/reproducible-path/gromacs-2024.4 -B/build/reproducible-path/gromacs-2024.4/build/basic --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2024.4/build/basic/CMakeFiles 74 /usr/bin/make -f CMakeFiles/Makefile2 CMakeFiles/tests.dir/all make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend /usr/bin/make -f src/external/googletest/googletest/CMakeFiles/gtest.dir/build.make src/external/googletest/googletest/CMakeFiles/gtest.dir/depend /usr/bin/make -f 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src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 0%] Built target energyanalysis [ 0%] Built target linearalgebra /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend [ 0%] Built target scanner [ 0%] Built target lmfit_objlib make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[4]: Leaving directory 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make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 8%] Built target colvars_objlib [ 9%] Built target options [ 10%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/taskassignment 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/usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && 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api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' make[4]: Nothing to be done for 'api/nblib/samples/CMakeFiles/methane-water-integration.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 67%] Built target argon-forces-integration [ 68%] Built target methane-water-integration cd /build/reproducible-path/gromacs-2024.4/build/basic/src/external/googletest/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file,CMakeFiles/gtest.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgtest.so.1.13.0 -o ../../../../lib/libgtest.so.1.13.0 "CMakeFiles/gtest.dir/src/gtest-all.cc.o" cd /build/reproducible-path/gromacs-2024.4/build/basic/src/external/googletest/googletest && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgtest.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 68%] Built target gtest /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock /build/reproducible-path/gromacs-2024.4/build/basic 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-I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest 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/usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o -MF CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o.d -o CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 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/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/densityfitting/tests/densityfitting.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build /usr/bin/make -f src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build.make src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem 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/usr/bin/make -f src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build.make src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/qmmm/tests/qmmminputgenerator.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" 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-I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest 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src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/densityfitting/tests/densityfittingamplitudelookup.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o -MF 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/usr/lib/x86_64-linux-gnu/libpthread.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 70%] Built target testutils-mpi-test cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/tests/colvarspreprocessor.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constr.cpp.o -MF CMakeFiles/mdlib-test.dir/constr.cpp.o.d -o CMakeFiles/mdlib-test.dir/constr.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/constr.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/arrayref.cpp.o -MF CMakeFiles/utility-test.dir/arrayref.cpp.o.d -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/arrayref.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biasgrid.cpp.o -MF CMakeFiles/awh-test.dir/biasgrid.cpp.o.d -o CMakeFiles/awh-test.dir/biasgrid.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/biasgrid.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/moduletest.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/densityfitting/tests/densityfittingforceprovider.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2024.4/src/testutils/tests/testasserts_tests.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulatorcomparison.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -DGMX_CP2K=0 -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/qmmm/tests/qmmmforceprovider.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests && /usr/bin/cmake -P CMakeFiles/nblib_test_infrastructure.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib_test_infrastructure.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../lib/libnblib_test_infrastructure.a CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o /usr/bin/ranlib ../../../lib/libnblib_test_infrastructure.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 70%] Built target nblib_test_infrastructure cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/constrtestdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/tests/colvarsforceprovider.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include 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src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biassharing.cpp.o -MF CMakeFiles/awh-test.dir/biassharing.cpp.o.d -o CMakeFiles/awh-test.dir/biassharing.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/biassharing.cpp /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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-I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/qmmm/tests/qmmm.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxlib/nonbonded/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nonbonded-fep-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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/usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 70%] Built target nonbonded-fep-test cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -MF CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o.d -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/trajectorycomparison.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biasstate.cpp.o -MF CMakeFiles/awh-test.dir/biasstate.cpp.o.d -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/biasstate.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -MF CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o.d -o CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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/build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/exclusions.cpp.o -MF CMakeFiles/nbnxm-test.dir/exclusions.cpp.o.d -o CMakeFiles/nbnxm-test.dir/exclusions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/exclusions.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/density_fitting_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/density_fitting_applied_forces-test.dir/link.d "CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/density_fitting_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.9.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 70%] Built target density_fitting_applied_forces-test cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/friction_metric.cpp.o -MF CMakeFiles/awh-test.dir/friction_metric.cpp.o.d -o CMakeFiles/awh-test.dir/friction_metric.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/friction_metric.cpp /usr/bin/c++ -g -O2 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directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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-DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o -MF CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o.d -o CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/energydrifttracker.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/qmmm_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/colvars_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" 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make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 70%] Built target colvars_applied_forces-test /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake "--color=" /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/qmmm_applied_forces-test.dir/link.d "CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/qmmm_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.9.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem 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src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -MF CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o.d -o CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/tests/haloexchange_mpi.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -MF CMakeFiles/mdlib-test.dir/energyoutput.cpp.o.d -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/energyoutput.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -MF CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o.d -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/tests/localatomsetmanager.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -P CMakeFiles/mdrun_test_infrastructure.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun_test_infrastructure.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o -MF CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o.d -o CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp /usr/bin/ar qc ../../../../lib/libmdrun_test_infrastructure.a CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o /usr/bin/ranlib ../../../../lib/libmdrun_test_infrastructure.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 70%] Built target mdrun_test_infrastructure cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/expanded.cpp.o -MF CMakeFiles/mdlib-test.dir/expanded.cpp.o.d -o CMakeFiles/mdlib-test.dir/expanded.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/expanded.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o -MF CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o.d -o CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/tests/position_restraints.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libonlinehelp-test-shared.a "CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o" "CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 70%] Built target onlinehelp-test-shared cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -MF CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o.d -o CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/freeenergyparameters.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/awh-test.dir/link.d "CMakeFiles/awh-test.dir/awh_setup.cpp.o" "CMakeFiles/awh-test.dir/bias.cpp.o" "CMakeFiles/awh-test.dir/biasgrid.cpp.o" "CMakeFiles/awh-test.dir/biassharing.cpp.o" "CMakeFiles/awh-test.dir/biasstate.cpp.o" "CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o" "CMakeFiles/awh-test.dir/friction_metric.cpp.o" "CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/awh-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.9.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 71%] Built target awh-test cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/booltype.cpp.o -MF CMakeFiles/utility-test.dir/booltype.cpp.o.d -o CMakeFiles/utility-test.dir/booltype.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/booltype.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask32.cpp.o -MF CMakeFiles/utility-test.dir/bitmask32.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/bitmask32.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o -MF CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o.d -o CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernelsetup.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/domdec-mpi-test.dir/link.d "CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o" "CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 72%] Built target domdec-mpi-test cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/domdec-test.dir/link.d "CMakeFiles/domdec-test.dir/hashedmap.cpp.o" "CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o" "CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 72%] Built target domdec-test /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make 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-DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/leapfrogtestdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask128.cpp.o -MF CMakeFiles/utility-test.dir/bitmask128.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/bitmask128.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include 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src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o -MF CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o.d -o CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/parrinellorahman.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src 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CMakeFiles/ewald-test.dir/pmegathertest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmegathertest.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem 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CMakeFiles/utility-test.dir/cstringutil.cpp.o.d -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/cstringutil.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settle.cpp.o -MF CMakeFiles/mdlib-test.dir/settle.cpp.o.d -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/settle.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/listed_forces-test.dir/link.d "CMakeFiles/listed_forces-test.dir/bonded.cpp.o" "CMakeFiles/listed_forces-test.dir/pairs.cpp.o" "CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o" "CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/listed_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 72%] Built target listed_forces-test /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fft/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests/fft.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/settletestdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY 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/usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 72%] Built target nbnxm-test /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory 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CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/tests/device_stream_manager.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -MF CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o.d -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/fixedcapacityvector.cpp /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/math/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include 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src/gromacs/math/tests/CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -MF CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o.d -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/arrayrefwithpadding.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o -MF CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/tests/pinnedmemorychecker.cpp cd 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/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/keyvaluetreetransform.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/updategroups.cpp.o -MF CMakeFiles/mdlib-test.dir/updategroups.cpp.o.d -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/updategroups.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o -MF CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o.d -o CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/tests/mockhardwaretopology.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pme.cpp.o -MF CMakeFiles/ewald-test.dir/pme.cpp.o.d -o CMakeFiles/ewald-test.dir/pme.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pme.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -MF CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/tests/devicetransfers.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/fft-test.dir/link.d "CMakeFiles/fft-test.dir/fft.cpp.o" "CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 74%] Built target fft-test cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest 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/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/updategroupscog.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -isystem 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CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o.d -o CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/tests/accessor_policy.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/ewald-test.dir/link.d "CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o" "CMakeFiles/ewald-test.dir/pmegathertest.cpp.o" "CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o" "CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o" "CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o" "CMakeFiles/ewald-test.dir/pme.cpp.o" "CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/logger.cpp.o -MF CMakeFiles/utility-test.dir/logger.cpp.o.d -o CMakeFiles/utility-test.dir/logger.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/logger.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/hardware-test.dir/link.d "CMakeFiles/hardware-test.dir/cpuinfo.cpp.o" "CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/device_management.cpp.o" "CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/tests/helpmanager.cpp [ 74%] Built target hardware-test cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoption.cpp.o -MF CMakeFiles/options-test.dir/filenameoption.cpp.o.d -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/tests/filenameoption.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/message_string_collector.cpp.o -MF CMakeFiles/utility-test.dir/message_string_collector.cpp.o.d -o CMakeFiles/utility-test.dir/message_string_collector.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/message_string_collector.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdlib-test.dir/link.d "CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o" "CMakeFiles/mdlib-test.dir/calcvir.cpp.o" "CMakeFiles/mdlib-test.dir/constr.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/ebin.cpp.o" "CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o" "CMakeFiles/mdlib-test.dir/energyoutput.cpp.o" "CMakeFiles/mdlib-test.dir/expanded.cpp.o" "CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrog.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o" "CMakeFiles/mdlib-test.dir/settle.cpp.o" "CMakeFiles/mdlib-test.dir/settletestdata.cpp.o" "CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/shake.cpp.o" "CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o" "CMakeFiles/mdlib-test.dir/updategroups.cpp.o" "CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o" "CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o" "CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 77%] Built target mdlib-test /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/com.cpp.o -MF CMakeFiles/pbcutil-test.dir/com.cpp.o.d -o CMakeFiles/pbcutil-test.dir/com.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/tests/com.cpp /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/random/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/random/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -MF CMakeFiles/random-test.dir/exponentialdistribution.cpp.o.d -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/random/tests/exponentialdistribution.cpp cd 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o -MF CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/tests/typecasts.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/mshift.cpp.o -MF CMakeFiles/pbcutil-test.dir/mshift.cpp.o.d -o CMakeFiles/pbcutil-test.dir/mshift.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/tests/mshift.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/normaldistribution.cpp.o -MF CMakeFiles/random-test.dir/normaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/random/tests/normaldistribution.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/gpu_utils-test.dir/link.d "CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o" "CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o" "CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o" "CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o" "CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o" "CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o" "CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 77%] Built target gpu_utils-test cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/seed.cpp.o -MF CMakeFiles/random-test.dir/seed.cpp.o.d -o CMakeFiles/random-test.dir/seed.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/random/tests/seed.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/onlinehelp-test.dir/link.d "CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o" "CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 77%] Built target onlinehelp-test /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory 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-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -MF CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/random/tests/tabulatednormaldistribution.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbc.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbc.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/tests/pbc.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/restraint/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/tests/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/tests/pbcenums.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdspan-test.dir/link.d "CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o" "CMakeFiles/mdspan-test.dir/extents.cpp.o" "CMakeFiles/mdspan-test.dir/extensions.cpp.o" "CMakeFiles/mdspan-test.dir/layouts.cpp.o" "CMakeFiles/mdspan-test.dir/mdspan.cpp.o" "CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 77%] Built target mdspan-test cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/invertmatrix.cpp.o -MF CMakeFiles/math-test.dir/invertmatrix.cpp.o.d -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/invertmatrix.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/restraintpotential-test.dir/link.d "CMakeFiles/restraintpotential-test.dir/manager.cpp.o" "CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 77%] Built target restraintpotential-test cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o -MF CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o.d -o CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/stringtoenumvalueconverter.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -MF CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o.d -o CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/forcebuffers.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o -MF CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o.d -o CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/multipletimestepping.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" 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../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 78%] Built target pbcutil-test cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/stringutil.cpp.o -MF CMakeFiles/utility-test.dir/stringutil.cpp.o.d -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/stringutil.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/neldermead.cpp.o -MF CMakeFiles/math-test.dir/neldermead.cpp.o.d -o CMakeFiles/math-test.dir/neldermead.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/neldermead.cpp /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2024.4/build/basic 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directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/pull.cpp.o -MF CMakeFiles/pull-test.dir/pull.cpp.o.d -o CMakeFiles/pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/tests/pull.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdtypes/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdtypes-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/timing/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/timing/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/timing/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/timing/tests/CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdtypes-test.dir/link.d "CMakeFiles/mdtypes-test.dir/enerdata.cpp.o" "CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o" "CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o" "CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o" "CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o" "CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdtypes-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 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/build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -MF CMakeFiles/random-test.dir/uniformintdistribution.cpp.o.d -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/random/tests/uniformintdistribution.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/timing/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/timing-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/table-test.dir/link.d "CMakeFiles/table-test.dir/splinetable.cpp.o" "CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 78%] Built target table-test cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -MF CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o.d -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/bootstrap_loadstore.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/timing-test.dir/link.d "CMakeFiles/timing-test.dir/timing.cpp.o" "CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/timing-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 78%] Built target timing-test cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/textreader.cpp.o -MF CMakeFiles/utility-test.dir/textreader.cpp.o.d -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/textreader.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/taskassignment-test.dir/link.d "CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o" "CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o ../CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o ../CMakeFiles/taskassignment.dir/findallgputasks.cpp.o ../CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o ../CMakeFiles/taskassignment.dir/resourcedivision.cpp.o ../CMakeFiles/taskassignment.dir/taskassignment.cpp.o ../CMakeFiles/taskassignment.dir/usergpuids.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 78%] Built target taskassignment-test cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar.cpp.o -MF CMakeFiles/simd-test.dir/scalar.cpp.o.d -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/scalar.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_util.cpp.o -MF CMakeFiles/simd-test.dir/scalar_util.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/scalar_util.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/idef.cpp.o -MF CMakeFiles/topology-test.dir/idef.cpp.o.d -o CMakeFiles/topology-test.dir/idef.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/idef.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/textwriter.cpp.o -MF CMakeFiles/utility-test.dir/textwriter.cpp.o.d -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/textwriter.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -MF CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o.d -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/random/tests/uniformrealdistribution.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/index.cpp.o -MF CMakeFiles/topology-test.dir/index.cpp.o.d -o CMakeFiles/topology-test.dir/index.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/index.cpp /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/compat/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/vectypes.cpp.o -MF CMakeFiles/math-test.dir/vectypes.cpp.o.d -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/vectypes.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem 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/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_math.cpp.o -MF CMakeFiles/simd-test.dir/scalar_math.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/scalar_math.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/timeunitmanager.cpp.o -MF CMakeFiles/options-test.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/tests/timeunitmanager.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/pull-test.dir/link.d "CMakeFiles/pull-test.dir/pull.cpp.o" "CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/pulling.dir/output.cpp.o ../CMakeFiles/pulling.dir/pull.cpp.o ../CMakeFiles/pulling.dir/pull_rotation.cpp.o ../CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o ../CMakeFiles/pulling.dir/pullutil.cpp.o ../CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lmuparser -lm ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/treesupport.cpp.o -MF CMakeFiles/options-test.dir/treesupport.cpp.o.d -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/tests/treesupport.cpp [ 78%] Built target pull-test cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/pointers.cpp.o -MF CMakeFiles/compat-test.dir/pointers.cpp.o.d -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/tests/pointers.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/random-test.dir/link.d "CMakeFiles/random-test.dir/exponentialdistribution.cpp.o" "CMakeFiles/random-test.dir/gammadistribution.cpp.o" "CMakeFiles/random-test.dir/normaldistribution.cpp.o" "CMakeFiles/random-test.dir/seed.cpp.o" "CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o" "CMakeFiles/random-test.dir/threefry.cpp.o" "CMakeFiles/random-test.dir/uniformintdistribution.cpp.o" "CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o" "CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 78%] Built target random-test cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd.cpp.o -MF CMakeFiles/simd-test.dir/simd.cpp.o.d -o CMakeFiles/simd-test.dir/simd.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/simd.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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-DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/symtab.cpp.o -MF CMakeFiles/topology-test.dir/symtab.cpp.o.d -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/symtab.cpp /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/simd_floatingpoint.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/compat-test.dir/link.d "CMakeFiles/compat-test.dir/mp11.cpp.o" "CMakeFiles/compat-test.dir/pointers.cpp.o" "CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 78%] Built target compat-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/tests/gmx_chi.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/topsort.cpp.o -MF CMakeFiles/topology-test.dir/topsort.cpp.o.d -o CMakeFiles/topology-test.dir/topsort.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/topsort.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem 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/build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/utility-test.dir/link.d "CMakeFiles/utility-test.dir/alignedallocator.cpp.o" "CMakeFiles/utility-test.dir/arrayref.cpp.o" "CMakeFiles/utility-test.dir/booltype.cpp.o" "CMakeFiles/utility-test.dir/bitmask32.cpp.o" "CMakeFiles/utility-test.dir/bitmask64.cpp.o" "CMakeFiles/utility-test.dir/bitmask128.cpp.o" "CMakeFiles/utility-test.dir/cstringutil.cpp.o" "CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o" "CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o" "CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o" "CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o" "CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o" "CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o" "CMakeFiles/utility-test.dir/listoflists.cpp.o" "CMakeFiles/utility-test.dir/logger.cpp.o" "CMakeFiles/utility-test.dir/message_string_collector.cpp.o" "CMakeFiles/utility-test.dir/path.cpp.o" "CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o" "CMakeFiles/utility-test.dir/range.cpp.o" "CMakeFiles/utility-test.dir/strconvert.cpp.o" "CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o" "CMakeFiles/utility-test.dir/stringutil.cpp.o" "CMakeFiles/utility-test.dir/template_mp.cpp.o" "CMakeFiles/utility-test.dir/textreader.cpp.o" "CMakeFiles/utility-test.dir/textwriter.cpp.o" "CMakeFiles/utility-test.dir/typetraits.cpp.o" "CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 79%] Built target utility-test cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/tests/gmx_mindist.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_memory.cpp.o -MF CMakeFiles/simd-test.dir/simd_memory.cpp.o.d -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/simd_memory.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem 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/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/genconf.cpp /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/options-test.dir/link.d "CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o" "CMakeFiles/options-test.dir/filenameoption.cpp.o" "CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o" "CMakeFiles/options-test.dir/option.cpp.o" "CMakeFiles/options-test.dir/optionsassigner.cpp.o" "CMakeFiles/options-test.dir/repeatingsection.cpp.o" "CMakeFiles/options-test.dir/timeunitmanager.cpp.o" "CMakeFiles/options-test.dir/treesupport.cpp.o" "CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 79%] Built target options-test cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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CMakeFiles/topology-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/topology-test.dir/link.d "CMakeFiles/topology-test.dir/atoms.cpp.o" "CMakeFiles/topology-test.dir/exclusionblocks.cpp.o" "CMakeFiles/topology-test.dir/idef.cpp.o" "CMakeFiles/topology-test.dir/index.cpp.o" "CMakeFiles/topology-test.dir/mtop.cpp.o" "CMakeFiles/topology-test.dir/symtab.cpp.o" "CMakeFiles/topology-test.dir/topsort.cpp.o" "CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 81%] Built target topology-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f 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make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src 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../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/simd4_floatingpoint.cpp [ 81%] Built target gmxana-test /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2024.4/build/basic 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src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -MF CMakeFiles/correlations-test.dir/correlationdataset.cpp.o.d -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/tests/correlationdataset.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 81%] Built target pdb2gmx2-test cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include 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src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/simd4_vector_operations.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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-DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -MF CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/legacyenergy.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/math-test.dir/link.d "CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o" "CMakeFiles/math-test.dir/boxmatrix.cpp.o" "CMakeFiles/math-test.dir/coordinatetransformation.cpp.o" "CMakeFiles/math-test.dir/densityfit.cpp.o" "CMakeFiles/math-test.dir/dofit.cpp.o" "CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o" "CMakeFiles/math-test.dir/functions.cpp.o" "CMakeFiles/math-test.dir/gausstransform.cpp.o" "CMakeFiles/math-test.dir/densityfittingforce.cpp.o" "CMakeFiles/math-test.dir/invertmatrix.cpp.o" "CMakeFiles/math-test.dir/matrix.cpp.o" "CMakeFiles/math-test.dir/multidimarray.cpp.o" "CMakeFiles/math-test.dir/neldermead.cpp.o" "CMakeFiles/math-test.dir/optimization.cpp.o" "CMakeFiles/math-test.dir/paddedvector.cpp.o" "CMakeFiles/math-test.dir/vectypes.cpp.o" "CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 82%] Built target math-test cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -MF CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o.d -o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/tests/outputadaptercontainer.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" 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CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o.d -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g 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/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY 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'/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 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-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/helpwriting.cpp.o -MF CMakeFiles/tool-test.dir/helpwriting.cpp.o.d -o CMakeFiles/tool-test.dir/helpwriting.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/tools/tests/helpwriting.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/requirements.cpp.o -MF CMakeFiles/coordinateio-test.dir/requirements.cpp.o.d -o CMakeFiles/coordinateio-test.dir/requirements.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/tests/requirements.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include 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/build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/energyanalysis-test.dir/link.d "CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o" "CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o" "CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 82%] Built target energyanalysis-test /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/selection/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake "--color=" /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/simd-test.dir/link.d "CMakeFiles/simd-test.dir/base.cpp.o" "CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o" "CMakeFiles/simd-test.dir/scalar.cpp.o" "CMakeFiles/simd-test.dir/scalar_util.cpp.o" "CMakeFiles/simd-test.dir/scalar_math.cpp.o" "CMakeFiles/simd-test.dir/simd.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o" "CMakeFiles/simd-test.dir/simd_integer.cpp.o" "CMakeFiles/simd-test.dir/simd_math.cpp.o" "CMakeFiles/simd-test.dir/simd_memory.cpp.o" "CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/simd4.cpp.o" "CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd4_math.cpp.o" "CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/make_ndx.cpp.o -MF CMakeFiles/tool-test.dir/make_ndx.cpp.o.d -o CMakeFiles/tool-test.dir/make_ndx.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/tools/tests/make_ndx.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/confio.cpp.o -MF CMakeFiles/fileio-test.dir/confio.cpp.o.d -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/confio.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/correlations-test.dir/link.d "CMakeFiles/correlations-test.dir/autocorr.cpp.o" "CMakeFiles/correlations-test.dir/correlationdataset.cpp.o" "CMakeFiles/correlations-test.dir/expfit.cpp.o" "CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o" "CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 85%] Built target correlations-test cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/interactiveMD.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/gmxpreprocess-test.dir/link.d "CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 86%] Built target gmxpreprocess-test cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/nbsearch.cpp.o -MF CMakeFiles/selection-test.dir/nbsearch.cpp.o.d -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/nbsearch.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/poscalc.cpp.o -MF CMakeFiles/selection-test.dir/poscalc.cpp.o.d -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/poscalc.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/report_methods.cpp.o -MF CMakeFiles/tool-test.dir/report_methods.cpp.o.d -o CMakeFiles/tool-test.dir/report_methods.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/tools/tests/report_methods.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -MF CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/checkpoint.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -MF CMakeFiles/coordinateio-test.dir/setatoms.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/tests/setatoms.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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-I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 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-I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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-I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 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-I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/convert-tpr.cpp.o -MF CMakeFiles/tool-test.dir/convert-tpr.cpp.o.d -o CMakeFiles/tool-test.dir/convert-tpr.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/tools/tests/convert-tpr.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-modules-test.dir/link.d "CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o" "CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o" "CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o" "CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-modules-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 86%] Built target mdrun-modules-test cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem 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CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem 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-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/toputils.cpp.o -MF CMakeFiles/selection-test.dir/toputils.cpp.o.d -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/toputils.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-output-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-output-test.dir/link.d "CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o" "CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o" "CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o" "CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o" "CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-output-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 86%] Built target mdrun-output-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/depend make[4]: Entering directory 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CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -MF CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/tests/setstarttime.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/dispersion_correction.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-io-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o -MF CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o.d -o CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/constantacceleration.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/tool-test.dir/link.d "CMakeFiles/tool-test.dir/dump.cpp.o" "CMakeFiles/tool-test.dir/helpwriting.cpp.o" "CMakeFiles/tool-test.dir/make_ndx.cpp.o" "CMakeFiles/tool-test.dir/report_methods.cpp.o" "CMakeFiles/tool-test.dir/trjconv.cpp.o" "CMakeFiles/tool-test.dir/convert-tpr.cpp.o" "CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 86%] Built target tool-test cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/ewaldsurfaceterm.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-io-test.dir/link.d "CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o" "CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o" "CMakeFiles/mdrun-io-test.dir/grompp.cpp.o" "CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o" "CMakeFiles/mdrun-io-test.dir/termination.cpp.o" "CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-io-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 87%] Built target mdrun-io-test cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -MF CMakeFiles/coordinateio-test.dir/settimestep.cpp.o.d -o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/tests/settimestep.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build.make 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-o CMakeFiles/minimize-test.dir/minimize.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/minimize.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem 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/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/coordinateio-test.dir/link.d "CMakeFiles/coordinateio-test.dir/builder.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o" "CMakeFiles/coordinateio-test.dir/register.cpp.o" "CMakeFiles/coordinateio-test.dir/requirements.cpp.o" "CMakeFiles/coordinateio-test.dir/setatoms.cpp.o" "CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o" "CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o" "CMakeFiles/coordinateio-test.dir/settimestep.cpp.o" "CMakeFiles/coordinateio-test.dir/testmodule.cpp.o" "CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 87%] Built target coordinateio-test cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/mrcdensitymap.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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-DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/rerun.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.d "CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-single-rank-algorithms-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/DependInfo.cmake "--color=" [ 87%] Built target mdrun-single-rank-algorithms-test cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/boxdeformation.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/multisim.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include 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-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/mrcdensitymapheader.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simple_mdrun.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/minimize-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-tpi-test.dir/link.d "CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o" "CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 89%] Built target mdrun-tpi-test cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/replicaexchange.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-test.dir/link.d "CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o" "CMakeFiles/mdrun-test.dir/swapcoords.cpp.o" "CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o" "CMakeFiles/mdrun-test.dir/freezegroups.cpp.o" "CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o" "CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o" "CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 89%] Built target mdrun-test cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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-I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-mpi-test.dir/link.d "CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 89%] Built target mdrun-mpi-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/periodicactions.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/periodicactions_coupling.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/periodicactions_basic.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -MF CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o.d -o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/fileioxdrserializer.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/tngio.cpp.o -MF CMakeFiles/fileio-test.dir/tngio.cpp.o.d -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/tngio.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/xvgio.cpp.o -MF CMakeFiles/fileio-test.dir/xvgio.cpp.o.d -o CMakeFiles/fileio-test.dir/xvgio.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/xvgio.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-multisim-test.dir/link.d "CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1 [ 89%] Built target mdrun-multisim-test cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat 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'/build/reproducible-path/gromacs-2024.4/build/basic' [ 89%] Built target mdrun-non-integrator-test cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include 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/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-pme-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-mpi-pme-test.dir/link.d "CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o" "CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-pme-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 89%] Built target mdrun-mpi-pme-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 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../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 90%] Built target mdrun-multisim-replex-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem 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src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem 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CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulator.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem 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../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-basic-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 90%] Built target mdrun-coordination-basic-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o -MF CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o.d -o CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/virtualsites.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-coupling-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. 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'/build/reproducible-path/gromacs-2024.4/build/basic' [ 90%] Built target mdrun-coordination-coupling-test /usr/bin/make -f api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build make[4]: 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api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/restraint.cpp.o -MF CMakeFiles/gmxapi-test.dir/restraint.cpp.o.d -o CMakeFiles/gmxapi-test.dir/restraint.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests/restraint.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/fileio-test.dir/link.d "CMakeFiles/fileio-test.dir/checkpoint.cpp.o" "CMakeFiles/fileio-test.dir/confio.cpp.o" "CMakeFiles/fileio-test.dir/filemd5.cpp.o" "CMakeFiles/fileio-test.dir/filetypes.cpp.o" "CMakeFiles/fileio-test.dir/mrcserializer.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o" "CMakeFiles/fileio-test.dir/readinp.cpp.o" "CMakeFiles/fileio-test.dir/timecontrol.cpp.o" "CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o" "CMakeFiles/fileio-test.dir/tngio.cpp.o" "CMakeFiles/fileio-test.dir/xvgio.cpp.o" "CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 90%] Built target fileio-test /usr/bin/make -f api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 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'/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/workflow/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include 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-I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o -MF CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o.d -o CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/integrator.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-constraints-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-coordination-constraints-test.dir/link.d "CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o" "CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-constraints-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 90%] Built target mdrun-coordination-constraints-test cd /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/workflow/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" 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/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests/stopsignaler.cpp /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-setup-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/CMakeFiles/nblib-setup-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/box.cpp.o -MF CMakeFiles/nblib-setup-test.dir/box.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/box.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/box.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-fep-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/system.cpp.o -MF CMakeFiles/gmxapi-test.dir/system.cpp.o.d -o CMakeFiles/gmxapi-test.dir/system.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests/system.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-fep-test.dir/link.d "CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o" "CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-fep-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 90%] Built target mdrun-fep-test cd /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/version.cpp.o -MF CMakeFiles/gmxapi-test.dir/version.cpp.o.d -o CMakeFiles/gmxapi-test.dir/version.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests/version.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-simulator-comparison-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/workflow-details-test.dir/link.d "CMakeFiles/workflow-details-test.dir/workflow.cpp.o" "CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi.so.0.4.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 91%] Built target workflow-details-test cd /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem 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/usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 91%] Built target mdrun-multisim-replex-equivalence-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o -MF CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o.d -o CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/tpr.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-simulator-comparison-test.dir/link.d "CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o" "CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-simulator-comparison-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 91%] Built target mdrun-simulator-comparison-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd 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-o ../../../../bin/mdrun-rotation-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 91%] Built target mdrun-rotation-test /usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2024.4/build/basic 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/traits.cpp.o -MF CMakeFiles/nblib-util-test.dir/traits.cpp.o.d -o CMakeFiles/nblib-util-test.dir/traits.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/util/tests/traits.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-vsites-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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/usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 91%] Built target gmxapi-test /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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api/nblib/tests/CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -MF CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/nbkernelsystem.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integrator-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -MF CMakeFiles/nblib-integration-test.dir/simstate.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/simstate.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat 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'/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/tests/gmxcalculator.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -MF CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/tests/threadaffinity.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-tpr-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/nblib-tpr-test.dir/link.d "CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o" "CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-tpr-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 91%] Built target nblib-tpr-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -MF CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/pbcholder.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -MF CMakeFiles/nblib-setup-test.dir/molecules.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/molecules.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/util/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-util-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/nblib-util-test.dir/link.d "CMakeFiles/nblib-util-test.dir/setup.cpp.o" "CMakeFiles/nblib-util-test.dir/traits.cpp.o" "CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-util-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 91%] Built target nblib-util-test cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-pull-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-pull-test.dir/link.d "CMakeFiles/mdrun-pull-test.dir/pull.cpp.o" "CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-pull-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 93%] Built target mdrun-pull-test cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o -MF CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/nbnxmsetup.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -MF CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/tests/analysisdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/tests/cmdlineparser.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integration-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrunutility-test.dir/link.d "CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o" "CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o" "CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 94%] Built target mdrunutility-test /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/moduletest.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/tests/helpers.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/topology.cpp.o -MF CMakeFiles/nblib-setup-test.dir/topology.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/topology.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/topology.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/nblib-integration-test.dir/link.d "CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o" "CMakeFiles/nblib-integration-test.dir/simstate.cpp.o" "CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integration-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 94%] Built target nblib-integration-test cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/tests/listedtesthelpers.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/virials.cpp.o -MF CMakeFiles/nblib-setup-test.dir/virials.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/virials.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrunutility-mpi-test.dir/link.d "CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o" "CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 94%] Built target mdrunutility-mpi-test cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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-I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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-I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection 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-I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/tests/shiftforces.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/commandline-test.dir/link.d "CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o" "CMakeFiles/commandline-test.dir/filenm.cpp.o" "CMakeFiles/commandline-test.dir/pargs.cpp.o" "CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 95%] Built target commandline-test cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/tests/transformations.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/analysisdata-test.dir/link.d "CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o" "CMakeFiles/analysisdata-test.dir/arraydata.cpp.o" "CMakeFiles/analysisdata-test.dir/average.cpp.o" "CMakeFiles/analysisdata-test.dir/histogram.cpp.o" "CMakeFiles/analysisdata-test.dir/lifetime.cpp.o" "CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 95%] Built target analysisdata-test cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/pairdist.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem 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CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/rdf.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 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-I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/select.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/scattering.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-setup-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/topologyinformation.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/nblib-setup-test.dir/link.d "CMakeFiles/nblib-setup-test.dir/box.cpp.o" "CMakeFiles/nblib-setup-test.dir/interactions.cpp.o" "CMakeFiles/nblib-setup-test.dir/particletype.cpp.o" "CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o" "CMakeFiles/nblib-setup-test.dir/molecules.cpp.o" "CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o" "CMakeFiles/nblib-setup-test.dir/topology.cpp.o" "CMakeFiles/nblib-setup-test.dir/virials.cpp.o" "CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-setup-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 97%] Built target nblib-setup-test /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/CMakeFiles/nblib-tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib-tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 97%] Built target nblib-tests cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src 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-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-listed-forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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../../../../bin/nblib-listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 98%] Built target nblib-listed-forces-test /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/trajectoryanalysis-test.dir/link.d "CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [100%] Built target trajectoryanalysis-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/CMakeFiles/tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [100%] Built target tests make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2024.4/build/basic/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' make[1]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' (cd build/basic; LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2024.4/build/basic/lib ctest -V) UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2024.4/build/basic/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2024.4/build/basic/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2024.4/build/basic/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2024.4/build/basic/DartConfiguration.tcl Test project /build/reproducible-path/gromacs-2024.4/build/basic Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: GmxapiExternalInterfaceTests 1: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/gmxapi-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/GmxapiExternalInterfaceTests.xml" 1: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests 1: Test timeout computed to be: 600 1: [==========] Running 9 tests from 1 test suite. 1: [----------] Global test environment set-up. 1: [----------] 9 tests from GmxApiTest 1: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -67109001 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: NOTE: 12 % of the run time was spent in pair search, 1: you might want to increase nstlist (this has no effect on accuracy) 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.176 0.088 199.8 1: (ns/day) (hour/ns) 1: Performance: 5.742 4.180 1: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (923 ms) 1: [ RUN ] GmxApiTest.RunnerBasicMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to 2041377518 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.046 0.023 199.5 1: (ns/day) (hour/ns) 1: Performance: 21.750 1.103 1: [ OK ] GmxApiTest.RunnerBasicMD (426 ms) 1: [ RUN ] GmxApiTest.RunnerReinitialize 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: 1: Received the remote INT/TERM signal, stopping within 200 steps 1: 1: Setting the LD random seed to -1075856618 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.038 0.019 199.4 1: (ns/day) (hour/ns) 1: Performance: 186.029 0.129 1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.047 0.024 199.4 1: (ns/day) (hour/ns) 1: Performance: 150.161 0.160 1: [ OK ] GmxApiTest.RunnerReinitialize (411 ms) 1: [ RUN ] GmxApiTest.RunnerChainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -1665221633 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.039 0.019 199.4 1: (ns/day) (hour/ns) 1: Performance: 26.051 0.921 1: trr version: GMX_trn_file (single precision) 1: 1: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 1: Setting nsteps to 4 1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 1: Input file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 2 1: Runtime for the run 0.00390625 ps 1: Run end step 2 1: Run end time 0.00390625 ps 1: 1: 1: Output file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 4 1: Runtime for the run 0.0078125 ps 1: Run end step 4 1: Run end time 0.0078125 ps 1: 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.067 0.033 199.7 1: (ns/day) (hour/ns) 1: Performance: 15.120 1.587 1: 1: [ OK ] GmxApiTest.RunnerChainedMD (423 ms) 1: [ RUN ] GmxApiTest.Status 1: [ OK ] GmxApiTest.Status (0 ms) 1: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 1: Changing nstlist from 10 to 1, rlist from 1.057 to 1 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: Setting the LD random seed to -1090576457 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.032 0.016 199.4 1: (ns/day) (hour/ns) 1: Performance: 53.379 0.450 1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 1: Overriding nsteps with value passed on the command line: 4 steps, 0.00781 ps 1: Changing nstlist from 10 to 1, rlist from 1.057 to 1 1: 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.032 0.016 198.9 1: (ns/day) (hour/ns) 1: Performance: 21.153 1.135 1: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (433 ms) 1: [ RUN ] GmxApiTest.SystemConstruction 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Setting the LD random seed to 2079847407 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: [ OK ] GmxApiTest.SystemConstruction (311 ms) 1: [ RUN ] GmxApiTest.SaneVersionComparisons 1: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms) 1: [ RUN ] GmxApiTest.VersionNamed0_1_Features 1: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) 1: [----------] 9 tests from GmxApiTest (2937 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 9 tests from 1 test suite ran. (3081 ms total) 1: [ PASSED ] 9 tests. 1/87 Test #1: GmxapiExternalInterfaceTests .............. Passed 3.77 sec test 2 Start 2: GmxapiInternalInterfaceTests 2: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/workflow-details-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/GmxapiInternalInterfaceTests.xml" 2: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/workflow/tests 2: Test timeout computed to be: 600 2: [==========] Running 2 tests from 1 test suite. 2: [----------] Global test environment set-up. 2: [----------] 2 tests from GmxApiTest 2: [ RUN ] GmxApiTest.BuildApiWorkflowImpl 2: Generating 1-4 interactions: fudge = 0.5 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Setting the LD random seed to 2111659062 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: [ OK ] GmxApiTest.BuildApiWorkflowImpl (308 ms) 2: [ RUN ] GmxApiTest.CreateApiWorkflow 2: Generating 1-4 interactions: fudge = 0.5 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Setting the LD random seed to -101845003 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: [ OK ] GmxApiTest.CreateApiWorkflow (269 ms) 2: [----------] 2 tests from GmxApiTest (578 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 2 tests from 1 test suite ran. (613 ms total) 2: [ PASSED ] 2 tests. 2/87 Test #2: GmxapiInternalInterfaceTests .............. Passed 0.64 sec test 3 Start 3: NbLibListedForcesTests 3: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/nblib-listed-forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/NbLibListedForcesTests.xml" 3: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/listed_forces/tests 3: Test timeout computed to be: 600 3: [==========] Running 44 tests from 22 test suites. 3: [----------] Global test environment set-up. 3: [----------] 8 tests from NBlibTest 3: [ RUN ] NBlibTest.BondTypesOperatorEqualWorks 3: [ OK ] NBlibTest.BondTypesOperatorEqualWorks (0 ms) 3: [ RUN ] NBlibTest.BondTypesLessThanWorks 3: [ OK ] NBlibTest.BondTypesLessThanWorks (0 ms) 3: [ RUN ] NBlibTest.CanSplitListedWork 3: [ OK ] NBlibTest.CanSplitListedWork (0 ms) 3: [ RUN ] NBlibTest.ListedForceBuffer 3: [ OK ] NBlibTest.ListedForceBuffer (0 ms) 3: [ RUN ] NBlibTest.ListedForceCalculatorCanConstruct 3: [ OK ] NBlibTest.ListedForceCalculatorCanConstruct (3 ms) 3: [ RUN ] NBlibTest.GmxToNblibConversionAllTypes 3: [ OK ] NBlibTest.GmxToNblibConversionAllTypes (3 ms) 3: [ RUN ] NBlibTest.EndToEndListedComparison 3: [ OK ] NBlibTest.EndToEndListedComparison (1 ms) 3: [ RUN ] NBlibTest.shiftForcesAreCorrect 3: [ OK ] NBlibTest.shiftForcesAreCorrect (14 ms) 3: [----------] 8 tests from NBlibTest (22 ms total) 3: 3: [----------] 1 test from Kernels 3: [ RUN ] Kernels.HarmonicScalarKernelCanCompute 3: [ OK ] Kernels.HarmonicScalarKernelCanCompute (0 ms) 3: [----------] 1 test from Kernels (0 ms total) 3: 3: [----------] 1 test from FourCenter 3: [ RUN ] FourCenter.ListedForcesProperDihedralTest 3: [ OK ] FourCenter.ListedForcesProperDihedralTest (0 ms) 3: [----------] 1 test from FourCenter (0 ms total) 3: 3: [----------] 7 tests from ThreeCenter 3: [ RUN ] ThreeCenter.ListedForcesG96AngleTest 3: [ OK ] ThreeCenter.ListedForcesG96AngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesHarmonicAngleTest 3: [ OK ] ThreeCenter.ListedForcesHarmonicAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesLinearAngleTest 3: [ OK ] ThreeCenter.ListedForcesLinearAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesCrossBondBondTest 3: [ OK ] ThreeCenter.ListedForcesCrossBondBondTest (3 ms) 3: [ RUN ] ThreeCenter.ListedForcesCrossBondAngleTest 3: [ OK ] ThreeCenter.ListedForcesCrossBondAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesQuarticAngleTest 3: [ OK ] ThreeCenter.ListedForcesQuarticAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesRestrictedAngleTest 3: [ OK ] ThreeCenter.ListedForcesRestrictedAngleTest (0 ms) 3: [----------] 7 tests from ThreeCenter (7 ms total) 3: 3: [----------] 5 tests from TwoCenter 3: [ RUN ] TwoCenter.ListedForcesHarmonicBondTest 3: [ OK ] TwoCenter.ListedForcesHarmonicBondTest (1 ms) 3: [ RUN ] TwoCenter.ListedForcesG96BondTest 3: [ OK ] TwoCenter.ListedForcesG96BondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesCubicBondTest 3: [ OK ] TwoCenter.ListedForcesCubicBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesMorseBondTest 3: [ OK ] TwoCenter.ListedForcesMorseBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesFeneBondTest 3: [ OK ] TwoCenter.ListedForcesFeneBondTest (0 ms) 3: [----------] 5 tests from TwoCenter (4 ms total) 3: 3: [----------] 5 tests from ListedExampleData 3: [ RUN ] ListedExampleData.ComputeHarmonicBondForces 3: [ OK ] ListedExampleData.ComputeHarmonicBondForces (0 ms) 3: [ RUN ] ListedExampleData.ComputeHarmonicBondEnergies 3: [ OK ] ListedExampleData.ComputeHarmonicBondEnergies (0 ms) 3: [ RUN ] ListedExampleData.ComputeHarmonicAngleForces 3: [ OK ] ListedExampleData.ComputeHarmonicAngleForces (1 ms) 3: [ RUN ] ListedExampleData.CanReduceForces 3: [ OK ] ListedExampleData.CanReduceForces (0 ms) 3: [ RUN ] ListedExampleData.CanReduceEnergies 3: [ OK ] ListedExampleData.CanReduceEnergies (0 ms) 3: [----------] 5 tests from ListedExampleData (3 ms total) 3: 3: [----------] 1 test from LinearChainDataFixture 3: [ RUN ] LinearChainDataFixture.Multithreading 3: [ OK ] LinearChainDataFixture.Multithreading (27 ms) 3: [----------] 1 test from LinearChainDataFixture (27 ms total) 3: 3: [----------] 2 tests from ListedShims 3: [ RUN ] ListedShims.ParameterConversion 3: [ OK ] ListedShims.ParameterConversion (0 ms) 3: [ RUN ] ListedShims.GmxToNblibConversion 3: [ OK ] ListedShims.GmxToNblibConversion (0 ms) 3: [----------] 2 tests from ListedShims (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1, where TypeParam = nblib::G96BondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2, where TypeParam = nblib::CubicBondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3, where TypeParam = nblib::MorseBondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5, where TypeParam = nblib::AngleInteractionType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6, where TypeParam = nblib::CosineParamAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7, where TypeParam = nblib::CosineParamAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9, where TypeParam = nblib::QuarticAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10, where TypeParam = nblib::CrossBondBond 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11, where TypeParam = nblib::CrossBondAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12, where TypeParam = nblib::ProperDihedral 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12 (0 ms total) 3: 3: [----------] 1 test from ListedTransformations 3: [ RUN ] ListedTransformations.SortInteractionIndices 3: [ OK ] ListedTransformations.SortInteractionIndices (0 ms) 3: [----------] 1 test from ListedTransformations (0 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 44 tests from 22 test suites ran. (68 ms total) 3: [ PASSED ] 44 tests. 3/87 Test #3: NbLibListedForcesTests .................... Passed 0.09 sec test 4 Start 4: NbLibSamplesTestArgon 4: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/argon-forces-integration 4: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/samples 4: Test timeout computed to be: 1500 4: initial forces on particle 0: x 0.000000 y 0.000000 z 0.000000 4: final forces on particle 0: x -0.412993 y -1.098256 z -0.113191 4: initial position of particle 0: x 0.794000 y 1.439000 z 0.610000 4: final position of particle 0: x 0.789162 y 1.271508 z 0.819867 4/87 Test #4: NbLibSamplesTestArgon ..................... Passed 0.04 sec test 5 Start 5: NbLibSamplesTestMethaneWater 5: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/methane-water-integration 5: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/samples 5: Test timeout computed to be: 1500 5: initial position of particle 0: x 0.005000 y 0.600000 z 0.244000 5: final position of particle 9: x 77.358398 y 5.324913 z -80.600098 5/87 Test #5: NbLibSamplesTestMethaneWater .............. Passed 0.03 sec test 6 Start 6: NbLibUtilTests 6: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/nblib-util-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/NbLibUtilTests.xml" 6: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/util/tests 6: Test timeout computed to be: 30 6: [==========] Running 16 tests from 2 test suites. 6: [----------] Global test environment set-up. 6: [----------] 6 tests from NBlibTest 6: [ RUN ] NBlibTest.isRealValued 6: [ OK ] NBlibTest.isRealValued (0 ms) 6: [ RUN ] NBlibTest.checkNumericValuesHasNan 6: [ OK ] NBlibTest.checkNumericValuesHasNan (0 ms) 6: [ RUN ] NBlibTest.checkNumericValuesHasInf 6: [ OK ] NBlibTest.checkNumericValuesHasInf (0 ms) 6: [ RUN ] NBlibTest.GeneratedVelocitiesAreCorrect 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.GeneratedVelocitiesAreCorrect (1 ms) 6: [ RUN ] NBlibTest.generateVelocitySize 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.generateVelocitySize (0 ms) 6: [ RUN ] NBlibTest.generateVelocityCheckNumbers 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.generateVelocityCheckNumbers (0 ms) 6: [----------] 6 tests from NBlibTest (1 ms total) 6: 6: [----------] 10 tests from NblibTraitsUtils 6: [ RUN ] NblibTraitsUtils.FuseTwo 6: [ OK ] NblibTraitsUtils.FuseTwo (0 ms) 6: [ RUN ] NblibTraitsUtils.Fuse 6: [ OK ] NblibTraitsUtils.Fuse (0 ms) 6: [ RUN ] NblibTraitsUtils.Repeat 6: [ OK ] NblibTraitsUtils.Repeat (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTuple1 6: [ OK ] NblibTraitsUtils.FindIndexTuple1 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTuple2 6: [ OK ] NblibTraitsUtils.FindIndexTuple2 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeList1 6: [ OK ] NblibTraitsUtils.FindIndexTypeList1 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeList2 6: [ OK ] NblibTraitsUtils.FindIndexTypeList2 (0 ms) 6: [ RUN ] NblibTraitsUtils.Contains 6: [ OK ] NblibTraitsUtils.Contains (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTupleRepeated 6: [ OK ] NblibTraitsUtils.FindIndexTupleRepeated (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeListRepeated 6: [ OK ] NblibTraitsUtils.FindIndexTypeListRepeated (0 ms) 6: [----------] 10 tests from NblibTraitsUtils (0 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 16 tests from 2 test suites ran. (1 ms total) 6: [ PASSED ] 16 tests. 6/87 Test #6: NbLibUtilTests ............................ Passed 0.02 sec test 7 Start 7: NbLibSetupTests 7: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/nblib-setup-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/NbLibSetupTests.xml" 7: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests 7: Test timeout computed to be: 600 7: [==========] Running 57 tests from 3 test suites. 7: [----------] Global test environment set-up. 7: [----------] 41 tests from NBlibTest 7: [ RUN ] NBlibTest.CubicBoxCannotHaveNaN 7: [ OK ] NBlibTest.CubicBoxCannotHaveNaN (0 ms) 7: [ RUN ] NBlibTest.CubicBoxCannotHaveInf 7: [ OK ] NBlibTest.CubicBoxCannotHaveInf (0 ms) 7: [ RUN ] NBlibTest.RectangularBoxCannotHaveNaN 7: [ OK ] NBlibTest.RectangularBoxCannotHaveNaN (0 ms) 7: [ RUN ] NBlibTest.RectangularBoxCannotHaveInf 7: [ OK ] NBlibTest.RectangularBoxCannotHaveInf (0 ms) 7: [ RUN ] NBlibTest.CubicBoxWorks 7: [ OK ] NBlibTest.CubicBoxWorks (0 ms) 7: [ RUN ] NBlibTest.BoxEqual 7: [ OK ] NBlibTest.BoxEqual (0 ms) 7: [ RUN ] NBlibTest.NonBondedForceParamsCorrect 7: [ OK ] NBlibTest.NonBondedForceParamsCorrect (0 ms) 7: [ RUN ] NBlibTest.CanMergeInteractions 7: [ OK ] NBlibTest.CanMergeInteractions (0 ms) 7: [ RUN ] NBlibTest.ParticleTypeNameCanBeConstructed 7: [ OK ] NBlibTest.ParticleTypeNameCanBeConstructed (0 ms) 7: [ RUN ] NBlibTest.ParticleTypeMassCanBeConstructed 7: [ OK ] NBlibTest.ParticleTypeMassCanBeConstructed (0 ms) 7: [ RUN ] NBlibTest.PbcHolderWorks 7: [ OK ] NBlibTest.PbcHolderWorks (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName (0 ms) 7: [ RUN ] NBlibTest.CanGetNumParticlesInMolecule 7: [ OK ] NBlibTest.CanGetNumParticlesInMolecule (0 ms) 7: [ RUN ] NBlibTest.CanConstructExclusionListFromNames 7: [ OK ] NBlibTest.CanConstructExclusionListFromNames (0 ms) 7: [ RUN ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed 7: [ OK ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed (0 ms) 7: [ RUN ] NBlibTest.AtWorks 7: [ OK ] NBlibTest.AtWorks (0 ms) 7: [ RUN ] NBlibTest.AtThrows 7: [ OK ] NBlibTest.AtThrows (1 ms) 7: [ RUN ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass 7: [ OK ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass (0 ms) 7: [ RUN ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass 7: [ OK ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass (0 ms) 7: [ RUN ] NBlibTest.MoleculeNoThrowsSameParticleTypeName 7: [ OK ] NBlibTest.MoleculeNoThrowsSameParticleTypeName (0 ms) 7: [ RUN ] NBlibTest.CanAddInteractions 7: [ OK ] NBlibTest.CanAddInteractions (0 ms) 7: [ RUN ] NBlibTest.CanAddUreyBradley 7: [ OK ] NBlibTest.CanAddUreyBradley (0 ms) 7: [ RUN ] NBlibTest.TopologyHasNumParticles 7: [ OK ] NBlibTest.TopologyHasNumParticles (0 ms) 7: [ RUN ] NBlibTest.TopologyHasCharges 7: [ OK ] NBlibTest.TopologyHasCharges (0 ms) 7: [ RUN ] NBlibTest.TopologyHasMasses 7: [ OK ] NBlibTest.TopologyHasMasses (0 ms) 7: [ RUN ] NBlibTest.TopologyHasParticleTypes 7: [ OK ] NBlibTest.TopologyHasParticleTypes (0 ms) 7: [ RUN ] NBlibTest.TopologyHasParticleTypeIds 7: [ OK ] NBlibTest.TopologyHasParticleTypeIds (0 ms) 7: [ RUN ] NBlibTest.TopologyThrowsIdenticalParticleType 7: [ OK ] NBlibTest.TopologyThrowsIdenticalParticleType (0 ms) 7: [ RUN ] NBlibTest.TopologyHasExclusions 7: [ OK ] NBlibTest.TopologyHasExclusions (0 ms) 7: [ RUN ] NBlibTest.TopologyHasSequencing 7: [ OK ] NBlibTest.TopologyHasSequencing (0 ms) 7: [ RUN ] NBlibTest.TopologyCanAggregateBonds 7: [ OK ] NBlibTest.TopologyCanAggregateBonds (0 ms) 7: [ RUN ] NBlibTest.TopologyCanSequencePairIDs 7: [ OK ] NBlibTest.TopologyCanSequencePairIDs (0 ms) 7: [ RUN ] NBlibTest.TopologySequenceIdThrows 7: No particle O-Atom in residue SOL in molecule SOL found 7: [ OK ] NBlibTest.TopologySequenceIdThrows (0 ms) 7: [ RUN ] NBlibTest.TopologyCanEliminateDuplicateBonds 7: [ OK ] NBlibTest.TopologyCanEliminateDuplicateBonds (0 ms) 7: [ RUN ] NBlibTest.TopologyListedInteractions 7: [ OK ] NBlibTest.TopologyListedInteractions (0 ms) 7: [ RUN ] NBlibTest.TopologyListedInteractionsMultipleTypes 7: [ OK ] NBlibTest.TopologyListedInteractionsMultipleTypes (0 ms) 7: [ RUN ] NBlibTest.TopologyInvalidParticleInInteractionThrows 7: No particle Iron in residue SOL in molecule SOL found 7: [ OK ] NBlibTest.TopologyInvalidParticleInInteractionThrows (0 ms) 7: [ RUN ] NBlibTest.toGmxExclusionBlockWorks 7: [ OK ] NBlibTest.toGmxExclusionBlockWorks (0 ms) 7: [----------] 41 tests from NBlibTest (3 ms total) 7: 7: [----------] 15 tests from NbnxmSetupTest 7: [ RUN ] NbnxmSetupTest.findNumEnergyGroups 7: [ OK ] NbnxmSetupTest.findNumEnergyGroups (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumNo 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumNo (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM (0 ms) 7: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsAuto 7: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsAuto (0 ms) 7: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsCount 7: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsCount (0 ms) 7: [ RUN ] NbnxmSetupTest.canCreateKernelSetupPlain 7: [ OK ] NbnxmSetupTest.canCreateKernelSetupPlain (0 ms) 7: [ RUN ] NbnxmSetupTest.canCreateParticleInfoAllVdv 7: [ OK ] NbnxmSetupTest.canCreateParticleInfoAllVdv (0 ms) 7: [ RUN ] NbnxmSetupTest.ewaldCoeffWorks 7: [ OK ] NbnxmSetupTest.ewaldCoeffWorks (0 ms) 7: [ RUN ] NbnxmSetupTest.updateForcerecWorks 7: [ OK ] NbnxmSetupTest.updateForcerecWorks (0 ms) 7: [ RUN ] NbnxmSetupTest.canCheckKernelSetup 7: [ OK ] NbnxmSetupTest.canCheckKernelSetup (0 ms) 7: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM 7: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM (0 ms) 7: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM 7: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM (0 ms) 7: [ RUN ] NbnxmSetupTest.CanCreateNbnxmCPU 7: [ OK ] NbnxmSetupTest.CanCreateNbnxmCPU (0 ms) 7: [----------] 15 tests from NbnxmSetupTest (0 ms total) 7: 7: [----------] 1 test from VirialsTest 7: [ RUN ] VirialsTest.computeVirialTensorWorks 7: [ OK ] VirialsTest.computeVirialTensorWorks (0 ms) 7: [----------] 1 test from VirialsTest (0 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 57 tests from 3 test suites ran. (4 ms total) 7: [ PASSED ] 57 tests. 7/87 Test #7: NbLibSetupTests ........................... Passed 0.07 sec test 8 Start 8: NbLibTprTests 8: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/nblib-tpr-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/NbLibTprTests.xml" 8: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests 8: Test timeout computed to be: 30 8: [==========] Running 4 tests from 1 test suite. 8: [----------] Global test environment set-up. 8: [----------] 4 tests from TprReaderTest 8: [ RUN ] TprReaderTest.SimDBTprIsCreated 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.SimDBTprIsCreated (31 ms) 8: [ RUN ] TprReaderTest.Spc2Reads 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Generating 1-4 interactions: fudge = 0.5 8: Number of degrees of freedom in T-Coupling group System is 9.00 8: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: NVE simulation: will use the initial temperature of 2573.591 K for 8: determining the Verlet buffer size 8: 8: 8: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: You are using a plain Coulomb cut-off, which might produce artifacts. 8: You might want to consider using PME electrostatics. 8: 8: 8: 8: There were 4 NOTEs 8: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 8: Generated 3 of the 3 non-bonded parameter combinations 8: 8: Generated 3 of the 3 1-4 parameter combinations 8: 8: Excluding 2 bonded neighbours molecule type 'SOL' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.Spc2Reads (19 ms) 8: [ RUN ] TprReaderTest.ArgonImportedDataIsCorrect 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.ArgonImportedDataIsCorrect (16 ms) 8: [ RUN ] TprReaderTest.FCfromTprDataWorks 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.FCfromTprDataWorks (19 ms) 8: [----------] 4 tests from TprReaderTest (87 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 4 tests from 1 test suite ran. (119 ms total) 8: [ PASSED ] 4 tests. 8/87 Test #8: NbLibTprTests ............................. Passed 0.14 sec test 9 Start 9: NbLibIntegrationTests 9: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/nblib-integration-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/NbLibIntegrationTests.xml" 9: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests 9: Test timeout computed to be: 600 9: [==========] Running 20 tests from 1 test suite. 9: [----------] Global test environment set-up. 9: [----------] 20 tests from NBlibTest 9: [ RUN ] NBlibTest.GmxForceCalculatorCanCompute 9: [ OK ] NBlibTest.GmxForceCalculatorCanCompute (10 ms) 9: [ RUN ] NBlibTest.ArgonVirialsAreCorrect 9: [ OK ] NBlibTest.ArgonVirialsAreCorrect (1 ms) 9: [ RUN ] NBlibTest.ArgonEnergiesAreCorrect 9: [ OK ] NBlibTest.ArgonEnergiesAreCorrect (1 ms) 9: [ RUN ] NBlibTest.SpcMethanolEnergiesAreCorrect 9: [ OK ] NBlibTest.SpcMethanolEnergiesAreCorrect (3 ms) 9: [ RUN ] NBlibTest.SpcMethanolForcesAreCorrect 9: [ OK ] NBlibTest.SpcMethanolForcesAreCorrect (1 ms) 9: [ RUN ] NBlibTest.ExpectedNumberOfForces 9: [ OK ] NBlibTest.ExpectedNumberOfForces (0 ms) 9: [ RUN ] NBlibTest.CanIntegrateSystem 9: [ OK ] NBlibTest.CanIntegrateSystem (0 ms) 9: [ RUN ] NBlibTest.UpdateChangesForces 9: [ OK ] NBlibTest.UpdateChangesForces (0 ms) 9: [ RUN ] NBlibTest.ArgonOplsaForcesAreCorrect 9: [ OK ] NBlibTest.ArgonOplsaForcesAreCorrect (1 ms) 9: [ RUN ] NBlibTest.ArgonGromos43A1ForcesAreCorrect 9: [ OK ] NBlibTest.ArgonGromos43A1ForcesAreCorrect (1 ms) 9: [ RUN ] NBlibTest.CanConstructSimulationState 9: [ OK ] NBlibTest.CanConstructSimulationState (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateNAN 9: [ OK ] NBlibTest.SimulationStateThrowsCoordinateNAN (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateINF 9: [ OK ] NBlibTest.SimulationStateThrowsCoordinateINF (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsVelocityNAN 9: [ OK ] NBlibTest.SimulationStateThrowsVelocityNAN (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsVelocityINF 9: [ OK ] NBlibTest.SimulationStateThrowsVelocityINF (0 ms) 9: [ RUN ] NBlibTest.SimulationStateCanMove 9: [ OK ] NBlibTest.SimulationStateCanMove (0 ms) 9: [ RUN ] NBlibTest.SimulationStateCanAssign 9: [ OK ] NBlibTest.SimulationStateCanAssign (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasBox 9: [ OK ] NBlibTest.SimulationStateHasBox (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasCorrectCoordinates 9: [ OK ] NBlibTest.SimulationStateHasCorrectCoordinates (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasCorrectVelocities 9: [ OK ] NBlibTest.SimulationStateHasCorrectVelocities (0 ms) 9: [----------] 20 tests from NBlibTest (23 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 20 tests from 1 test suite ran. (23 ms total) 9: [ PASSED ] 20 tests. 9/87 Test #9: NbLibIntegrationTests ..................... Passed 0.05 sec test 10 Start 10: NbLibIntegratorTests 10: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/nblib-integrator-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/NbLibIntegratorTests.xml" 10: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests 10: Test timeout computed to be: 600 10: [==========] Running 1 test from 1 test suite. 10: [----------] Global test environment set-up. 10: [----------] 1 test from NBlibTest 10: [ RUN ] NBlibTest.IntegratorWorks 10: [ OK ] NBlibTest.IntegratorWorks (0 ms) 10: [----------] 1 test from NBlibTest (0 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 1 test from 1 test suite ran. (0 ms total) 10: [ PASSED ] 1 test. 10/87 Test #10: NbLibIntegratorTests ...................... Passed 0.02 sec test 11 Start 11: TestUtilsUnitTests 11: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/testutils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/TestUtilsUnitTests.xml" 11: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/testutils/tests 11: Test timeout computed to be: 30 11: [==========] Running 59 tests from 5 test suites. 11: [----------] Global test environment set-up. 11: [----------] 10 tests from InteractiveTestHelperTest 11: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 11: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (6 ms) 11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (1 ms) 11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 11: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 11: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 11: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 11: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 11: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 11: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (0 ms) 11: [----------] 10 tests from InteractiveTestHelperTest (10 ms total) 11: 11: [----------] 34 tests from ReferenceDataTest 11: [ RUN ] ReferenceDataTest.HandlesSimpleData 11: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 11: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 11: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesStringBlockData 11: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesVectorData 11: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSequenceData 11: [ OK ] ReferenceDataTest.HandlesSequenceData (1 ms) 11: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 11: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesIncorrectData 11: [ OK ] ReferenceDataTest.HandlesIncorrectData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 11: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMissingData 11: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUncheckedData 11: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 11: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 11: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesAnys 11: [ OK ] ReferenceDataTest.HandlesAnys (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 11: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 11: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 11: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue 11: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType 11: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (6 ms) 11: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 11: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 11: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (1 ms) 11: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 11: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 11: [ OK ] ReferenceDataTest.HandlesEmptyStrings (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 11: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 11: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 11: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 11: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 11: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesReadingValues 11: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (0 ms) 11: [----------] 34 tests from ReferenceDataTest (14 ms total) 11: 11: [----------] 7 tests from FloatingPointDifferenceTest 11: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 11: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 11: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 11: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 11: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 11: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 11: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 11: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 11: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 11: 11: [----------] 4 tests from FloatingPointToleranceTest 11: [ RUN ] FloatingPointToleranceTest.UlpTolerance 11: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 11: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 11: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 11: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 11: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 11: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 11: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 11: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 11: 11: [----------] 4 tests from XvgTests 11: [ RUN ] XvgTests.CreateFile 11: [ OK ] XvgTests.CreateFile (0 ms) 11: [ RUN ] XvgTests.CheckMissing 11: [ OK ] XvgTests.CheckMissing (0 ms) 11: [ RUN ] XvgTests.CheckExtra 11: [ OK ] XvgTests.CheckExtra (0 ms) 11: [ RUN ] XvgTests.ReadIncorrect 11: [ OK ] XvgTests.ReadIncorrect (0 ms) 11: [----------] 4 tests from XvgTests (0 ms total) 11: 11: [----------] Global test environment tear-down 11: [==========] 59 tests from 5 test suites ran. (25 ms total) 11: [ PASSED ] 59 tests. 11/87 Test #11: TestUtilsUnitTests ........................ Passed 0.05 sec test 12 Start 12: TestUtilsMpiUnitTests 12: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/TestUtilsMpiUnitTests.xml" 12: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/testutils/tests 12: Test timeout computed to be: 30 12: [==========] Running 1 test from 1 test suite. 12: [----------] Global test environment set-up. 12: [----------] 1 test from MpiSelfTest 12: [ RUN ] MpiSelfTest.Runs 12: [ OK ] MpiSelfTest.Runs (23 ms) 12: [----------] 1 test from MpiSelfTest (23 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 1 test from 1 test suite ran. (23 ms total) 12: [ PASSED ] 1 test. 12/87 Test #12: TestUtilsMpiUnitTests ..................... Passed 0.05 sec test 13 Start 13: UtilityUnitTests 13: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/utility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/UtilityUnitTests.xml" 13: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests 13: Test timeout computed to be: 30 13: [==========] Running 400 tests from 62 test suites. 13: [----------] Global test environment set-up. 13: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/0.Move 13: [ OK ] AllocatorTest/0.Move (0 ms) 13: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 13: [----------] 5 tests from AllocatorTest/0 (0 ms total) 13: 13: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/1.Move 13: [ OK ] AllocatorTest/1.Move (0 ms) 13: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 13: [----------] 5 tests from AllocatorTest/1 (0 ms total) 13: 13: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/2.Move 13: [ OK ] AllocatorTest/2.Move (0 ms) 13: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 13: [----------] 5 tests from AllocatorTest/2 (0 ms total) 13: 13: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/3.Move 13: [ OK ] AllocatorTest/3.Move (0 ms) 13: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 13: [----------] 5 tests from AllocatorTest/3 (0 ms total) 13: 13: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 13: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/4.Move 13: [ OK ] AllocatorTest/4.Move (0 ms) 13: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 13: [----------] 5 tests from AllocatorTest/4 (0 ms total) 13: 13: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> 13: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/5.Move 13: [ OK ] AllocatorTest/5.Move (0 ms) 13: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 13: [----------] 5 tests from AllocatorTest/5 (0 ms total) 13: 13: [----------] 1 test from AllocatorUntypedTest 13: [ RUN ] AllocatorUntypedTest.Comparison 13: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 13: [----------] 1 test from AllocatorUntypedTest (0 ms total) 13: 13: [----------] 4 tests from EmptyArrayRefTest 13: [ RUN ] EmptyArrayRefTest.IsEmpty 13: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 13: [ RUN ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty 13: [ OK ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty (0 ms) 13: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr 13: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr (0 ms) 13: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull 13: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull (0 ms) 13: [----------] 4 tests from EmptyArrayRefTest (0 ms total) 13: 13: [----------] 1 test from EmptyConstArrayRefTest 13: [ RUN ] EmptyConstArrayRefTest.IsEmpty 13: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 13: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/8 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/14 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 13: 13: [----------] 8 tests from BoolType 13: [ RUN ] BoolType.ImplicitConversion 13: [ OK ] BoolType.ImplicitConversion (0 ms) 13: [ RUN ] BoolType.FalseByDefault 13: [ OK ] BoolType.FalseByDefault (0 ms) 13: [ RUN ] BoolType.Assignment 13: [ OK ] BoolType.Assignment (0 ms) 13: [ RUN ] BoolType.Copy 13: [ OK ] BoolType.Copy (0 ms) 13: [ RUN ] BoolType.ArrayRefCanBeCreated 13: [ OK ] BoolType.ArrayRefCanBeCreated (0 ms) 13: [ RUN ] BoolType.CanBeCastToBool 13: [ OK ] BoolType.CanBeCastToBool (0 ms) 13: [ RUN ] BoolType.HasSizeOfBool 13: [ OK ] BoolType.HasSizeOfBool (0 ms) 13: [ RUN ] BoolType.HasAlignmentOfBool 13: [ OK ] BoolType.HasAlignmentOfBool (0 ms) 13: [----------] 8 tests from BoolType (0 ms total) 13: 13: [----------] 4 tests from ArrayRefFromBoolTypeVector 13: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructEmpty 13: [ OK ] ArrayRefFromBoolTypeVector.CanConstructEmpty (0 ms) 13: [ RUN ] ArrayRefFromBoolTypeVector.Works 13: [ OK ] ArrayRefFromBoolTypeVector.Works (0 ms) 13: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty 13: [ OK ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty (0 ms) 13: [ RUN ] ArrayRefFromBoolTypeVector.ConstWorks 13: [ OK ] ArrayRefFromBoolTypeVector.ConstWorks (0 ms) 13: [----------] 4 tests from ArrayRefFromBoolTypeVector (0 ms total) 13: 13: [----------] 7 tests from CStringUtilityTest 13: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison 13: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms) 13: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength 13: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms) 13: [ RUN ] CStringUtilityTest.strip_comment 13: [ OK ] CStringUtilityTest.strip_comment (0 ms) 13: [ RUN ] CStringUtilityTest.upstring 13: [ OK ] CStringUtilityTest.upstring (0 ms) 13: [ RUN ] CStringUtilityTest.ltrim 13: [ OK ] CStringUtilityTest.ltrim (0 ms) 13: [ RUN ] CStringUtilityTest.rtrim 13: [ OK ] CStringUtilityTest.rtrim (0 ms) 13: [ RUN ] CStringUtilityTest.trim 13: [ OK ] CStringUtilityTest.trim (0 ms) 13: [----------] 7 tests from CStringUtilityTest (0 ms total) 13: 13: [----------] 2 tests from DefaultInitializationAllocator 13: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization 13: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms) 13: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization 13: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms) 13: [----------] 2 tests from DefaultInitializationAllocator (0 ms total) 13: 13: [----------] 4 tests from EnumerationHelpersTest 13: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks 13: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms) 13: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks 13: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms) 13: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe 13: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms) 13: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks 13: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms) 13: [----------] 4 tests from EnumerationHelpersTest (0 ms total) 13: 13: [----------] 9 tests from FixedCapacityVectorTest 13: [ RUN ] FixedCapacityVectorTest.IsEmpty 13: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms) 13: [ RUN ] FixedCapacityVectorTest.PushWorks 13: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.PopWorks 13: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ClearWorks 13: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks 13: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.AtThrows 13: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms) 13: [ RUN ] FixedCapacityVectorTest.IteratorWorks 13: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks 13: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks 13: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms) 13: [----------] 9 tests from FixedCapacityVectorTest (0 ms total) 13: 13: [----------] 5 tests from InMemorySerializerTest 13: [ RUN ] InMemorySerializerTest.Roundtrip 13: [ OK ] InMemorySerializerTest.Roundtrip (0 ms) 13: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap 13: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms) 13: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap 13: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms) 13: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap 13: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms) 13: [ RUN ] InMemorySerializerTest.SizeIsCorrect 13: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms) 13: [----------] 5 tests from InMemorySerializerTest (0 ms total) 13: 13: [----------] 4 tests from KeyValueTreeSerializerTest 13: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 13: [ OK ] KeyValueTreeSerializerTest.EmptyTree (3 ms) 13: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 13: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms) 13: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 13: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms) 13: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 13: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms) 13: [----------] 4 tests from KeyValueTreeSerializerTest (5 ms total) 13: 13: [----------] 7 tests from TreeValueTransformTest 13: [ RUN ] TreeValueTransformTest.SimpleTransforms 13: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms) 13: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 13: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms) 13: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 13: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (2 ms) 13: [ RUN ] TreeValueTransformTest.ObjectFromString 13: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms) 13: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 13: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms) 13: [ RUN ] TreeValueTransformTest.ScopedTransformRules 13: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) 13: [ RUN ] TreeValueTransformTest.CanAssignUserMultiValue 13: [ OK ] TreeValueTransformTest.CanAssignUserMultiValue (0 ms) 13: [----------] 7 tests from TreeValueTransformTest (6 ms total) 13: 13: [----------] 1 test from TreeValueTransformErrorTest 13: [ RUN ] TreeValueTransformErrorTest.ConversionError 13: [ OK ] TreeValueTransformErrorTest.ConversionError (2 ms) 13: [----------] 1 test from TreeValueTransformErrorTest (2 ms total) 13: 13: [----------] 9 tests from ListOfLists 13: [ RUN ] ListOfLists.EmptyListOfListsWorks 13: [ OK ] ListOfLists.EmptyListOfListsWorks (0 ms) 13: [ RUN ] ListOfLists.AppendWorks 13: [ OK ] ListOfLists.AppendWorks (0 ms) 13: [ RUN ] ListOfLists.EmptyListWorks 13: [ OK ] ListOfLists.EmptyListWorks (0 ms) 13: [ RUN ] ListOfLists.AppendAccessWorks 13: [ OK ] ListOfLists.AppendAccessWorks (0 ms) 13: [ RUN ] ListOfLists.ClearWorks 13: [ OK ] ListOfLists.ClearWorks (0 ms) 13: [ RUN ] ListOfLists.OutOfRangeAccessThrows 13: [ OK ] ListOfLists.OutOfRangeAccessThrows (0 ms) 13: [ RUN ] ListOfLists.FrontAndBackWork 13: [ OK ] ListOfLists.FrontAndBackWork (0 ms) 13: [ RUN ] ListOfLists.ExtractsAndRestores 13: [ OK ] ListOfLists.ExtractsAndRestores (0 ms) 13: [ RUN ] ListOfLists.AppendsListOfListsWithOffset 13: [ OK ] ListOfLists.AppendsListOfListsWithOffset (0 ms) 13: [----------] 9 tests from ListOfLists (0 ms total) 13: 13: [----------] 7 tests from LoggerTest 13: [ RUN ] LoggerTest.EmptyLoggerWorks 13: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 13: [ RUN ] LoggerTest.LogsToStream 13: [ OK ] LoggerTest.LogsToStream (0 ms) 13: [ RUN ] LoggerTest.LogsToFile 13: [ OK ] LoggerTest.LogsToFile (1 ms) 13: [ RUN ] LoggerTest.LevelFilteringWorks 13: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) 13: [ RUN ] LoggerTest.LogsToMultipleStreams 13: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) 13: [ RUN ] LoggerTest.LogsToMultipleFiles 13: [ OK ] LoggerTest.LogsToMultipleFiles (0 ms) 13: [ RUN ] LoggerTest.LogsToStreamAndFile 13: [ OK ] LoggerTest.LogsToStreamAndFile (6 ms) 13: [----------] 7 tests from LoggerTest (11 ms total) 13: 13: [----------] 7 tests from MessageStringCollectorTest 13: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext 13: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext 13: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddStringMessages 13: [ OK ] MessageStringCollectorTest.CanAddStringMessages (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddCharMessagesConditionally 13: [ OK ] MessageStringCollectorTest.CanAddCharMessagesConditionally (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddStringMessagesConditionally 13: [ OK ] MessageStringCollectorTest.CanAddStringMessagesConditionally (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanMoveConstruct 13: [ OK ] MessageStringCollectorTest.CanMoveConstruct (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanMoveAssign 13: [ OK ] MessageStringCollectorTest.CanMoveAssign (0 ms) 13: [----------] 7 tests from MessageStringCollectorTest (0 ms total) 13: 13: [----------] 1 test from PathTest 13: [ RUN ] PathTest.StripSourcePrefixWorks 13: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 13: [----------] 1 test from PathTest (0 ms total) 13: 13: [----------] 2 tests from PhysicalNodeCommunicatorTest 13: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 13: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 13: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 13: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 13: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 13: 13: [----------] 5 tests from Range 13: [ RUN ] Range.EmptyRangeWorks 13: [ OK ] Range.EmptyRangeWorks (0 ms) 13: [ RUN ] Range.NonEmptyRangeWorks 13: [ OK ] Range.NonEmptyRangeWorks (0 ms) 13: [ RUN ] Range.BeginEnd 13: [ OK ] Range.BeginEnd (0 ms) 13: [ RUN ] Range.IsInRangeWorks 13: [ OK ] Range.IsInRangeWorks (0 ms) 13: [ RUN ] Range.IteratorWorks 13: [ OK ] Range.IteratorWorks (0 ms) 13: [----------] 5 tests from Range (0 ms total) 13: 13: [----------] 7 tests from StringConvert 13: [ RUN ] StringConvert.NoResultFromEptyString 13: [ OK ] StringConvert.NoResultFromEptyString (0 ms) 13: [ RUN ] StringConvert.ThreeFloatsSuccessfully 13: [ OK ] StringConvert.ThreeFloatsSuccessfully (0 ms) 13: [ RUN ] StringConvert.OneIntSucessfully 13: [ OK ] StringConvert.OneIntSucessfully (0 ms) 13: [ RUN ] StringConvert.FloatAsStringToIntArrayThrows 13: [ OK ] StringConvert.FloatAsStringToIntArrayThrows (0 ms) 13: [ RUN ] StringConvert.ThrowsWhenWrongSize 13: [ OK ] StringConvert.ThrowsWhenWrongSize (0 ms) 13: [ RUN ] StringConvert.StringIdentityTransformWithArrayThrows 13: [ OK ] StringConvert.StringIdentityTransformWithArrayThrows (0 ms) 13: [ RUN ] StringConvert.StringIdentityTransformWithArrayOkay 13: [ OK ] StringConvert.StringIdentityTransformWithArrayOkay (0 ms) 13: [----------] 7 tests from StringConvert (0 ms total) 13: 13: [----------] 7 tests from StringToEnumValueConverterTest 13: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping 13: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping 13: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping 13: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping 13: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping 13: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping 13: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CustomConverterWorks 13: [ OK ] StringToEnumValueConverterTest.CustomConverterWorks (0 ms) 13: [----------] 7 tests from StringToEnumValueConverterTest (0 ms total) 13: 13: [----------] 9 tests from StringUtilityTest 13: [ RUN ] StringUtilityTest.StartsWith 13: [ OK ] StringUtilityTest.StartsWith (0 ms) 13: [ RUN ] StringUtilityTest.EndsWith 13: [ OK ] StringUtilityTest.EndsWith (0 ms) 13: [ RUN ] StringUtilityTest.StripSuffixIfPresent 13: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 13: [ RUN ] StringUtilityTest.StripString 13: [ OK ] StringUtilityTest.StripString (0 ms) 13: [ RUN ] StringUtilityTest.SplitString 13: [ OK ] StringUtilityTest.SplitString (0 ms) 13: [ RUN ] StringUtilityTest.SplitDelimitedString 13: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 13: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 13: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) 13: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive 13: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms) 13: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength 13: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms) 13: [----------] 9 tests from StringUtilityTest (0 ms total) 13: 13: [----------] 2 tests from FormatStringTest 13: [ RUN ] FormatStringTest.HandlesBasicFormatting 13: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 13: [ RUN ] FormatStringTest.HandlesLongStrings 13: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 13: [----------] 2 tests from FormatStringTest (0 ms total) 13: 13: [----------] 1 test from StringFormatterTest 13: [ RUN ] StringFormatterTest.HandlesBasicFormatting 13: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 13: [----------] 1 test from StringFormatterTest (0 ms total) 13: 13: [----------] 1 test from formatAndJoinTest 13: [ RUN ] formatAndJoinTest.Works 13: [ OK ] formatAndJoinTest.Works (0 ms) 13: [----------] 1 test from formatAndJoinTest (0 ms total) 13: 13: [----------] 1 test from JoinStringsTest 13: [ RUN ] JoinStringsTest.Works 13: [ OK ] JoinStringsTest.Works (0 ms) 13: [----------] 1 test from JoinStringsTest (0 ms total) 13: 13: [----------] 6 tests from ReplaceAllTest 13: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 13: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesNoMatches 13: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 13: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 13: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 13: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 13: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 13: [----------] 6 tests from ReplaceAllTest (0 ms total) 13: 13: [----------] 10 tests from TextLineWrapperTest 13: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 13: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 13: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 13: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 13: [ RUN ] TextLineWrapperTest.WrapsCorrectly 13: [ OK ] TextLineWrapperTest.WrapsCorrectly (4 ms) 13: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 13: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesIndent 13: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 13: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 13: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 13: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) 13: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 13: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) 13: [----------] 10 tests from TextLineWrapperTest (8 ms total) 13: 13: [----------] 3 tests from TemplateMPTest 13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnum 13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnum (0 ms) 13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionBool 13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionBool (0 ms) 13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnumBool 13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnumBool (0 ms) 13: [----------] 3 tests from TemplateMPTest (0 ms total) 13: 13: [----------] 6 tests from TextWriterTest 13: [ RUN ] TextWriterTest.WritesLines 13: [ OK ] TextWriterTest.WritesLines (0 ms) 13: [ RUN ] TextWriterTest.WritesLinesInParts 13: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) 13: [ RUN ] TextWriterTest.WritesWrappedLines 13: [ OK ] TextWriterTest.WritesWrappedLines (0 ms) 13: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 13: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) 13: [ RUN ] TextWriterTest.TracksNewlines 13: [ OK ] TextWriterTest.TracksNewlines (0 ms) 13: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 13: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) 13: [----------] 6 tests from TextWriterTest (3 ms total) 13: 13: [----------] 1 test from TypeTraitsTest 13: [ RUN ] TypeTraitsTest.IsIntegralConstant 13: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 13: [----------] 1 test from TypeTraitsTest (0 ms total) 13: 13: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 13: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 13: 13: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 13: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 13: 13: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 13: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) 13: 13: [----------] 11 tests from WithInputPaths/PathSearchTest 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 (1 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 (0 ms) 13: [----------] 11 tests from WithInputPaths/PathSearchTest (7 ms total) 13: 13: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 13: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (0 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 400 tests from 62 test suites ran. (53 ms total) 13: [ PASSED ] 400 tests. 13: 13: YOU HAVE 1 DISABLED TEST 13: 13/87 Test #13: UtilityUnitTests .......................... Passed 0.08 sec test 14 Start 14: UtilityMpiUnitTests 14: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/utility-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/UtilityMpiUnitTests.xml" 14: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests 14: Test timeout computed to be: 30 14: [==========] Running 2 tests from 1 test suite. 14: [----------] Global test environment set-up. 14: [----------] 2 tests from PhysicalNodeCommunicatorTest 14: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 14: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (3 ms) 14: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 14: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (3 ms) 14: [----------] 2 tests from PhysicalNodeCommunicatorTest (7 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 2 tests from 1 test suite ran. (7 ms total) 14: [ PASSED ] 2 tests. 14/87 Test #14: UtilityMpiUnitTests ....................... Passed 0.03 sec test 15 Start 15: GmxlibTests 15: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/nonbonded-fep-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/GmxlibTests.xml" 15: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxlib/nonbonded/tests 15: Test timeout computed to be: 30 15: [==========] Running 78 tests from 2 test suites. 15: [----------] Global test environment set-up. 15: [----------] 72 tests from NBInteraction/NonbondedFepTest 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/0 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/0 (2 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/1 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/1 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/2 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/2 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/3 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/3 (2 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/4 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/4 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/5 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/5 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/6 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/6 (2 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/7 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/7 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/8 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/8 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/9 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/9 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/10 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/10 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/11 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/11 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/12 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/12 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/13 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/13 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/14 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/14 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/15 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/15 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/16 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/16 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/17 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/17 (2 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/18 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/18 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/19 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/19 (2 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/20 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/20 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/21 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/21 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/22 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/22 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/23 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/23 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/24 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/24 (2 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/25 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/25 (3 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/26 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/26 (3 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/27 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/27 (2 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/28 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/28 (2 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/29 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/29 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/30 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/30 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/31 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/31 (3 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/32 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/32 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/33 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/33 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/34 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/34 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/35 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/35 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/36 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/36 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/37 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/37 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/38 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/38 (14 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/39 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/39 (9 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/40 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/40 (8 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/41 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/41 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/42 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/42 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/43 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/43 (2 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/44 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/44 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/45 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/45 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/46 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/46 (2 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/47 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/47 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/48 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/48 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/49 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/49 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/50 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/50 (2 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/51 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/51 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/52 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/52 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/53 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/53 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/54 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/54 (3 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/55 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/55 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/56 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/56 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/57 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/57 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/58 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/58 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/59 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/59 (2 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/60 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/60 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/61 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/61 (2 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/62 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/62 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/63 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/63 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/64 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/64 (8 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/65 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/65 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/66 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/66 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/67 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/67 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/68 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/68 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/69 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/69 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/70 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/70 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/71 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/71 (2 ms) 15: [----------] 72 tests from NBInteraction/NonbondedFepTest (155 ms total) 15: 15: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 (2 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 (1 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 (1 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 (4 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 (0 ms) 15: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest (13 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 78 tests from 2 test suites ran. (171 ms total) 15: [ PASSED ] 78 tests. 15/87 Test #15: GmxlibTests ............................... Passed 0.22 sec test 16 Start 16: MdlibUnitTest 16: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdlib-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdlibUnitTest.xml" 16: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests 16: Test timeout computed to be: 30 16: [==========] Running 999 tests from 25 test suites. 16: [----------] Global test environment set-up. 16: [----------] 2 tests from EffectiveAtomDensity 16: [ RUN ] EffectiveAtomDensity.VolumeIndependence 16: [ OK ] EffectiveAtomDensity.VolumeIndependence (0 ms) 16: [ RUN ] EffectiveAtomDensity.WeightingWorks 16: [ OK ] EffectiveAtomDensity.WeightingWorks (0 ms) 16: [----------] 2 tests from EffectiveAtomDensity (0 ms total) 16: 16: [----------] 2 tests from AtomNonbondedAndKineticProperties 16: [ RUN ] AtomNonbondedAndKineticProperties.IsAccurate 16: [ OK ] AtomNonbondedAndKineticProperties.IsAccurate (0 ms) 16: [ RUN ] AtomNonbondedAndKineticProperties.ConstraintsWork 16: [ OK ] AtomNonbondedAndKineticProperties.ConstraintsWork (0 ms) 16: [----------] 2 tests from AtomNonbondedAndKineticProperties (0 ms total) 16: 16: [----------] 1 test from VerletBufferConstraintTest 16: [ RUN ] VerletBufferConstraintTest.EqualMasses 16: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) 16: [----------] 1 test from VerletBufferConstraintTest (0 ms total) 16: 16: [----------] 6 tests from CalcvirTest 16: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBox 16: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBox (1 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew 16: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX (1 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY (1 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ (0 ms) 16: [----------] 6 tests from CalcvirTest (6 ms total) 16: 16: [----------] 2 tests from PrEbinTest 16: [ RUN ] PrEbinTest.HandlesAverages 16: [ OK ] PrEbinTest.HandlesAverages (1 ms) 16: [ RUN ] PrEbinTest.HandlesEmptyAverages 16: [ OK ] PrEbinTest.HandlesEmptyAverages (1 ms) 16: [----------] 2 tests from PrEbinTest (3 ms total) 16: 16: [----------] 3 tests from EnergyDriftTracker 16: [ RUN ] EnergyDriftTracker.emptyWorks 16: [ OK ] EnergyDriftTracker.emptyWorks (0 ms) 16: [ RUN ] EnergyDriftTracker.onePointWorks 16: [ OK ] EnergyDriftTracker.onePointWorks (0 ms) 16: [ RUN ] EnergyDriftTracker.manyPointsWorks 16: [ OK ] EnergyDriftTracker.manyPointsWorks (0 ms) 16: [----------] 3 tests from EnergyDriftTracker (0 ms total) 16: 16: [----------] 4 tests from ShakeTest 16: [ RUN ] ShakeTest.ConstrainsOneBond 16: [ OK ] ShakeTest.ConstrainsOneBond (0 ms) 16: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 16: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 16: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 16: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 16: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 16: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 16: [----------] 4 tests from ShakeTest (0 ms total) 16: 16: [----------] 1 test from NullSignalTest 16: [ RUN ] NullSignalTest.NullSignallerWorks 16: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) 16: [----------] 1 test from NullSignalTest (0 ms total) 16: 16: [----------] 7 tests from SignalTest 16: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 16: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 16: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 16: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 16: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 16: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 16: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 16: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 16: [----------] 7 tests from SignalTest (0 ms total) 16: 16: [----------] 13 tests from UpdateGroupsTest 16: [ RUN ] UpdateGroupsTest.WithEthaneUA 16: [ OK ] UpdateGroupsTest.WithEthaneUA (0 ms) 16: [ RUN ] UpdateGroupsTest.WithMethane 16: [ OK ] UpdateGroupsTest.WithMethane (0 ms) 16: [ RUN ] UpdateGroupsTest.WithEthane 16: [ OK ] UpdateGroupsTest.WithEthane (0 ms) 16: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane 16: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane (0 ms) 16: [ RUN ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups 16: [ OK ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups (0 ms) 16: [ RUN ] UpdateGroupsTest.WithWaterThreeSite 16: [ OK ] UpdateGroupsTest.WithWaterThreeSite (0 ms) 16: [ RUN ] UpdateGroupsTest.WithWaterFourSite 16: [ OK ] UpdateGroupsTest.WithWaterFourSite (0 ms) 16: [ RUN ] UpdateGroupsTest.WithFourAtomsWithSettle 16: [ OK ] UpdateGroupsTest.WithFourAtomsWithSettle (0 ms) 16: [ RUN ] UpdateGroupsTest.WithWaterFlexAngle 16: [ OK ] UpdateGroupsTest.WithWaterFlexAngle (0 ms) 16: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle 16: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle (0 ms) 16: [ RUN ] UpdateGroupsTest.WithTwoMoltypes 16: [ OK ] UpdateGroupsTest.WithTwoMoltypes (0 ms) 16: [ RUN ] UpdateGroupsTest.LogsWhenSizesAreInvalid 16: [ OK ] UpdateGroupsTest.LogsWhenSizesAreInvalid (0 ms) 16: [ RUN ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful 16: [ OK ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful (0 ms) 16: [----------] 13 tests from UpdateGroupsTest (0 ms total) 16: 16: [----------] 1 test from UpdateGroupsCog 16: [ RUN ] UpdateGroupsCog.ComputesCogs 16: [ OK ] UpdateGroupsCog.ComputesCogs (8 ms) 16: [----------] 1 test from UpdateGroupsCog (8 ms total) 16: 16: [----------] 2 tests from WholeMoleculeTransform 16: [ RUN ] WholeMoleculeTransform.MakesMoleculesWhole 16: [ OK ] WholeMoleculeTransform.MakesMoleculesWhole (0 ms) 16: [ RUN ] WholeMoleculeTransform.HandlesReordering 16: [ OK ] WholeMoleculeTransform.HandlesReordering (0 ms) 16: [----------] 2 tests from WholeMoleculeTransform (0 ms total) 16: 16: [----------] 14 tests from WithParameters/ConstraintsTest 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 (1 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 (1 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 (13 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 (12 ms) 16: [----------] 14 tests from WithParameters/ConstraintsTest (38 ms total) 16: 16: [----------] 11 tests from WithParameters/EnergyOutputTest 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0 16: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (13 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1 16: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (2 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2 16: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (3 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3 16: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (4 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4 16: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as single precision energy file 16: Reading energy frame 0 time 10.100 Reading energy frame 1 time 27.500 Reading energy frame 2 time 44.900 Reading energy frame 3 time 62.300 Reading energy frame 4 time 79.700 Reading energy frame 5 time 97.100 Reading energy frame 6 time 114.500 Reading energy frame 7 time 131.900 Reading energy frame 8 time 149.300 Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (5 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5 16: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (8 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6 16: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (6 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7 16: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (6 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8 16: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (5 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9 16: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (4 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10 16: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (9 ms) 16: [----------] 11 tests from WithParameters/EnergyOutputTest (70 ms total) 16: 16: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (6 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms) 16: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (7 ms total) 16: 16: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms) 16: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (0 ms total) 16: 16: [----------] 23 tests from WithParameters/FreeEnergyParameterTest 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 (0 ms) 16: [----------] 23 tests from WithParameters/FreeEnergyParameterTest (1 ms total) 16: 16: [----------] 16 tests from WithParameters/LeapFrogTest 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (5 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (4 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (6 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (4 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (4 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (8 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (2 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (2 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (2 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (6 ms) 16: [----------] 16 tests from WithParameters/LeapFrogTest (62 ms total) 16: 16: [----------] 140 tests from Cubic/ParrRahmTest 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (5 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (2 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 (8 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (2 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (2 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (2 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (2 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (2 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (2 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (2 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (2 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (2 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (5 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (2 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (2 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (2 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (2 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (5 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (2 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (2 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (2 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 (2 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from Cubic/ParrRahmTest (177 ms total) 16: 16: [----------] 140 tests from Rectilinear/ParrRahmTest 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (2 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (2 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (7 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (2 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (2 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (2 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (2 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (2 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (4 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (4 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (6 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (2 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (2 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 (2 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 (4 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 (5 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (2 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (2 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (2 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (2 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (2 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (2 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (2 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (4 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 (4 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from Rectilinear/ParrRahmTest (226 ms total) 16: 16: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (4 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 (4 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (4 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (5 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest (220 ms total) 16: 16: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (4 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (3 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (3 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (6 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (3 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 (3 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest (224 ms total) 16: 16: [----------] 140 tests from TruncOct/ParrRahmTest 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (3 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (4 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (2 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (2 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (2 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (2 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (2 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (3 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (2 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (2 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (2 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (3 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (2 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (3 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (2 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (2 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (3 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 (6 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 (4 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 (11 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 (2 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (5 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (3 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (3 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (2 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (3 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (2 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (3 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (2 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (2 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (2 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (3 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (3 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (2 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 (2 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (2 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 (4 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from TruncOct/ParrRahmTest (236 ms total) 16: 16: [----------] 140 tests from Other/ParrRahmTest 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (6 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (3 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (3 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (9 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (2 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (2 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (3 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (6 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (3 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (2 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (5 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (3 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (2 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (2 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (4 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 (4 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (2 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 (3 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (4 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 (3 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 (6 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (4 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (2 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (2 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (4 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (3 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (3 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (3 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (2 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (2 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (2 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (2 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (2 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (4 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (2 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (2 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (4 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (2 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (2 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 (2 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (4 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 (2 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 (2 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (2 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 (2 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from Other/ParrRahmTest (246 ms total) 16: 16: [----------] 13 tests from WithParameters/SettleTest 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (1 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (2 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (1 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (6 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (5 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (2 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (2 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (5 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (5 ms) 16: [----------] 13 tests from WithParameters/SettleTest (38 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 999 tests from 25 test suites ran. (1572 ms total) 16: [ PASSED ] 999 tests. 16/87 Test #16: MdlibUnitTest ............................. Passed 1.72 sec test 17 Start 17: AwhTest 17: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/awh-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/AwhTest.xml" 17: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/awh/tests 17: Test timeout computed to be: 30 17: [==========] Running 27 tests from 10 test suites. 17: [----------] Global test environment set-up. 17: [----------] 3 tests from SerializationTest 17: [ RUN ] SerializationTest.CanSerializeDimParams 17: [ OK ] SerializationTest.CanSerializeDimParams (0 ms) 17: [ RUN ] SerializationTest.CanSerializeBiasParams 17: [ OK ] SerializationTest.CanSerializeBiasParams (0 ms) 17: [ RUN ] SerializationTest.CanSerializeAwhParams 17: [ OK ] SerializationTest.CanSerializeAwhParams (0 ms) 17: [----------] 3 tests from SerializationTest (4 ms total) 17: 17: [----------] 1 test from BiasTest 17: [ RUN ] BiasTest.DetectsCovering 17: [ OK ] BiasTest.DetectsCovering (2 ms) 17: [----------] 1 test from BiasTest (2 ms total) 17: 17: [----------] 1 test from biasGridTest 17: [ RUN ] biasGridTest.neighborhood 17: [ OK ] biasGridTest.neighborhood (0 ms) 17: [----------] 1 test from biasGridTest (0 ms total) 17: 17: [----------] 2 tests from BiasSharingTest 17: [ RUN ] BiasSharingTest.SharingWorks 17: [ OK ] BiasSharingTest.SharingWorks (49 ms) 17: [ RUN ] BiasSharingTest.SharingScalingByMetricWorks 17: [ OK ] BiasSharingTest.SharingScalingByMetricWorks (15 ms) 17: [----------] 2 tests from BiasSharingTest (65 ms total) 17: 17: [----------] 2 tests from BiasFepLambdaStateTest 17: [ RUN ] BiasFepLambdaStateTest.DetectsCovering 17: [ OK ] BiasFepLambdaStateTest.DetectsCovering (1 ms) 17: [ RUN ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy 17: [ OK ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy (0 ms) 17: [----------] 2 tests from BiasFepLambdaStateTest (2 ms total) 17: 17: [----------] 8 tests from WithParameters/BiasTest 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 (5 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 (4 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 (1 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 (0 ms) 17: [----------] 8 tests from WithParameters/BiasTest (21 ms total) 17: 17: [----------] 2 tests from WithParameters/BiasStateTest 17: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 17: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms) 17: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 17: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (3 ms) 17: [----------] 2 tests from WithParameters/BiasStateTest (4 ms total) 17: 17: [----------] 1 test from WithParameters/UserInputTest 17: [ RUN ] WithParameters/UserInputTest.ParsesUser3DInput/0 17: [ OK ] WithParameters/UserInputTest.ParsesUser3DInput/0 (4 ms) 17: [----------] 1 test from WithParameters/UserInputTest (4 ms total) 17: 17: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 (5 ms) 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 (7 ms) 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 (7 ms) 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 (5 ms) 17: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest (47 ms total) 17: 17: [----------] 3 tests from WithParameters/FrictionMetricTest 17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/0 17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/0 (1 ms) 17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/1 17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/1 (1 ms) 17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/2 17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/2 (25 ms) 17: [----------] 3 tests from WithParameters/FrictionMetricTest (35 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 27 tests from 10 test suites ran. (188 ms total) 17: [ PASSED ] 27 tests. 17/87 Test #17: AwhTest ................................... Passed 0.22 sec test 18 Start 18: DensityFittingAppliedForcesUnitTest 18: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/density_fitting_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/DensityFittingAppliedForcesUnitTest.xml" 18: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/densityfitting/tests 18: Test timeout computed to be: 30 18: [==========] Running 18 tests from 4 test suites. 18: [----------] Global test environment set-up. 18: [----------] 2 tests from DensityFittingTest 18: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows 18: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (1 ms) 18: [ RUN ] DensityFittingTest.SingleAtom 18: [ OK ] DensityFittingTest.SingleAtom (2 ms) 18: [----------] 2 tests from DensityFittingTest (4 ms total) 18: 18: [----------] 7 tests from DensityFittingAmplitudeLookupTest 18: [ RUN ] DensityFittingAmplitudeLookupTest.Unity 18: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.Charge 18: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.Masses 18: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign 18: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct 18: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign 18: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct 18: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms) 18: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total) 18: 18: [----------] 1 test from DensityFittingForceProviderState 18: [ RUN ] DensityFittingForceProviderState.RoundTripSaving 18: [ OK ] DensityFittingForceProviderState.RoundTripSaving (0 ms) 18: [----------] 1 test from DensityFittingForceProviderState (0 ms total) 18: 18: [----------] 8 tests from DensityFittingOptionsTest 18: [ RUN ] DensityFittingOptionsTest.DefaultParameters 18: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms) 18: [ RUN ] DensityFittingOptionsTest.OptionSetsActive 18: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms) 18: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive 18: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 18: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive 18: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (0 ms) 18: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup 18: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 18: [ RUN ] DensityFittingOptionsTest.InternalsToKvt 18: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms) 18: [ RUN ] DensityFittingOptionsTest.KvtToInternal 18: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms) 18: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent 18: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms) 18: [----------] 8 tests from DensityFittingOptionsTest (0 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 18 tests from 4 test suites ran. (4 ms total) 18: [ PASSED ] 18 tests. 18/87 Test #18: DensityFittingAppliedForcesUnitTest ....... Passed 0.03 sec test 19 Start 19: QMMMAppliedForcesUnitTest 19: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/qmmm_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/QMMMAppliedForcesUnitTest.xml" 19: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests 19: Test timeout computed to be: 30 19: [==========] Running 21 tests from 5 test suites. 19: [----------] Global test environment set-up. 19: [----------] 3 tests from QMMMInputGeneratorTest 19: [ RUN ] QMMMInputGeneratorTest.CanConstruct 19: [ OK ] QMMMInputGeneratorTest.CanConstruct (0 ms) 19: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBENoLink 19: [ OK ] QMMMInputGeneratorTest.TwoWatersPBENoLink (3 ms) 19: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBEWithLink 19: [ OK ] QMMMInputGeneratorTest.TwoWatersPBEWithLink (0 ms) 19: [----------] 3 tests from QMMMInputGeneratorTest (4 ms total) 19: 19: [----------] 7 tests from QMMMTopologyPreprocessorTest 19: [ RUN ] QMMMTopologyPreprocessorTest.CanConstruct 19: [ OK ] QMMMTopologyPreprocessorTest.CanConstruct (0 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 21.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 19: Setting the LD random seed to -270139404 19: 19: Generated 10 of the 10 non-bonded parameter combinations 19: 19: Generated 10 of the 10 1-4 parameter combinations 19: 19: Excluding 2 bonded neighbours molecule type 'SOL' 19: Analysing residue names: 19: There are: 4 Water residues 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink (16 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 21.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 19: Setting the LD random seed to -25955074 19: 19: Generated 10 of the 10 non-bonded parameter combinations 19: 19: Generated 10 of the 10 1-4 parameter combinations 19: 19: Excluding 2 bonded neighbours molecule type 'SOL' 19: Analysing residue names: 19: There are: 4 Water residues 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink (7 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 21.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 19: Setting the LD random seed to -34154249 19: 19: Generated 10 of the 10 non-bonded parameter combinations 19: 19: Generated 10 of the 10 1-4 parameter combinations 19: 19: Excluding 2 bonded neighbours molecule type 'SOL' 19: Analysing residue names: 19: There are: 4 Water residues 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink (14 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 63.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 19: NVE simulation: will use the initial temperature of 129.093 K for 19: determining the Verlet buffer size 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 19: Setting the LD random seed to -1614746673 19: 19: Generated 2145 of the 2145 non-bonded parameter combinations 19: 19: Generated 2145 of the 2145 1-4 parameter combinations 19: 19: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 19: Analysing residue names: 19: There are: 3 Protein residues 19: Analysing Protein... 19: 19: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 19: 19: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 19: 19: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 19: 19: Note that mdrun will redetermine rlist based on the actual pair-list setup 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints (22 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: 19: NOTE 2 [file unknown]: 19: You are using constraints on all bonds, whereas the forcefield has been 19: parametrized only with constraints involving hydrogen atoms. We suggest 19: using constraints = h-bonds instead, this will also improve performance. 19: 19: 19: NOTE 3 [file unknown]: 19: For energy conservation with LINCS, lincs_iter should be 2 or larger. 19: 19: 19: Number of degrees of freedom in T-Coupling group rest is 42.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 19: NVE simulation: will use the initial temperature of 193.640 K for 19: determining the Verlet buffer size 19: 19: 19: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 5 NOTEs 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 19: Setting the LD random seed to 1526157759 19: 19: Generated 2145 of the 2145 non-bonded parameter combinations 19: 19: Generated 2145 of the 2145 1-4 parameter combinations 19: 19: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 19: 19: turning all bonds into constraints... 19: Analysing residue names: 19: There are: 3 Protein residues 19: Analysing Protein... 19: 19: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 19: 19: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 19: 19: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 19: 19: Note that mdrun will redetermine rlist based on the actual pair-list setup 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints (19 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.RemovingQMVsites 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Number of degrees of freedom in T-Coupling group rest is 45.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 19: Setting the LD random seed to -806494217 19: 19: Generated 3 of the 6 non-bonded parameter combinations 19: 19: Excluding 3 bonded neighbours molecule type 'VSTEST' 19: 19: Cleaning up constraints and constant bonded interactions with virtual sites 19: Analysing residue names: 19: There are: 1 Other residues 19: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.RemovingQMVsites (14 ms) 19: [----------] 7 tests from QMMMTopologyPreprocessorTest (95 ms total) 19: 19: [----------] 9 tests from QMMMOptionsTest 19: [ RUN ] QMMMOptionsTest.DefaultParameters 19: [ OK ] QMMMOptionsTest.DefaultParameters (0 ms) 19: [ RUN ] QMMMOptionsTest.OptionSetsActive 19: [ OK ] QMMMOptionsTest.OptionSetsActive (0 ms) 19: [ RUN ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive 19: [ OK ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 19: [ RUN ] QMMMOptionsTest.OutputDefaultValuesWhenActive 19: [ OK ] QMMMOptionsTest.OutputDefaultValuesWhenActive (2 ms) 19: [ RUN ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup 19: [ OK ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 19: [ RUN ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup 19: [ OK ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup (0 ms) 19: [ RUN ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup 19: [ OK ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup (1 ms) 19: [ RUN ] QMMMOptionsTest.InternalsToKvtAndBack 19: [ OK ] QMMMOptionsTest.InternalsToKvtAndBack (0 ms) 19: [ RUN ] QMMMOptionsTest.CP2KInputProcessing 19: [ OK ] QMMMOptionsTest.CP2KInputProcessing (3 ms) 19: [----------] 9 tests from QMMMOptionsTest (12 ms total) 19: 19: [----------] 1 test from QMMMForceProviderTest 19: [ RUN ] QMMMForceProviderTest.CanConstructOrNot 19: [ OK ] QMMMForceProviderTest.CanConstructOrNot (0 ms) 19: [----------] 1 test from QMMMForceProviderTest (0 ms total) 19: 19: [----------] 1 test from QMMMTest 19: [ RUN ] QMMMTest.ForceProviderLackingInputThrows 19: [ OK ] QMMMTest.ForceProviderLackingInputThrows (0 ms) 19: [----------] 1 test from QMMMTest (0 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 21 tests from 5 test suites ran. (113 ms total) 19: [ PASSED ] 21 tests. 19/87 Test #19: QMMMAppliedForcesUnitTest ................. Passed 0.14 sec test 20 Start 20: ColvarsAppliedForcesUnitTest 20: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/colvars_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/ColvarsAppliedForcesUnitTest.xml" 20: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests 20: Test timeout computed to be: 30 20: [==========] Running 16 tests from 4 test suites. 20: [----------] Global test environment set-up. 20: [----------] 1 test from ColvarsTest 20: [ RUN ] ColvarsTest.ForceProviderLackingInputThrows 20: [ OK ] ColvarsTest.ForceProviderLackingInputThrows (0 ms) 20: [----------] 1 test from ColvarsTest (0 ms total) 20: 20: [----------] 6 tests from ColvarsOptionsTest 20: [ RUN ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive 20: [ OK ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 20: [ RUN ] ColvarsOptionsTest.OutputDefaultValuesWhenActive 20: [ OK ] ColvarsOptionsTest.OutputDefaultValuesWhenActive (0 ms) 20: [ RUN ] ColvarsOptionsTest.OutputValuesWhenActive 20: [ OK ] ColvarsOptionsTest.OutputValuesWhenActive (0 ms) 20: [ RUN ] ColvarsOptionsTest.OptionSetsActive 20: [ OK ] ColvarsOptionsTest.OptionSetsActive (0 ms) 20: [ RUN ] ColvarsOptionsTest.InternalsToKvtAndBack 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 20: Setting the LD random seed to -2013856833 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsOptionsTest.InternalsToKvtAndBack (59 ms) 20: [ RUN ] ColvarsOptionsTest.RetrieveEdrFilename 20: [ OK ] ColvarsOptionsTest.RetrieveEdrFilename (0 ms) 20: [----------] 6 tests from ColvarsOptionsTest (61 ms total) 20: 20: [----------] 4 tests from ColvarsPreProcessorTest 20: [ RUN ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 20: Setting the LD random seed to -327266532 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess (7 ms) 20: [ RUN ] ColvarsPreProcessorTest.CheckValuesFourWaters 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 20: Setting the LD random seed to 2130697727 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.CheckValuesFourWaters (11 ms) 20: [ RUN ] ColvarsPreProcessorTest.CheckNestedInputFiles 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 20: Setting the LD random seed to 2113140669 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.CheckNestedInputFiles (12 ms) 20: [ RUN ] ColvarsPreProcessorTest.WrongColvarsInput 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 20: Setting the LD random seed to 1542978559 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.WrongColvarsInput (20 ms) 20: [----------] 4 tests from ColvarsPreProcessorTest (52 ms total) 20: 20: [----------] 5 tests from ColvarsForceProviderTest 20: [ RUN ] ColvarsForceProviderTest.CanConstructOrNot 20: [ OK ] ColvarsForceProviderTest.CanConstructOrNot (0 ms) 20: [ RUN ] ColvarsForceProviderTest.SimpleInputs 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 20: Setting the LD random seed to 926937006 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.SimpleInputs (3 ms) 20: [ RUN ] ColvarsForceProviderTest.WrongColvarsInput 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 20: Setting the LD random seed to -1413513307 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.WrongColvarsInput (7 ms) 20: [ RUN ] ColvarsForceProviderTest.CalculateForces4water 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 20: Setting the LD random seed to -269584387 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.CalculateForces4water (78 ms) 20: [ RUN ] ColvarsForceProviderTest.CalculateForcesAlanine 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 66.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 20: NVE simulation: will use the initial temperature of 300.368 K for 20: determining the Verlet buffer size 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 20: Setting the LD random seed to -659476 20: 20: Generated 2211 of the 2211 non-bonded parameter combinations 20: 20: Generated 2211 of the 2211 1-4 parameter combinations 20: 20: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 20: Analysing residue names: 20: There are: 2 Protein residues 20: Analysing Protein... 20: 20: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 20: 20: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 20: 20: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 20: 20: Note that mdrun will redetermine rlist based on the actual pair-list setup 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.CalculateForcesAlanine (96 ms) 20: [----------] 5 tests from ColvarsForceProviderTest (185 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 16 tests from 4 test suites ran. (300 ms total) 20: [ PASSED ] 16 tests. 20/87 Test #20: ColvarsAppliedForcesUnitTest .............. Passed 0.32 sec test 21 Start 21: AppliedForcesUnitTest 21: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/AppliedForcesUnitTest.xml" 21: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/tests 21: Test timeout computed to be: 30 21: [==========] Running 3 tests from 1 test suite. 21: [----------] Global test environment set-up. 21: [----------] 3 tests from ElectricFieldTest 21: [ RUN ] ElectricFieldTest.Static 21: [ OK ] ElectricFieldTest.Static (0 ms) 21: [ RUN ] ElectricFieldTest.Oscillating 21: [ OK ] ElectricFieldTest.Oscillating (0 ms) 21: [ RUN ] ElectricFieldTest.Pulsed 21: [ OK ] ElectricFieldTest.Pulsed (0 ms) 21: [----------] 3 tests from ElectricFieldTest (0 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 3 tests from 1 test suite ran. (0 ms total) 21: [ PASSED ] 3 tests. 21/87 Test #21: AppliedForcesUnitTest ..................... Passed 0.02 sec test 22 Start 22: ListedForcesTest 22: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/listed_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/ListedForcesTest.xml" 22: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/listed_forces/tests 22: Test timeout computed to be: 30 22: [==========] Running 132 tests from 9 test suites. 22: [----------] Global test environment set-up. 22: [----------] 24 tests from Bond/ListedForcesTest 22: [ RUN ] Bond/ListedForcesTest.Ifunc/0 22: [ OK ] Bond/ListedForcesTest.Ifunc/0 (2 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/1 22: [ OK ] Bond/ListedForcesTest.Ifunc/1 (3 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/2 22: [ OK ] Bond/ListedForcesTest.Ifunc/2 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/3 22: [ OK ] Bond/ListedForcesTest.Ifunc/3 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/4 22: [ OK ] Bond/ListedForcesTest.Ifunc/4 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/5 22: [ OK ] Bond/ListedForcesTest.Ifunc/5 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/6 22: [ OK ] Bond/ListedForcesTest.Ifunc/6 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/7 22: [ OK ] Bond/ListedForcesTest.Ifunc/7 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/8 22: [ OK ] Bond/ListedForcesTest.Ifunc/8 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/9 22: [ OK ] Bond/ListedForcesTest.Ifunc/9 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/10 22: [ OK ] Bond/ListedForcesTest.Ifunc/10 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/11 22: [ OK ] Bond/ListedForcesTest.Ifunc/11 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/12 22: [ OK ] Bond/ListedForcesTest.Ifunc/12 (4 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/13 22: [ OK ] Bond/ListedForcesTest.Ifunc/13 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/14 22: [ OK ] Bond/ListedForcesTest.Ifunc/14 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/15 22: [ OK ] Bond/ListedForcesTest.Ifunc/15 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/16 22: [ OK ] Bond/ListedForcesTest.Ifunc/16 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/17 22: [ OK ] Bond/ListedForcesTest.Ifunc/17 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/18 22: [ OK ] Bond/ListedForcesTest.Ifunc/18 (3 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/19 22: [ OK ] Bond/ListedForcesTest.Ifunc/19 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/20 22: [ OK ] Bond/ListedForcesTest.Ifunc/20 (1 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/21 22: [ OK ] Bond/ListedForcesTest.Ifunc/21 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/22 22: [ OK ] Bond/ListedForcesTest.Ifunc/22 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/23 22: [ OK ] Bond/ListedForcesTest.Ifunc/23 (0 ms) 22: [----------] 24 tests from Bond/ListedForcesTest (30 ms total) 22: 22: [----------] 33 tests from Angle/ListedForcesTest 22: [ RUN ] Angle/ListedForcesTest.Ifunc/0 22: [ OK ] Angle/ListedForcesTest.Ifunc/0 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/1 22: [ OK ] Angle/ListedForcesTest.Ifunc/1 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/2 22: [ OK ] Angle/ListedForcesTest.Ifunc/2 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/3 22: [ OK ] Angle/ListedForcesTest.Ifunc/3 (1 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/4 22: [ OK ] Angle/ListedForcesTest.Ifunc/4 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/5 22: [ OK ] Angle/ListedForcesTest.Ifunc/5 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/6 22: [ OK ] Angle/ListedForcesTest.Ifunc/6 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/7 22: [ OK ] Angle/ListedForcesTest.Ifunc/7 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/8 22: [ OK ] Angle/ListedForcesTest.Ifunc/8 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/9 22: [ OK ] Angle/ListedForcesTest.Ifunc/9 (1 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/10 22: [ OK ] Angle/ListedForcesTest.Ifunc/10 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/11 22: [ OK ] Angle/ListedForcesTest.Ifunc/11 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/12 22: [ OK ] Angle/ListedForcesTest.Ifunc/12 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/13 22: [ OK ] Angle/ListedForcesTest.Ifunc/13 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/14 22: [ OK ] Angle/ListedForcesTest.Ifunc/14 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/15 22: [ OK ] Angle/ListedForcesTest.Ifunc/15 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/16 22: [ OK ] Angle/ListedForcesTest.Ifunc/16 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/17 22: [ OK ] Angle/ListedForcesTest.Ifunc/17 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/18 22: [ OK ] Angle/ListedForcesTest.Ifunc/18 (1 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/19 22: [ OK ] Angle/ListedForcesTest.Ifunc/19 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/20 22: [ OK ] Angle/ListedForcesTest.Ifunc/20 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/21 22: [ OK ] Angle/ListedForcesTest.Ifunc/21 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/22 22: [ OK ] Angle/ListedForcesTest.Ifunc/22 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/23 22: [ OK ] Angle/ListedForcesTest.Ifunc/23 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/24 22: [ OK ] Angle/ListedForcesTest.Ifunc/24 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/25 22: [ OK ] Angle/ListedForcesTest.Ifunc/25 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/26 22: [ OK ] Angle/ListedForcesTest.Ifunc/26 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/27 22: [ OK ] Angle/ListedForcesTest.Ifunc/27 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/28 22: [ OK ] Angle/ListedForcesTest.Ifunc/28 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/29 22: [ OK ] Angle/ListedForcesTest.Ifunc/29 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/30 22: [ OK ] Angle/ListedForcesTest.Ifunc/30 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/31 22: [ OK ] Angle/ListedForcesTest.Ifunc/31 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/32 22: [ OK ] Angle/ListedForcesTest.Ifunc/32 (0 ms) 22: [----------] 33 tests from Angle/ListedForcesTest (44 ms total) 22: 22: [----------] 18 tests from Dihedral/ListedForcesTest 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/0 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/0 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/1 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/1 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/2 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/2 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/3 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/3 (1 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/4 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/4 (2 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/5 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/5 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/6 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/6 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/7 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/7 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/8 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/8 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/9 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/9 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/10 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/10 (1 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/11 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/11 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/12 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/12 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/13 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/13 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/14 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/14 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/15 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/15 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/16 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/16 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/17 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/17 (0 ms) 22: [----------] 18 tests from Dihedral/ListedForcesTest (24 ms total) 22: 22: [----------] 12 tests from Polarize/ListedForcesTest 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/0 22: [ OK ] Polarize/ListedForcesTest.Ifunc/0 (0 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/1 22: [ OK ] Polarize/ListedForcesTest.Ifunc/1 (0 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/2 22: [ OK ] Polarize/ListedForcesTest.Ifunc/2 (2 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/3 22: [ OK ] Polarize/ListedForcesTest.Ifunc/3 (0 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/4 22: [ OK ] Polarize/ListedForcesTest.Ifunc/4 (0 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/5 22: [ OK ] Polarize/ListedForcesTest.Ifunc/5 (0 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/6 22: [ OK ] Polarize/ListedForcesTest.Ifunc/6 (0 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/7 22: [ OK ] Polarize/ListedForcesTest.Ifunc/7 (0 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/8 22: [ OK ] Polarize/ListedForcesTest.Ifunc/8 (0 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/9 22: [ OK ] Polarize/ListedForcesTest.Ifunc/9 (0 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/10 22: [ OK ] Polarize/ListedForcesTest.Ifunc/10 (0 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/11 22: [ OK ] Polarize/ListedForcesTest.Ifunc/11 (0 ms) 22: [----------] 12 tests from Polarize/ListedForcesTest (16 ms total) 22: 22: [----------] 18 tests from Restraints/ListedForcesTest 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/0 22: [ OK ] Restraints/ListedForcesTest.Ifunc/0 (1 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/1 22: [ OK ] Restraints/ListedForcesTest.Ifunc/1 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/2 22: [ OK ] Restraints/ListedForcesTest.Ifunc/2 (1 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/3 22: [ OK ] Restraints/ListedForcesTest.Ifunc/3 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/4 22: [ OK ] Restraints/ListedForcesTest.Ifunc/4 (1 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/5 22: [ OK ] Restraints/ListedForcesTest.Ifunc/5 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/6 22: [ OK ] Restraints/ListedForcesTest.Ifunc/6 (1 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/7 22: [ OK ] Restraints/ListedForcesTest.Ifunc/7 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/8 22: [ OK ] Restraints/ListedForcesTest.Ifunc/8 (3 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/9 22: [ OK ] Restraints/ListedForcesTest.Ifunc/9 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/10 22: [ OK ] Restraints/ListedForcesTest.Ifunc/10 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/11 22: [ OK ] Restraints/ListedForcesTest.Ifunc/11 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/12 22: [ OK ] Restraints/ListedForcesTest.Ifunc/12 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/13 22: [ OK ] Restraints/ListedForcesTest.Ifunc/13 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/14 22: [ OK ] Restraints/ListedForcesTest.Ifunc/14 (1 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/15 22: [ OK ] Restraints/ListedForcesTest.Ifunc/15 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/16 22: [ OK ] Restraints/ListedForcesTest.Ifunc/16 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/17 22: [ OK ] Restraints/ListedForcesTest.Ifunc/17 (0 ms) 22: [----------] 18 tests from Restraints/ListedForcesTest (32 ms total) 22: 22: [----------] 3 tests from BondZeroLength/ListedForcesTest 22: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/0 22: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/0 (0 ms) 22: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/1 22: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/1 (0 ms) 22: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/2 22: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/2 (0 ms) 22: [----------] 3 tests from BondZeroLength/ListedForcesTest (2 ms total) 22: 22: [----------] 3 tests from AngleZero/ListedForcesTest 22: [ RUN ] AngleZero/ListedForcesTest.Ifunc/0 22: [ OK ] AngleZero/ListedForcesTest.Ifunc/0 (0 ms) 22: [ RUN ] AngleZero/ListedForcesTest.Ifunc/1 22: [ OK ] AngleZero/ListedForcesTest.Ifunc/1 (0 ms) 22: [ RUN ] AngleZero/ListedForcesTest.Ifunc/2 22: [ OK ] AngleZero/ListedForcesTest.Ifunc/2 (0 ms) 22: [----------] 3 tests from AngleZero/ListedForcesTest (2 ms total) 22: 22: [----------] 12 tests from 14Interaction/ListedForcesPairsTest 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/0 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/0 (0 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/1 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/1 (1 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/2 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/2 (0 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/3 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/3 (0 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/4 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/4 (0 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/5 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/5 (0 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/6 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/6 (0 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/7 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/7 (0 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/8 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/8 (0 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/9 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/9 (0 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/10 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/10 (0 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/11 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/11 (4 ms) 22: [----------] 12 tests from 14Interaction/ListedForcesPairsTest (20 ms total) 22: 22: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest 22: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 22: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 (1 ms) 22: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 22: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 (0 ms) 22: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 22: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 (1 ms) 22: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 22: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 (0 ms) 22: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 22: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 (0 ms) 22: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 22: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 (2 ms) 22: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 22: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 (0 ms) 22: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 22: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 (2 ms) 22: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 22: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 (0 ms) 22: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest (15 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 132 tests from 9 test suites ran. (190 ms total) 22: [ PASSED ] 132 tests. 22/87 Test #22: ListedForcesTest .......................... Passed 0.23 sec test 23 Start 23: NbnxmTests 23: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/nbnxm-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/NbnxmTests.xml" 23: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/nbnxm/tests 23: Test timeout computed to be: 30 23: [==========] Running 80 tests from 3 test suites. 23: [----------] Global test environment set-up. 23: [----------] 18 tests from KernelSetupTest 23: [ RUN ] KernelSetupTest.getCoulombKernelTypeRF 23: [ OK ] KernelSetupTest.getCoulombKernelTypeRF (0 ms) 23: [ RUN ] KernelSetupTest.getCoulombKernelTypeCut 23: [ OK ] KernelSetupTest.getCoulombKernelTypeCut (0 ms) 23: [ RUN ] KernelSetupTest.getCoulombKernelTypeTable 23: [ OK ] KernelSetupTest.getCoulombKernelTypeTable (0 ms) 23: [ RUN ] KernelSetupTest.getCoulombKernelTypeTableTwin 23: [ OK ] KernelSetupTest.getCoulombKernelTypeTableTwin (0 ms) 23: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwald 23: [ OK ] KernelSetupTest.getCoulombKernelTypeEwald (0 ms) 23: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwaldTwin 23: [ OK ] KernelSetupTest.getCoulombKernelTypeEwaldTwin (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone 23: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift 23: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone 23: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift 23: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone 23: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift 23: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutThrows 23: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutThrows (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch 23: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypePmeGeom 23: [ OK ] KernelSetupTest.getVdwKernelTypePmeGeom (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypePmeNone 23: [ OK ] KernelSetupTest.getVdwKernelTypePmeNone (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch 23: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypeAllCountThrows 23: [ OK ] KernelSetupTest.getVdwKernelTypeAllCountThrows (0 ms) 23: [----------] 18 tests from KernelSetupTest (1 ms total) 23: 23: [----------] 60 tests from NbnxmKernelTest 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwCutCombGeom 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwCutCombGeom (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwCutCombLB 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwCutCombLB (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwCutCombNone 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwCutCombNone (5 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwForceSwitch 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwForceSwitch (11 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwPotSwitch 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwPotSwitch (11 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwEwaldCombGeom 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwEwaldCombGeom (11 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwCutCombGeom 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwCutCombGeom (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwCutCombLB 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwCutCombLB (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwCutCombNone 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwCutCombNone (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwForceSwitch 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwForceSwitch (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwPotSwitch 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwPotSwitch (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwEwaldCombGeom 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwEwaldCombGeom (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwCutCombGeom 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwCutCombLB 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwCutCombLB (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwCutCombNone 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwCutCombNone (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwForceSwitch 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwForceSwitch (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwPotSwitch 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwPotSwitch (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwEwaldCombGeom 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwCutCombGeom 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwCutCombGeom (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwCutCombLB 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwCutCombLB (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwCutCombNone 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwCutCombNone (15 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwForceSwitch 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwForceSwitch (22 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwPotSwitch 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwPotSwitch (28 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwEwaldCombGeom 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwEwaldCombGeom (13 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwCutCombGeom 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwCutCombLB 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwCutCombLB (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwCutCombNone 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwCutCombNone (12 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwForceSwitch 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwForceSwitch (10 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwPotSwitch 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwPotSwitch (12 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwEwaldCombGeom 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwEwaldCombGeom (16 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwCutCombGeom 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwCutCombGeom (6 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwCutCombLB 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwCutCombLB (7 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwCutCombNone 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwCutCombNone (9 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwForceSwitch 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwForceSwitch (1 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwPotSwitch 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwPotSwitch (3 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwEwaldCombGeom 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwEwaldCombGeom (4 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwCutCombGeom 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwCutCombGeom (9 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwCutCombLB 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwCutCombLB (7 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwCutCombNone 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwCutCombNone (10 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwForceSwitch 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwForceSwitch (5 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwPotSwitch 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwPotSwitch (3 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwEwaldCombGeom 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwEwaldCombGeom (4 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwCutCombGeom 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwCutCombGeom (5 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwCutCombLB 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwCutCombLB (5 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwCutCombNone 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwCutCombNone (2 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwForceSwitch 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwForceSwitch (2 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwPotSwitch 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwPotSwitch (2 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwEwaldCombGeom 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwEwaldCombGeom (5 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwCutCombGeom 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwCutCombGeom (4 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwCutCombLB 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwCutCombLB (6 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwCutCombNone 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwCutCombNone (3 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwForceSwitch 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwForceSwitch (5 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwPotSwitch 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwPotSwitch (2 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwEwaldCombGeom 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwEwaldCombGeom (2 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwCutCombGeom 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwCutCombGeom (2 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwCutCombLB 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwCutCombLB (2 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwCutCombNone 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwCutCombNone (7 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwForceSwitch 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwForceSwitch (2 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwPotSwitch 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwPotSwitch (3 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwEwaldCombGeom 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwEwaldCombGeom (3 ms) 23: [----------] 60 tests from NbnxmKernelTest (324 ms total) 23: 23: [----------] 2 tests from WithParameters/CpuListDiagonalExclusionsTest 23: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 23: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 (0 ms) 23: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 23: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 (0 ms) 23: [----------] 2 tests from WithParameters/CpuListDiagonalExclusionsTest (0 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 80 tests from 3 test suites ran. (325 ms total) 23: [ PASSED ] 80 tests. 23/87 Test #23: NbnxmTests ................................ Passed 0.38 sec test 24 Start 24: CommandLineUnitTests 24: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/commandline-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/CommandLineUnitTests.xml" 24: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/commandline/tests 24: Test timeout computed to be: 30 24: [==========] Running 60 tests from 7 test suites. 24: [----------] Global test environment set-up. 24: [----------] 3 tests from CommandLineHelpModuleTest 24: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 24: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (2 ms) 24: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 24: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (0 ms) 24: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 24: [ OK ] CommandLineHelpModuleTest.ExportsHelp (2 ms) 24: [----------] 3 tests from CommandLineHelpModuleTest (6 ms total) 24: 24: [----------] 7 tests from CommandLineHelpWriterTest 24: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 24: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (2 ms) 24: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 24: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms) 24: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 24: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (1 ms) 24: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 24: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms) 24: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 24: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) 24: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 24: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms) 24: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues 24: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms) 24: [----------] 7 tests from CommandLineHelpWriterTest (6 ms total) 24: 24: [----------] 6 tests from CommandLineModuleManagerTest 24: [ RUN ] CommandLineModuleManagerTest.RunsModule 24: [ OK ] CommandLineModuleManagerTest.RunsModule (4 ms) 24: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 24: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 24: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 24: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 24: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 24: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) 24: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 24: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 24: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 24: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 24: [----------] 6 tests from CommandLineModuleManagerTest (5 ms total) 24: 24: [----------] 13 tests from CommandLineParserTest 24: [ RUN ] CommandLineParserTest.HandlesSingleValues 24: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 24: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 24: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 24: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 24: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 24: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 24: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms) 24: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 24: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 24: [ RUN ] CommandLineParserTest.HandlesString 24: [ OK ] CommandLineParserTest.HandlesString (0 ms) 24: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 24: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) 24: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 24: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 24: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 24: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 24: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 24: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 24: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 24: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 24: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 24: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 24: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 24: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 24: [----------] 13 tests from CommandLineParserTest (0 ms total) 24: 24: [----------] 6 tests from CommandLineProgramContextTest 24: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 24: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) 24: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 24: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 24: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 24: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 24: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 24: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 24: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 24: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) 24: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 24: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 24: [----------] 6 tests from CommandLineProgramContextTest (0 ms total) 24: 24: [----------] 3 tests from OutputNamesTest 24: [ RUN ] OutputNamesTest.CanBeSuffixed 24: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms) 24: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend 24: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms) 24: [ RUN ] OutputNamesTest.CanHavePartNumberAdded 24: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms) 24: [----------] 3 tests from OutputNamesTest (0 ms total) 24: 24: [----------] 22 tests from ParseCommonArgsTest 24: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 24: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 24: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 24: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 24: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 24: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum 24: [ OK ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 24: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 24: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 24: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 24: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 24: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 24: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 24: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 24: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 24: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 24: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 24: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 24: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 24: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 24: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 24: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 24: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (0 ms) 24: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 24: Value is /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/commandline/tests/Testing/Temporary/ParseCommonArgsTest_AcceptsUnknownTrajectoryExtension.foo 24: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) 24: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 24: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (0 ms) 24: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 24: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (1 ms) 24: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 24: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 24: [----------] 22 tests from ParseCommonArgsTest (3 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 60 tests from 7 test suites ran. (22 ms total) 24: [ PASSED ] 60 tests. 24/87 Test #24: CommandLineUnitTests ...................... Passed 0.05 sec test 25 Start 25: DomDecTests 25: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/domdec-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/DomDecTests.xml" 25: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/domdec/tests 25: Test timeout computed to be: 30 25: [==========] Running 9 tests from 2 test suites. 25: [----------] Global test environment set-up. 25: [----------] 7 tests from HashedMap 25: [ RUN ] HashedMap.InsertsFinds 25: [ OK ] HashedMap.InsertsFinds (0 ms) 25: [ RUN ] HashedMap.NegativeKeysWork 25: [ OK ] HashedMap.NegativeKeysWork (0 ms) 25: [ RUN ] HashedMap.InsertsErases 25: [ OK ] HashedMap.InsertsErases (0 ms) 25: [ RUN ] HashedMap.InsertsOrAssigns 25: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 25: [ RUN ] HashedMap.Clears 25: [ OK ] HashedMap.Clears (0 ms) 25: [ RUN ] HashedMap.LinkedEntries 25: [ OK ] HashedMap.LinkedEntries (0 ms) 25: [ RUN ] HashedMap.ResizesTable 25: [ OK ] HashedMap.ResizesTable (0 ms) 25: [----------] 7 tests from HashedMap (0 ms total) 25: 25: [----------] 2 tests from LocalAtomSetManager 25: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 25: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 25: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 25: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 25: [----------] 2 tests from LocalAtomSetManager (0 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 9 tests from 2 test suites ran. (0 ms total) 25: [ PASSED ] 9 tests. 25/87 Test #25: DomDecTests ............................... Passed 0.03 sec test 26 Start 26: DomDecMpiTests 26: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/domdec-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/DomDecMpiTests.xml" 26: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/domdec/tests 26: Test timeout computed to be: 30 26: [==========] Running 4 tests from 1 test suite. 26: [----------] Global test environment set-up. 26: [----------] 4 tests from HaloExchangeTest 26: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith1Pulse 26: [ OK ] HaloExchangeTest.Coordinates1dHaloWith1Pulse (23 ms) 26: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith2Pulses 26: [ OK ] HaloExchangeTest.Coordinates1dHaloWith2Pulses (23 ms) 26: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim 26: [ OK ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim (31 ms) 26: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 26: [ OK ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 (47 ms) 26: [----------] 4 tests from HaloExchangeTest (127 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 4 tests from 1 test suite ran. (127 ms total) 26: [ PASSED ] 4 tests. 26/87 Test #26: DomDecMpiTests ............................ Passed 0.19 sec test 27 Start 27: EwaldUnitTests 27: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/ewald-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/EwaldUnitTests.xml" 27: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/ewald/tests 27: Test timeout computed to be: 30 27: [==========] Running 407 tests from 9 test suites. 27: [----------] Global test environment set-up. 27: [----------] 6 tests from SeparatePmeRanksPermittedTest 27: [ RUN ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons 27: [ OK ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons (0 ms) 27: [ RUN ] SeparatePmeRanksPermittedTest.CanBeDisabled 27: [ OK ] SeparatePmeRanksPermittedTest.CanBeDisabled (0 ms) 27: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag 27: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag (0 ms) 27: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonText 27: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonText (0 ms) 27: [ RUN ] SeparatePmeRanksPermittedTest.TwoDisableReasonText 27: [ OK ] SeparatePmeRanksPermittedTest.TwoDisableReasonText (0 ms) 27: [ RUN ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText 27: [ OK ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText (0 ms) 27: [----------] 6 tests from SeparatePmeRanksPermittedTest (0 ms total) 27: 27: [----------] 108 tests from Pme_SplineAndSpreadTest 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline (21 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline (4 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline (2 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline (7 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline (6 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline (3 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline (3 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline (2 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline (3 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline (3 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline (10 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread (2 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline (4 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline (8 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread (2 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (2 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline (2 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline (2 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline (5 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (5 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline (3 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline (2 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline (2 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline (4 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline (3 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline (2 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline (3 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (5 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline (6 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline (3 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread (6 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 27: [----------] 108 tests from Pme_SplineAndSpreadTest (277 ms total) 27: 27: [----------] 64 tests from Pme_SolveTest 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (5 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (1 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (4 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (3 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (4 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (3 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (2 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (3 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [----------] 64 tests from Pme_SolveTest (41 ms total) 27: 27: [----------] 32 tests from PmeDiffEwaldQ_SolveTest 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (4 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (6 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [----------] 32 tests from PmeDiffEwaldQ_SolveTest (20 ms total) 27: 27: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (1 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 27: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest (24 ms total) 27: 27: [----------] 64 tests from PmeDiffEps_SolveTest 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (3 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (3 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (1 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [----------] 64 tests from PmeDiffEps_SolveTest (36 ms total) 27: 27: [----------] 72 tests from Pme_GatherTest 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom (1 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (2 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom (1 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (2 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom (3 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (6 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (5 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 27: [----------] 72 tests from Pme_GatherTest (66 ms total) 27: 27: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 27: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 27: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms) 27: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 27: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 27: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 27: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 27: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 27: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (1 ms) 27: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 27: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 27: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (1 ms total) 27: 27: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (14 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (3 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (7 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (1 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (2 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (4 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (2 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (4 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (7 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (1 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (2 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (7 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (7 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (1 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (1 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (2 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (6 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (1 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (5 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (2 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (5 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (1 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (1 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (4 ms) 27: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (110 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 407 tests from 9 test suites ran. (579 ms total) 27: [ PASSED ] 311 tests. 27: [ SKIPPED ] 96 tests, listed below: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27/87 Test #27: EwaldUnitTests ............................ Passed 0.65 sec test 28 Start 28: FFTUnitTests 28: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/fft-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/FFTUnitTests.xml" 28: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fft/tests 28: Test timeout computed to be: 1920 28: [==========] Running 15 tests from 4 test suites. 28: [----------] Global test environment set-up. 28: [----------] 2 tests from ManyFFTTest 28: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 28: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (6 ms) 28: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 28: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (25 ms) 28: [----------] 2 tests from ManyFFTTest (33 ms total) 28: 28: [----------] 1 test from FFTTest 28: [ RUN ] FFTTest.Real2DLength18_15Test 28: [ OK ] FFTTest.Real2DLength18_15Test (4 ms) 28: [----------] 1 test from FFTTest (9 ms total) 28: 28: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 28: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 28: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (4 ms) 28: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 28: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (1 ms) 28: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 28: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (1 ms) 28: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 28: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (3 ms) 28: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 28: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (2 ms) 28: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 28: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (1 ms) 28: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 28: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (1 ms) 28: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 28: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (1 ms) 28: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 28: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (17 ms) 28: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 28: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (24 ms) 28: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (74 ms total) 28: 28: [----------] 2 tests from Works/ParameterizedFFTTest3D 28: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 28: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 (2 ms) 28: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 28: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 (1 ms) 28: [----------] 2 tests from Works/ParameterizedFFTTest3D (7 ms total) 28: 28: [----------] Global test environment tear-down 28: [==========] 15 tests from 4 test suites ran. (131 ms total) 28: [ PASSED ] 15 tests. 28/87 Test #28: FFTUnitTests .............................. Passed 0.20 sec test 29 Start 29: GpuUtilsUnitTests 29: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/gpu_utils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/GpuUtilsUnitTests.xml" 29: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gpu_utils/tests 29: Test timeout computed to be: 30 29: [==========] Running 64 tests from 22 test suites. 29: [----------] Global test environment set-up. 29: [----------] 2 tests from ClfftInitializer 29: [ RUN ] ClfftInitializer.SingleInitializationWorks 29: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms) 29: [ RUN ] ClfftInitializer.TwoInitializationsWork 29: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms) 29: [----------] 2 tests from ClfftInitializer (0 ms total) 29: 29: [----------] 1 test from DevicesAvailable 29: [ RUN ] DevicesAvailable.ShouldBeAbleToRunOnDevice 29: [ OK ] DevicesAvailable.ShouldBeAbleToRunOnDevice (0 ms) 29: [----------] 1 test from DevicesAvailable (0 ms total) 29: 29: [----------] 1 test from DeviceStreamManagerTest 29: [ RUN ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice 29: [ OK ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice (0 ms) 29: [----------] 1 test from DeviceStreamManagerTest (0 ms total) 29: 29: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 29: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 29: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 29: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 29: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 29: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 29: 29: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float 29: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 29: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 29: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 29: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 29: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 29: 29: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 29: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 29: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 29: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 29: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 29: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 29: 29: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 29: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 29: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 29: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 29: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 29: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 29: 29: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 29: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 29: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 29: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 29: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 29: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 29: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 29: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 29: 29: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float 29: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 29: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 29: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 29: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 29: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 29: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 29: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 29: 29: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 29: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 29: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 29: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 29: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 29: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 29: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 29: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 29: 29: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 29: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 29: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 29: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 29: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/0.Swap 29: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/0.Comparison 29: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 29: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 29: 29: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float 29: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 29: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 29: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 29: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/1.Swap 29: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/1.Comparison 29: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 29: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 29: 29: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 29: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 29: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 29: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 29: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/2.Swap 29: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/2.Comparison 29: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 29: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 29: 29: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 29: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 29: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 29: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 29: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/3.Swap 29: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/3.Comparison 29: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 29: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 29: 29: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 29: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 29: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 29: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 29: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 29: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 29: 29: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float 29: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 29: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 29: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 29: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 29: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 29: 29: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 29: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 29: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 29: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 29: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 29: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 29: 29: [----------] 1 test from HostAllocatorUntypedTest 29: [ RUN ] HostAllocatorUntypedTest.Comparison 29: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 29: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 29: 29: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 29: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 29: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 29: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 29: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/0.Move 29: [ OK ] AllocatorTest/0.Move (0 ms) 29: [----------] 4 tests from AllocatorTest/0 (0 ms total) 29: 29: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 29: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 29: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 29: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 29: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/1.Move 29: [ OK ] AllocatorTest/1.Move (0 ms) 29: [----------] 4 tests from AllocatorTest/1 (0 ms total) 29: 29: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> 29: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 29: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 29: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 29: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/2.Move 29: [ OK ] AllocatorTest/2.Move (0 ms) 29: [----------] 4 tests from AllocatorTest/2 (0 ms total) 29: 29: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 29: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 29: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 29: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 29: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/3.Move 29: [ OK ] AllocatorTest/3.Move (0 ms) 29: [----------] 4 tests from AllocatorTest/3 (0 ms total) 29: 29: [----------] Global test environment tear-down 29: [==========] 64 tests from 22 test suites ran. (0 ms total) 29: [ PASSED ] 64 tests. 29/87 Test #29: GpuUtilsUnitTests ......................... Passed 0.07 sec test 30 Start 30: HardwareUnitTests 30: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/hardware-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/HardwareUnitTests.xml" 30: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/hardware/tests 30: Test timeout computed to be: 30 30: [==========] Running 21 tests from 9 test suites. 30: [----------] Global test environment set-up. 30: [----------] 1 test from CpuInfoTest 30: [ RUN ] CpuInfoTest.SupportLevel 30: [ OK ] CpuInfoTest.SupportLevel (4 ms) 30: [----------] 1 test from CpuInfoTest (4 ms total) 30: 30: [----------] 4 tests from HardwareTopologyTest 30: [ RUN ] HardwareTopologyTest.Execute 30: [ OK ] HardwareTopologyTest.Execute (34 ms) 30: [ RUN ] HardwareTopologyTest.HwlocExecute 30: [ OK ] HardwareTopologyTest.HwlocExecute (34 ms) 30: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 30: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (31 ms) 30: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 30: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (20 ms) 30: [----------] 4 tests from HardwareTopologyTest (125 ms total) 30: 30: [----------] 1 test from DevicesManagerTest 30: [ RUN ] DevicesManagerTest.Serialization 30: [ OK ] DevicesManagerTest.Serialization (0 ms) 30: [----------] 1 test from DevicesManagerTest (0 ms total) 30: 30: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest 30: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 30: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 (17 ms) 30: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 30: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 (1 ms) 30: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 30: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 (1 ms) 30: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 30: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) 30: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 30: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) 30: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest (23 ms total) 30: 30: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest 30: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 30: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 (18 ms) 30: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 30: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 (1 ms) 30: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 30: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 (1 ms) 30: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 30: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 (1 ms) 30: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 30: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 (1 ms) 30: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest (29 ms total) 30: 30: [----------] 2 tests from Core12900K/MockHardwareTopologyTest 30: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 30: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 (10 ms) 30: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 30: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 (8 ms) 30: [----------] 2 tests from Core12900K/MockHardwareTopologyTest (19 ms total) 30: 30: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest 30: [ RUN ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 30: [ OK ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (47 ms) 30: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest (48 ms total) 30: 30: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest 30: [ RUN ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 30: [ OK ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (128 ms) 30: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest (128 ms total) 30: 30: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest 30: [ RUN ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 30: [ OK ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (237 ms) 30: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest (238 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 21 tests from 9 test suites ran. (618 ms total) 30: [ PASSED ] 21 tests. 30/87 Test #30: HardwareUnitTests ......................... Passed 0.65 sec test 31 Start 31: MathUnitTests 31: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/math-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MathUnitTests.xml" 31: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/math/tests 31: Test timeout computed to be: 30 31: [==========] Running 304 tests from 38 test suites. 31: [----------] Global test environment set-up. 31: [----------] 1 test from EmptyArrayRefWithPaddingTest 31: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 31: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 31: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 31: 31: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 31: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 31: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 31: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 31: 31: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 31: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 31: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 31: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 31: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 31: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 31: 31: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 31: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 31: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 31: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 31: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 31: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 31: 31: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 31: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 31: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 31: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 31: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 31: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 31: 31: [----------] 2 tests from InvertBoxMatrixTest 31: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 31: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 31: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 31: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 31: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 31: 31: [----------] 11 tests from TranslateAndScaleTest 31: [ RUN ] TranslateAndScaleTest.identityTransformation 31: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms) 31: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling 31: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms) 31: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation 31: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms) 31: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial 31: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms) 31: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector 31: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector (0 ms) 31: [ RUN ] TranslateAndScaleTest.scalingIdentity 31: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms) 31: [ RUN ] TranslateAndScaleTest.scalingNonTrivial 31: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms) 31: [ RUN ] TranslateAndScaleTest.scalingNonTrivialSingleVector 31: [ OK ] TranslateAndScaleTest.scalingNonTrivialSingleVector (0 ms) 31: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero 31: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms) 31: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero 31: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms) 31: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector 31: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector (0 ms) 31: [----------] 11 tests from TranslateAndScaleTest (0 ms total) 31: 31: [----------] 3 tests from AffineTransformationTest 31: [ RUN ] AffineTransformationTest.identityTransformYieldsSameVectors 31: [ OK ] AffineTransformationTest.identityTransformYieldsSameVectors (0 ms) 31: [ RUN ] AffineTransformationTest.applyTransformationToVectors 31: [ OK ] AffineTransformationTest.applyTransformationToVectors (0 ms) 31: [ RUN ] AffineTransformationTest.retrieveGradient 31: [ OK ] AffineTransformationTest.retrieveGradient (0 ms) 31: [----------] 3 tests from AffineTransformationTest (0 ms total) 31: 31: [----------] 14 tests from DensitySimilarityTest 31: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect 31: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms) 31: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect 31: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms) 31: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch 31: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms) 31: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch 31: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms) 31: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect 31: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms) 31: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero 31: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms) 31: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect 31: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms) 31: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect 31: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (1 ms) 31: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne 31: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (35 ms) 31: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated 31: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (30 ms) 31: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated 31: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (1 ms) 31: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect 31: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (5 ms) 31: [ RUN ] DensitySimilarityTest.NormalizationCorrect 31: [ OK ] DensitySimilarityTest.NormalizationCorrect (0 ms) 31: [ RUN ] DensitySimilarityTest.NormalizationAllNonPositive 31: [ OK ] DensitySimilarityTest.NormalizationAllNonPositive (0 ms) 31: [----------] 14 tests from DensitySimilarityTest (74 ms total) 31: 31: [----------] 6 tests from StructureSimilarityTest 31: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 31: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 31: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 31: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 31: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 31: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 31: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 31: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 31: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 31: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 31: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 31: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 31: [----------] 6 tests from StructureSimilarityTest (0 ms total) 31: 31: [----------] 8 tests from ExponentialMovingAverage 31: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero 31: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms) 31: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative 31: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms) 31: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue 31: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms) 31: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue 31: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms) 31: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly 31: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms) 31: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing 31: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms) 31: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect 31: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms) 31: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree 31: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms) 31: [----------] 8 tests from ExponentialMovingAverage (0 ms total) 31: 31: [----------] 21 tests from FunctionTest 31: [ RUN ] FunctionTest.StaticLog2 31: [ OK ] FunctionTest.StaticLog2 (0 ms) 31: [ RUN ] FunctionTest.Log2I32Bit 31: [ OK ] FunctionTest.Log2I32Bit (0 ms) 31: [ RUN ] FunctionTest.Log2I64Bit 31: [ OK ] FunctionTest.Log2I64Bit (0 ms) 31: [ RUN ] FunctionTest.GreatestCommonDivisor 31: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 31: [ RUN ] FunctionTest.InvsqrtFloat 31: [ OK ] FunctionTest.InvsqrtFloat (0 ms) 31: [ RUN ] FunctionTest.InvsqrtDouble 31: [ OK ] FunctionTest.InvsqrtDouble (0 ms) 31: [ RUN ] FunctionTest.InvsqrtInteger 31: [ OK ] FunctionTest.InvsqrtInteger (0 ms) 31: [ RUN ] FunctionTest.InvcbrtFloat 31: [ OK ] FunctionTest.InvcbrtFloat (0 ms) 31: [ RUN ] FunctionTest.InvcbrtDouble 31: [ OK ] FunctionTest.InvcbrtDouble (0 ms) 31: [ RUN ] FunctionTest.InvcbrtInteger 31: [ OK ] FunctionTest.InvcbrtInteger (0 ms) 31: [ RUN ] FunctionTest.SixthrootFloat 31: [ OK ] FunctionTest.SixthrootFloat (5 ms) 31: [ RUN ] FunctionTest.SixthrootDouble 31: [ OK ] FunctionTest.SixthrootDouble (0 ms) 31: [ RUN ] FunctionTest.SixthrootInteger 31: [ OK ] FunctionTest.SixthrootInteger (0 ms) 31: [ RUN ] FunctionTest.InvsixthrootFloat 31: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) 31: [ RUN ] FunctionTest.InvsixthrootDouble 31: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) 31: [ RUN ] FunctionTest.InvsixthrootInteger 31: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) 31: [ RUN ] FunctionTest.Powers 31: [ OK ] FunctionTest.Powers (0 ms) 31: [ RUN ] FunctionTest.ErfInvFloat 31: [ OK ] FunctionTest.ErfInvFloat (0 ms) 31: [ RUN ] FunctionTest.ErfInvDouble 31: [ OK ] FunctionTest.ErfInvDouble (3 ms) 31: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 31: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) 31: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 31: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms) 31: [----------] 21 tests from FunctionTest (20 ms total) 31: 31: [----------] 1 test from FunctionTestIntegerTypes/0, where TypeParam = char 31: [ RUN ] FunctionTestIntegerTypes/0.IsPowerOfTwo 31: [ OK ] FunctionTestIntegerTypes/0.IsPowerOfTwo (0 ms) 31: [----------] 1 test from FunctionTestIntegerTypes/0 (0 ms total) 31: 31: [----------] 1 test from FunctionTestIntegerTypes/1, where TypeParam = unsigned char 31: [ RUN ] FunctionTestIntegerTypes/1.IsPowerOfTwo 31: [ OK ] FunctionTestIntegerTypes/1.IsPowerOfTwo (0 ms) 31: [----------] 1 test from FunctionTestIntegerTypes/1 (0 ms total) 31: 31: [----------] 1 test from FunctionTestIntegerTypes/2, where TypeParam = int 31: [ RUN ] FunctionTestIntegerTypes/2.IsPowerOfTwo 31: [ OK ] FunctionTestIntegerTypes/2.IsPowerOfTwo (0 ms) 31: [----------] 1 test from FunctionTestIntegerTypes/2 (0 ms total) 31: 31: [----------] 1 test from FunctionTestIntegerTypes/3, where TypeParam = unsigned int 31: [ RUN ] FunctionTestIntegerTypes/3.IsPowerOfTwo 31: [ OK ] FunctionTestIntegerTypes/3.IsPowerOfTwo (0 ms) 31: [----------] 1 test from FunctionTestIntegerTypes/3 (0 ms total) 31: 31: [----------] 1 test from FunctionTestIntegerTypes/4, where TypeParam = long 31: [ RUN ] FunctionTestIntegerTypes/4.IsPowerOfTwo 31: [ OK ] FunctionTestIntegerTypes/4.IsPowerOfTwo (0 ms) 31: [----------] 1 test from FunctionTestIntegerTypes/4 (0 ms total) 31: 31: [----------] 1 test from FunctionTestIntegerTypes/5, where TypeParam = unsigned long 31: [ RUN ] FunctionTestIntegerTypes/5.IsPowerOfTwo 31: [ OK ] FunctionTestIntegerTypes/5.IsPowerOfTwo (0 ms) 31: [----------] 1 test from FunctionTestIntegerTypes/5 (0 ms total) 31: 31: [----------] 4 tests from GaussianOn1DLattice 31: [ RUN ] GaussianOn1DLattice.sumsCloseToOne 31: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms) 31: [ RUN ] GaussianOn1DLattice.isCorrect 31: [ OK ] GaussianOn1DLattice.isCorrect (0 ms) 31: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero 31: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms) 31: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange 31: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms) 31: [----------] 4 tests from GaussianOn1DLattice (0 ms total) 31: 31: [----------] 9 tests from GaussTransformTest 31: [ RUN ] GaussTransformTest.isZeroUponConstruction 31: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms) 31: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss 31: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms) 31: [ RUN ] GaussTransformTest.isZeroAfterSettingZero 31: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms) 31: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX 31: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms) 31: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY 31: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms) 31: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ 31: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms) 31: [ RUN ] GaussTransformTest.complementaryGaussAddToZero 31: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms) 31: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues 31: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms) 31: [ RUN ] GaussTransformTest.view 31: [ OK ] GaussTransformTest.view (0 ms) 31: [----------] 9 tests from GaussTransformTest (0 ms total) 31: 31: [----------] 3 tests from DensityFittingForce 31: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity 31: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms) 31: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections 31: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms) 31: [ RUN ] DensityFittingForce.pullsTowardsDerivative 31: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms) 31: [----------] 3 tests from DensityFittingForce (0 ms total) 31: 31: [----------] 2 tests from InvertMatrixTest 31: [ RUN ] InvertMatrixTest.IdentityIsImpotent 31: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 31: [ RUN ] InvertMatrixTest.ComputesInverse 31: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 31: [----------] 2 tests from InvertMatrixTest (0 ms total) 31: 31: [----------] 17 tests from MatrixTest 31: [ RUN ] MatrixTest.canSetFromArray 31: [ OK ] MatrixTest.canSetFromArray (0 ms) 31: [ RUN ] MatrixTest.canSetStaticallyFromList 31: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms) 31: [ RUN ] MatrixTest.canConstructAndFill 31: [ OK ] MatrixTest.canConstructAndFill (0 ms) 31: [ RUN ] MatrixTest.canSetValues 31: [ OK ] MatrixTest.canSetValues (0 ms) 31: [ RUN ] MatrixTest.canCopyAssign 31: [ OK ] MatrixTest.canCopyAssign (0 ms) 31: [ RUN ] MatrixTest.canSwap 31: [ OK ] MatrixTest.canSwap (0 ms) 31: [ RUN ] MatrixTest.staticMultiDimArrayExtent 31: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms) 31: [ RUN ] MatrixTest.determinantWorks 31: [ OK ] MatrixTest.determinantWorks (0 ms) 31: [ RUN ] MatrixTest.noninvertableDeterminantIsZero 31: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms) 31: [ RUN ] MatrixTest.determinantOfDiagonalMatrix 31: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms) 31: [ RUN ] MatrixTest.traceWorks 31: [ OK ] MatrixTest.traceWorks (0 ms) 31: [ RUN ] MatrixTest.transposeWorks 31: [ OK ] MatrixTest.transposeWorks (0 ms) 31: [ RUN ] MatrixTest.transposeOfSymmetricMatrix 31: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms) 31: [ RUN ] MatrixTest.canCreateFromLegacyMatrix 31: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms) 31: [ RUN ] MatrixTest.canFillLegacyMatrix 31: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms) 31: [ RUN ] MatrixTest.IdentityMatrix 31: [ OK ] MatrixTest.IdentityMatrix (0 ms) 31: [ RUN ] MatrixTest.MatrixVectorMultiplication 31: [ OK ] MatrixTest.MatrixVectorMultiplication (0 ms) 31: [----------] 17 tests from MatrixTest (0 ms total) 31: 31: [----------] 25 tests from MultiDimArrayTest 31: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic 31: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms) 31: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic 31: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms) 31: [ RUN ] MultiDimArrayTest.canSetValuesInStatic 31: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms) 31: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic 31: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms) 31: [ RUN ] MultiDimArrayTest.canMoveConstructStatic 31: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms) 31: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic 31: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms) 31: [ RUN ] MultiDimArrayTest.canMoveAssignStatic 31: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms) 31: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic 31: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms) 31: [ RUN ] MultiDimArrayTest.canCopyConstructStatic 31: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms) 31: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic 31: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms) 31: [ RUN ] MultiDimArrayTest.canCopyAssignStatic 31: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms) 31: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic 31: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms) 31: [ RUN ] MultiDimArrayTest.canSwapStatic 31: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms) 31: [ RUN ] MultiDimArrayTest.canSwapDynamic 31: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms) 31: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent 31: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms) 31: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent 31: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms) 31: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent 31: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms) 31: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue 31: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms) 31: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray 31: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms) 31: [ RUN ] MultiDimArrayTest.conversionToView 31: [ OK ] MultiDimArrayTest.conversionToView (0 ms) 31: [ RUN ] MultiDimArrayTest.conversionToConstView 31: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms) 31: [ RUN ] MultiDimArrayTest.viewBegin 31: [ OK ] MultiDimArrayTest.viewBegin (0 ms) 31: [ RUN ] MultiDimArrayTest.viewEnd 31: [ OK ] MultiDimArrayTest.viewEnd (0 ms) 31: [ RUN ] MultiDimArrayTest.constViewConstBegin 31: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms) 31: [ RUN ] MultiDimArrayTest.constViewConstEnd 31: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms) 31: [----------] 25 tests from MultiDimArrayTest (0 ms total) 31: 31: [----------] 4 tests from MultiDimArrayToMdSpanTest 31: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan 31: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms) 31: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan 31: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms) 31: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan 31: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms) 31: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan 31: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms) 31: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total) 31: 31: [----------] 9 tests from NelderMeadSimplexTest 31: [ RUN ] NelderMeadSimplexTest.BestVertex 31: [ OK ] NelderMeadSimplexTest.BestVertex (0 ms) 31: [ RUN ] NelderMeadSimplexTest.WorstVertex 31: [ OK ] NelderMeadSimplexTest.WorstVertex (0 ms) 31: [ RUN ] NelderMeadSimplexTest.SecondWorstValue 31: [ OK ] NelderMeadSimplexTest.SecondWorstValue (0 ms) 31: [ RUN ] NelderMeadSimplexTest.ReflectionPoint 31: [ OK ] NelderMeadSimplexTest.ReflectionPoint (0 ms) 31: [ RUN ] NelderMeadSimplexTest.EvaluateExpansionPoint 31: [ OK ] NelderMeadSimplexTest.EvaluateExpansionPoint (0 ms) 31: [ RUN ] NelderMeadSimplexTest.EvaluateContractionPoint 31: [ OK ] NelderMeadSimplexTest.EvaluateContractionPoint (0 ms) 31: [ RUN ] NelderMeadSimplexTest.SwapOutWorst 31: [ OK ] NelderMeadSimplexTest.SwapOutWorst (0 ms) 31: [ RUN ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest 31: [ OK ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest (0 ms) 31: [ RUN ] NelderMeadSimplexTest.OrientedLength 31: [ OK ] NelderMeadSimplexTest.OrientedLength (0 ms) 31: [----------] 9 tests from NelderMeadSimplexTest (0 ms total) 31: 31: [----------] 2 tests from NelderMead 31: [ RUN ] NelderMead.Optimizes2DFunctionCorrectly 31: [ OK ] NelderMead.Optimizes2DFunctionCorrectly (0 ms) 31: [ RUN ] NelderMead.Optimizes3DFunctorCorrectly 31: [ OK ] NelderMead.Optimizes3DFunctorCorrectly (0 ms) 31: [----------] 2 tests from NelderMead (0 ms total) 31: 31: [----------] 11 tests from PaddedVectorTest/0, where TypeParam = std::allocator 31: [ RUN ] PaddedVectorTest/0.DefaultConstructorWorks 31: [ OK ] PaddedVectorTest/0.DefaultConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/0.ResizeWorks 31: [ OK ] PaddedVectorTest/0.ResizeWorks (0 ms) 31: [ RUN ] PaddedVectorTest/0.ReserveWorks 31: [ OK ] PaddedVectorTest/0.ReserveWorks (0 ms) 31: [ RUN ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve 31: [ OK ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve (0 ms) 31: [ RUN ] PaddedVectorTest/0.MoveConstructorWorks 31: [ OK ] PaddedVectorTest/0.MoveConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks 31: [ OK ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/0.MoveAssignmentWorks 31: [ OK ] PaddedVectorTest/0.MoveAssignmentWorks (0 ms) 31: [ RUN ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical 31: [ OK ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical (0 ms) 31: [ RUN ] PaddedVectorTest/0.CanCopyAssign 31: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 31: [ RUN ] PaddedVectorTest/0.CanMoveAssign 31: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 31: [ RUN ] PaddedVectorTest/0.CanSwap 31: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 31: [----------] 11 tests from PaddedVectorTest/0 (0 ms total) 31: 31: [----------] 11 tests from PaddedVectorTest/1, where TypeParam = std::allocator 31: [ RUN ] PaddedVectorTest/1.DefaultConstructorWorks 31: [ OK ] PaddedVectorTest/1.DefaultConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/1.ResizeWorks 31: [ OK ] PaddedVectorTest/1.ResizeWorks (0 ms) 31: [ RUN ] PaddedVectorTest/1.ReserveWorks 31: [ OK ] PaddedVectorTest/1.ReserveWorks (0 ms) 31: [ RUN ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve 31: [ OK ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve (0 ms) 31: [ RUN ] PaddedVectorTest/1.MoveConstructorWorks 31: [ OK ] PaddedVectorTest/1.MoveConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks 31: [ OK ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/1.MoveAssignmentWorks 31: [ OK ] PaddedVectorTest/1.MoveAssignmentWorks (0 ms) 31: [ RUN ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical 31: [ OK ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical (0 ms) 31: [ RUN ] PaddedVectorTest/1.CanCopyAssign 31: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 31: [ RUN ] PaddedVectorTest/1.CanMoveAssign 31: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 31: [ RUN ] PaddedVectorTest/1.CanSwap 31: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 31: [----------] 11 tests from PaddedVectorTest/1 (0 ms total) 31: 31: [----------] 11 tests from PaddedVectorTest/2, where TypeParam = std::allocator 31: [ RUN ] PaddedVectorTest/2.DefaultConstructorWorks 31: [ OK ] PaddedVectorTest/2.DefaultConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/2.ResizeWorks 31: [ OK ] PaddedVectorTest/2.ResizeWorks (0 ms) 31: [ RUN ] PaddedVectorTest/2.ReserveWorks 31: [ OK ] PaddedVectorTest/2.ReserveWorks (0 ms) 31: [ RUN ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve 31: [ OK ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve (0 ms) 31: [ RUN ] PaddedVectorTest/2.MoveConstructorWorks 31: [ OK ] PaddedVectorTest/2.MoveConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks 31: [ OK ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/2.MoveAssignmentWorks 31: [ OK ] PaddedVectorTest/2.MoveAssignmentWorks (0 ms) 31: [ RUN ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical 31: [ OK ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical (0 ms) 31: [ RUN ] PaddedVectorTest/2.CanCopyAssign 31: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 31: [ RUN ] PaddedVectorTest/2.CanMoveAssign 31: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 31: [ RUN ] PaddedVectorTest/2.CanSwap 31: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 31: [----------] 11 tests from PaddedVectorTest/2 (3 ms total) 31: 31: [----------] 11 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 31: [ RUN ] PaddedVectorTest/3.DefaultConstructorWorks 31: [ OK ] PaddedVectorTest/3.DefaultConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/3.ResizeWorks 31: [ OK ] PaddedVectorTest/3.ResizeWorks (0 ms) 31: [ RUN ] PaddedVectorTest/3.ReserveWorks 31: [ OK ] PaddedVectorTest/3.ReserveWorks (0 ms) 31: [ RUN ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve 31: [ OK ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve (0 ms) 31: [ RUN ] PaddedVectorTest/3.MoveConstructorWorks 31: [ OK ] PaddedVectorTest/3.MoveConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks 31: [ OK ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/3.MoveAssignmentWorks 31: [ OK ] PaddedVectorTest/3.MoveAssignmentWorks (0 ms) 31: [ RUN ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical 31: [ OK ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical (0 ms) 31: [ RUN ] PaddedVectorTest/3.CanCopyAssign 31: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 31: [ RUN ] PaddedVectorTest/3.CanMoveAssign 31: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 31: [ RUN ] PaddedVectorTest/3.CanSwap 31: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 31: [----------] 11 tests from PaddedVectorTest/3 (0 ms total) 31: 31: [----------] 11 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 31: [ RUN ] PaddedVectorTest/4.DefaultConstructorWorks 31: [ OK ] PaddedVectorTest/4.DefaultConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/4.ResizeWorks 31: [ OK ] PaddedVectorTest/4.ResizeWorks (0 ms) 31: [ RUN ] PaddedVectorTest/4.ReserveWorks 31: [ OK ] PaddedVectorTest/4.ReserveWorks (0 ms) 31: [ RUN ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve 31: [ OK ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve (0 ms) 31: [ RUN ] PaddedVectorTest/4.MoveConstructorWorks 31: [ OK ] PaddedVectorTest/4.MoveConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks 31: [ OK ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/4.MoveAssignmentWorks 31: [ OK ] PaddedVectorTest/4.MoveAssignmentWorks (0 ms) 31: [ RUN ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical 31: [ OK ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical (0 ms) 31: [ RUN ] PaddedVectorTest/4.CanCopyAssign 31: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 31: [ RUN ] PaddedVectorTest/4.CanMoveAssign 31: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 31: [ RUN ] PaddedVectorTest/4.CanSwap 31: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 31: [----------] 11 tests from PaddedVectorTest/4 (0 ms total) 31: 31: [----------] 11 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 31: [ RUN ] PaddedVectorTest/5.DefaultConstructorWorks 31: [ OK ] PaddedVectorTest/5.DefaultConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/5.ResizeWorks 31: [ OK ] PaddedVectorTest/5.ResizeWorks (0 ms) 31: [ RUN ] PaddedVectorTest/5.ReserveWorks 31: [ OK ] PaddedVectorTest/5.ReserveWorks (0 ms) 31: [ RUN ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve 31: [ OK ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve (0 ms) 31: [ RUN ] PaddedVectorTest/5.MoveConstructorWorks 31: [ OK ] PaddedVectorTest/5.MoveConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks 31: [ OK ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/5.MoveAssignmentWorks 31: [ OK ] PaddedVectorTest/5.MoveAssignmentWorks (0 ms) 31: [ RUN ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical 31: [ OK ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical (0 ms) 31: [ RUN ] PaddedVectorTest/5.CanCopyAssign 31: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 31: [ RUN ] PaddedVectorTest/5.CanMoveAssign 31: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 31: [ RUN ] PaddedVectorTest/5.CanSwap 31: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 31: [----------] 11 tests from PaddedVectorTest/5 (0 ms total) 31: 31: [----------] 11 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 31: [ RUN ] PaddedVectorTest/6.DefaultConstructorWorks 31: [ OK ] PaddedVectorTest/6.DefaultConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/6.ResizeWorks 31: [ OK ] PaddedVectorTest/6.ResizeWorks (0 ms) 31: [ RUN ] PaddedVectorTest/6.ReserveWorks 31: [ OK ] PaddedVectorTest/6.ReserveWorks (0 ms) 31: [ RUN ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve 31: [ OK ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve (0 ms) 31: [ RUN ] PaddedVectorTest/6.MoveConstructorWorks 31: [ OK ] PaddedVectorTest/6.MoveConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks 31: [ OK ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/6.MoveAssignmentWorks 31: [ OK ] PaddedVectorTest/6.MoveAssignmentWorks (0 ms) 31: [ RUN ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical 31: [ OK ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical (0 ms) 31: [ RUN ] PaddedVectorTest/6.CanCopyAssign 31: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 31: [ RUN ] PaddedVectorTest/6.CanMoveAssign 31: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 31: [ RUN ] PaddedVectorTest/6.CanSwap 31: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 31: [----------] 11 tests from PaddedVectorTest/6 (0 ms total) 31: 31: [----------] 11 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 31: [ RUN ] PaddedVectorTest/7.DefaultConstructorWorks 31: [ OK ] PaddedVectorTest/7.DefaultConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/7.ResizeWorks 31: [ OK ] PaddedVectorTest/7.ResizeWorks (0 ms) 31: [ RUN ] PaddedVectorTest/7.ReserveWorks 31: [ OK ] PaddedVectorTest/7.ReserveWorks (0 ms) 31: [ RUN ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve 31: [ OK ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve (0 ms) 31: [ RUN ] PaddedVectorTest/7.MoveConstructorWorks 31: [ OK ] PaddedVectorTest/7.MoveConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks 31: [ OK ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/7.MoveAssignmentWorks 31: [ OK ] PaddedVectorTest/7.MoveAssignmentWorks (0 ms) 31: [ RUN ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical 31: [ OK ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical (0 ms) 31: [ RUN ] PaddedVectorTest/7.CanCopyAssign 31: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 31: [ RUN ] PaddedVectorTest/7.CanMoveAssign 31: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 31: [ RUN ] PaddedVectorTest/7.CanSwap 31: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 31: [----------] 11 tests from PaddedVectorTest/7 (0 ms total) 31: 31: [----------] 11 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 31: [ RUN ] PaddedVectorTest/8.DefaultConstructorWorks 31: [ OK ] PaddedVectorTest/8.DefaultConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/8.ResizeWorks 31: [ OK ] PaddedVectorTest/8.ResizeWorks (0 ms) 31: [ RUN ] PaddedVectorTest/8.ReserveWorks 31: [ OK ] PaddedVectorTest/8.ReserveWorks (0 ms) 31: [ RUN ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve 31: [ OK ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve (0 ms) 31: [ RUN ] PaddedVectorTest/8.MoveConstructorWorks 31: [ OK ] PaddedVectorTest/8.MoveConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks 31: [ OK ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/8.MoveAssignmentWorks 31: [ OK ] PaddedVectorTest/8.MoveAssignmentWorks (0 ms) 31: [ RUN ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical 31: [ OK ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical (0 ms) 31: [ RUN ] PaddedVectorTest/8.CanCopyAssign 31: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 31: [ RUN ] PaddedVectorTest/8.CanMoveAssign 31: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 31: [ RUN ] PaddedVectorTest/8.CanSwap 31: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 31: [----------] 11 tests from PaddedVectorTest/8 (0 ms total) 31: 31: [----------] 11 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 31: [ RUN ] PaddedVectorTest/9.DefaultConstructorWorks 31: [ OK ] PaddedVectorTest/9.DefaultConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/9.ResizeWorks 31: [ OK ] PaddedVectorTest/9.ResizeWorks (0 ms) 31: [ RUN ] PaddedVectorTest/9.ReserveWorks 31: [ OK ] PaddedVectorTest/9.ReserveWorks (0 ms) 31: [ RUN ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve 31: [ OK ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve (0 ms) 31: [ RUN ] PaddedVectorTest/9.MoveConstructorWorks 31: [ OK ] PaddedVectorTest/9.MoveConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks 31: [ OK ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/9.MoveAssignmentWorks 31: [ OK ] PaddedVectorTest/9.MoveAssignmentWorks (0 ms) 31: [ RUN ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical 31: [ OK ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical (0 ms) 31: [ RUN ] PaddedVectorTest/9.CanCopyAssign 31: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 31: [ RUN ] PaddedVectorTest/9.CanMoveAssign 31: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 31: [ RUN ] PaddedVectorTest/9.CanSwap 31: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 31: [----------] 11 tests from PaddedVectorTest/9 (0 ms total) 31: 31: [----------] 40 tests from RVecTest 31: [ RUN ] RVecTest.CanBeStoredInVector 31: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 31: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 31: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 31: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 31: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 31: [ RUN ] RVecTest.WorksAsMutable_rvec 31: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 31: [ RUN ] RVecTest.WorksAs_rvec_Array 31: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 31: [ RUN ] RVecTest.ComparesEqual 31: [ OK ] RVecTest.ComparesEqual (0 ms) 31: [ RUN ] RVecTest.ComparesUnequal 31: [ OK ] RVecTest.ComparesUnequal (0 ms) 31: [ RUN ] RVecTest.CanAddRVecToRvec 31: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 31: [ RUN ] RVecTest.CanAddAssignRVecToRvec 31: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 31: [ RUN ] RVecTest.CanSubtractRVecFromRvec 31: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 31: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 31: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 31: [ RUN ] RVecTest.CanDotProductRVecByRvec 31: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 31: [ RUN ] RVecTest.CanCrossProductRVecByRvec 31: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 31: [ RUN ] RVecTest.CanDivideRVecInplace 31: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 31: [ RUN ] RVecTest.CanScaleRVec 31: [ OK ] RVecTest.CanScaleRVec (0 ms) 31: [ RUN ] RVecTest.CanDivideRVec 31: [ OK ] RVecTest.CanDivideRVec (0 ms) 31: [ RUN ] RVecTest.CanDoUnitvFromRVec 31: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 31: [ RUN ] RVecTest.CanSqLengthOfRVec 31: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 31: [ RUN ] RVecTest.CanLengthOfRVec 31: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 31: [ RUN ] RVecTest.CanCastToRVec 31: [ OK ] RVecTest.CanCastToRVec (0 ms) 31: [ RUN ] RVecTest.CanCastToDVec 31: [ OK ] RVecTest.CanCastToDVec (0 ms) 31: [ RUN ] RVecTest.CanLeftScalarMultiply 31: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 31: [ RUN ] RVecTest.CanRightScalarMultiply 31: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 31: [ RUN ] RVecTest.CanGetUnitvFromRVec 31: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 31: [ RUN ] RVecTest.CanGetSqLengthOfRVec 31: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 31: [ RUN ] RVecTest.CanGetLengthOfRVec 31: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 31: [ RUN ] RVecTest.CanDoCrossProductOfRVec 31: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 31: [ RUN ] RVecTest.CanDoDotProductOfRVec 31: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 31: [ RUN ] RVecTest.CanScaleByVector 31: [ OK ] RVecTest.CanScaleByVector (0 ms) 31: [ RUN ] RVecTest.CanNegate 31: [ OK ] RVecTest.CanNegate (0 ms) 31: [ RUN ] RVecTest.asIVec 31: [ OK ] RVecTest.asIVec (0 ms) 31: [ RUN ] RVecTest.elementWiseMin 31: [ OK ] RVecTest.elementWiseMin (0 ms) 31: [ RUN ] RVecTest.elementWiseMax 31: [ OK ] RVecTest.elementWiseMax (0 ms) 31: [ RUN ] RVecTest.WorksAs_dvec_Reference 31: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 31: [ RUN ] RVecTest.WorksAs_ivec_Reference 31: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 31: [ RUN ] RVecTest.WorksAs_rvec_Reference 31: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 31: [ RUN ] RVecTest.CopyConstructorWorks 31: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 31: [ RUN ] RVecTest.CopyAssignmentWorks 31: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 31: [ RUN ] RVecTest.MoveConstructorWorks 31: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 31: [ RUN ] RVecTest.MoveAssignmentWorks 31: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 31: [----------] 40 tests from RVecTest (0 ms total) 31: 31: [----------] Global test environment tear-down 31: [==========] 304 tests from 38 test suites ran. (102 ms total) 31: [ PASSED ] 304 tests. 31/87 Test #31: MathUnitTests ............................. Passed 0.13 sec test 32 Start 32: MdrunUtilityUnitTests 32: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrunutility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunUtilityUnitTests.xml" 32: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdrunutility/tests 32: Test timeout computed to be: 30 32: [==========] Running 21 tests from 2 test suites. 32: [----------] Global test environment set-up. 32: [----------] 4 tests from MDModulesNotifierTest 32: [ RUN ] MDModulesNotifierTest.AddConsumer 32: [ OK ] MDModulesNotifierTest.AddConsumer (0 ms) 32: [ RUN ] MDModulesNotifierTest.AddConsumerWithPointerParameter 32: [ OK ] MDModulesNotifierTest.AddConsumerWithPointerParameter (0 ms) 32: [ RUN ] MDModulesNotifierTest.AddTwoDifferentConsumers 32: [ OK ] MDModulesNotifierTest.AddTwoDifferentConsumers (0 ms) 32: [ RUN ] MDModulesNotifierTest.AddConsumerOfTwoResources 32: [ OK ] MDModulesNotifierTest.AddConsumerOfTwoResources (0 ms) 32: [----------] 4 tests from MDModulesNotifierTest (0 ms total) 32: 32: [----------] 17 tests from ThreadAffinityTest 32: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 32: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 32: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 32: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 32: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 32: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms) 32: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 32: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 32: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 32: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) 32: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 32: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms) 32: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 32: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 32: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 32: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) 32: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 32: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 32: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 32: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms) 32: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 32: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) 32: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 32: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (0 ms) 32: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 32: NOTE: Affinity setting failed. 32: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) 32: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 32: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (1 ms) 32: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 32: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (0 ms) 32: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 32: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (0 ms) 32: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 32: NOTE: Affinity setting for 1/2 threads failed. 32: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (0 ms) 32: [----------] 17 tests from ThreadAffinityTest (3 ms total) 32: 32: [----------] Global test environment tear-down 32: [==========] 21 tests from 2 test suites ran. (3 ms total) 32: [ PASSED ] 21 tests. 32/87 Test #32: MdrunUtilityUnitTests ..................... Passed 0.03 sec test 33 Start 33: MdrunUtilityMpiUnitTests 33: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 33: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdrunutility/tests 33: Test timeout computed to be: 30 33: [==========] Running 13 tests from 2 test suites. 33: [----------] Global test environment set-up. 33: [----------] 6 tests from ThreadAffinityMultiRankTest 33: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 33: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (174 ms) 33: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 33: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (74 ms) 33: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 33: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (65 ms) 33: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 33: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (39 ms) 33: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 33: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (4 ms) 33: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 33: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (3 ms) 33: [----------] 6 tests from ThreadAffinityMultiRankTest (362 ms total) 33: 33: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 33: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly 33: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly (4 ms) 33: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly 33: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly (3 ms) 33: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain 33: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain (4 ms) 33: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly 33: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly (3 ms) 33: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly 33: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly (7 ms) 33: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly 33: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly (4 ms) 33: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly 33: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly (3 ms) 33: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (32 ms total) 33: 33: [----------] Global test environment tear-down 33: [==========] 13 tests from 2 test suites ran. (394 ms total) 33: [ PASSED ] 13 tests. 33/87 Test #33: MdrunUtilityMpiUnitTests .................. Passed 0.41 sec test 34 Start 34: MDSpanTests 34: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdspan-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MDSpanTests.xml" 34: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdspan/tests 34: Test timeout computed to be: 30 34: [==========] Running 32 tests from 7 test suites. 34: [----------] Global test environment set-up. 34: [----------] 4 tests from BasicAccessorPolicy 34: [ RUN ] BasicAccessorPolicy.Decay 34: [ OK ] BasicAccessorPolicy.Decay (0 ms) 34: [ RUN ] BasicAccessorPolicy.Access 34: [ OK ] BasicAccessorPolicy.Access (0 ms) 34: [ RUN ] BasicAccessorPolicy.Offset 34: [ OK ] BasicAccessorPolicy.Offset (0 ms) 34: [ RUN ] BasicAccessorPolicy.CopyAccessor 34: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms) 34: [----------] 4 tests from BasicAccessorPolicy (0 ms total) 34: 34: [----------] 4 tests from ExtentsTest 34: [ RUN ] ExtentsTest.Construction 34: [ OK ] ExtentsTest.Construction (0 ms) 34: [ RUN ] ExtentsTest.PurelyStatic 34: [ OK ] ExtentsTest.PurelyStatic (0 ms) 34: [ RUN ] ExtentsTest.RankNought 34: [ OK ] ExtentsTest.RankNought (0 ms) 34: [ RUN ] ExtentsTest.Assignment 34: [ OK ] ExtentsTest.Assignment (0 ms) 34: [----------] 4 tests from ExtentsTest (0 ms total) 34: 34: [----------] 8 tests from MdSpanExtension 34: [ RUN ] MdSpanExtension.SlicingAllStatic 34: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms) 34: [ RUN ] MdSpanExtension.SlicingDynamic 34: [ OK ] MdSpanExtension.SlicingDynamic (0 ms) 34: [ RUN ] MdSpanExtension.SlicingAllStatic3D 34: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms) 34: [ RUN ] MdSpanExtension.SlicingEqualsView3D 34: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms) 34: [ RUN ] MdSpanExtension.additionWorks 34: [ OK ] MdSpanExtension.additionWorks (0 ms) 34: [ RUN ] MdSpanExtension.subtractionWorks 34: [ OK ] MdSpanExtension.subtractionWorks (0 ms) 34: [ RUN ] MdSpanExtension.multiplicationWorks 34: [ OK ] MdSpanExtension.multiplicationWorks (0 ms) 34: [ RUN ] MdSpanExtension.divisionWorks 34: [ OK ] MdSpanExtension.divisionWorks (0 ms) 34: [----------] 8 tests from MdSpanExtension (0 ms total) 34: 34: [----------] 3 tests from LayoutTests 34: [ RUN ] LayoutTests.LayoutRightConstruction 34: [ OK ] LayoutTests.LayoutRightConstruction (0 ms) 34: [ RUN ] LayoutTests.LayoutRightProperties 34: [ OK ] LayoutTests.LayoutRightProperties (0 ms) 34: [ RUN ] LayoutTests.LayoutRightOperator 34: [ OK ] LayoutTests.LayoutRightOperator (0 ms) 34: [----------] 3 tests from LayoutTests (0 ms total) 34: 34: [----------] 1 test from MdSpanTest 34: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly 34: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms) 34: [----------] 1 test from MdSpanTest (0 ms total) 34: 34: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 34: [ RUN ] MdSpanTest/0.Rank 34: [ OK ] MdSpanTest/0.Rank (0 ms) 34: [ RUN ] MdSpanTest/0.DynamicRank 34: [ OK ] MdSpanTest/0.DynamicRank (0 ms) 34: [ RUN ] MdSpanTest/0.Extents 34: [ OK ] MdSpanTest/0.Extents (0 ms) 34: [ RUN ] MdSpanTest/0.Strides 34: [ OK ] MdSpanTest/0.Strides (0 ms) 34: [ RUN ] MdSpanTest/0.Properties 34: [ OK ] MdSpanTest/0.Properties (0 ms) 34: [ RUN ] MdSpanTest/0.Operator 34: [ OK ] MdSpanTest/0.Operator (0 ms) 34: [----------] 6 tests from MdSpanTest/0 (0 ms total) 34: 34: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 34: [ RUN ] MdSpanTest/1.Rank 34: [ OK ] MdSpanTest/1.Rank (0 ms) 34: [ RUN ] MdSpanTest/1.DynamicRank 34: [ OK ] MdSpanTest/1.DynamicRank (0 ms) 34: [ RUN ] MdSpanTest/1.Extents 34: [ OK ] MdSpanTest/1.Extents (0 ms) 34: [ RUN ] MdSpanTest/1.Strides 34: [ OK ] MdSpanTest/1.Strides (0 ms) 34: [ RUN ] MdSpanTest/1.Properties 34: [ OK ] MdSpanTest/1.Properties (0 ms) 34: [ RUN ] MdSpanTest/1.Operator 34: [ OK ] MdSpanTest/1.Operator (0 ms) 34: [----------] 6 tests from MdSpanTest/1 (0 ms total) 34: 34: [----------] Global test environment tear-down 34: [==========] 32 tests from 7 test suites ran. (0 ms total) 34: [ PASSED ] 32 tests. 34/87 Test #34: MDSpanTests ............................... Passed 0.04 sec test 35 Start 35: MdtypesUnitTest 35: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdtypes-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdtypesUnitTest.xml" 35: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdtypes/tests 35: Test timeout computed to be: 30 35: [==========] Running 97 tests from 7 test suites. 35: [----------] Global test environment set-up. 35: [----------] 4 tests from ForeingLambdaTermsDhdl 35: [ RUN ] ForeingLambdaTermsDhdl.RateCheckWorks 35: [ OK ] ForeingLambdaTermsDhdl.RateCheckWorks (0 ms) 35: [ RUN ] ForeingLambdaTermsDhdl.AllLinear 35: [ OK ] ForeingLambdaTermsDhdl.AllLinear (0 ms) 35: [ RUN ] ForeingLambdaTermsDhdl.AllLinearNegative 35: [ OK ] ForeingLambdaTermsDhdl.AllLinearNegative (0 ms) 35: [ RUN ] ForeingLambdaTermsDhdl.SeparateVdwCoul 35: [ OK ] ForeingLambdaTermsDhdl.SeparateVdwCoul (0 ms) 35: [----------] 4 tests from ForeingLambdaTermsDhdl (0 ms total) 35: 35: [----------] 4 tests from ObservablesReducerTest 35: [ RUN ] ObservablesReducerTest.CanMoveAssign 35: [ OK ] ObservablesReducerTest.CanMoveAssign (0 ms) 35: [ RUN ] ObservablesReducerTest.CanMoveConstruct 35: [ OK ] ObservablesReducerTest.CanMoveConstruct (0 ms) 35: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers 35: [ OK ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers (0 ms) 35: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber 35: [ OK ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber (0 ms) 35: [----------] 4 tests from ObservablesReducerTest (0 ms total) 35: 35: [----------] 2 tests from CheckpointDataTest 35: [ RUN ] CheckpointDataTest.SingleDataTest 35: [ OK ] CheckpointDataTest.SingleDataTest (20 ms) 35: [ RUN ] CheckpointDataTest.MultiDataTest 35: [ OK ] CheckpointDataTest.MultiDataTest (187 ms) 35: [----------] 2 tests from CheckpointDataTest (207 ms total) 35: 35: [----------] 7 tests from ForceBuffers 35: [ RUN ] ForceBuffers.ConstructsUnpinned 35: [ OK ] ForceBuffers.ConstructsUnpinned (0 ms) 35: [ RUN ] ForceBuffers.ConstructsPinned 35: [ OK ] ForceBuffers.ConstructsPinned (0 ms) 35: [ RUN ] ForceBuffers.ConstructsEmpty 35: [ OK ] ForceBuffers.ConstructsEmpty (0 ms) 35: [ RUN ] ForceBuffers.ResizeWorks 35: [ OK ] ForceBuffers.ResizeWorks (0 ms) 35: [ RUN ] ForceBuffers.PaddingWorks 35: [ OK ] ForceBuffers.PaddingWorks (0 ms) 35: [ RUN ] ForceBuffers.CopyWorks 35: [ OK ] ForceBuffers.CopyWorks (0 ms) 35: [ RUN ] ForceBuffers.CopyDoesNotPin 35: [ OK ] ForceBuffers.CopyDoesNotPin (0 ms) 35: [----------] 7 tests from ForceBuffers (0 ms total) 35: 35: [----------] 5 tests from MultipleTimeStepping 35: [ RUN ] MultipleTimeStepping.ChecksNumLevels 35: [ OK ] MultipleTimeStepping.ChecksNumLevels (0 ms) 35: [ RUN ] MultipleTimeStepping.SelectsForceGroups 35: [ OK ] MultipleTimeStepping.SelectsForceGroups (0 ms) 35: [ RUN ] MultipleTimeStepping.ChecksStepFactor 35: [ OK ] MultipleTimeStepping.ChecksStepFactor (0 ms) 35: [ RUN ] MultipleTimeStepping.ChecksPmeIsAtLastLevel 35: [ OK ] MultipleTimeStepping.ChecksPmeIsAtLastLevel (0 ms) 35: [ RUN ] MultipleTimeStepping.ChecksIntegrator 35: [ OK ] MultipleTimeStepping.ChecksIntegrator (0 ms) 35: [----------] 5 tests from MultipleTimeStepping (0 ms total) 35: 35: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 (0 ms) 35: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest (0 ms total) 35: 35: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/0 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/0 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/1 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/1 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/2 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/2 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/3 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/3 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/4 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/4 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/5 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/5 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/6 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/6 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/7 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/7 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/8 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/8 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/9 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/9 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/10 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/10 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/11 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/11 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/12 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/12 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/13 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/13 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/14 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/14 (0 ms) 35: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest (0 ms total) 35: 35: [----------] Global test environment tear-down 35: [==========] 97 tests from 7 test suites ran. (208 ms total) 35: [ PASSED ] 97 tests. 35/87 Test #35: MdtypesUnitTest ........................... Passed 0.23 sec test 36 Start 36: OnlineHelpUnitTests 36: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/onlinehelp-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/OnlineHelpUnitTests.xml" 36: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/onlinehelp/tests 36: Test timeout computed to be: 30 36: [==========] Running 22 tests from 4 test suites. 36: [----------] Global test environment set-up. 36: [----------] 6 tests from TextTableFormatterTest 36: [ RUN ] TextTableFormatterTest.HandlesBasicCase 36: [ OK ] TextTableFormatterTest.HandlesBasicCase (3 ms) 36: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 36: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms) 36: [ RUN ] TextTableFormatterTest.HandlesIndentation 36: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) 36: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 36: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (1 ms) 36: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 36: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms) 36: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 36: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) 36: [----------] 6 tests from TextTableFormatterTest (7 ms total) 36: 36: [----------] 3 tests from HelpManagerTest 36: [ RUN ] HelpManagerTest.HandlesRootTopic 36: [ OK ] HelpManagerTest.HandlesRootTopic (7 ms) 36: [ RUN ] HelpManagerTest.HandlesSubTopics 36: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 36: [ RUN ] HelpManagerTest.HandlesInvalidTopics 36: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) 36: [----------] 3 tests from HelpManagerTest (8 ms total) 36: 36: [----------] 2 tests from HelpTopicFormattingTest 36: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 36: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms) 36: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 36: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) 36: [----------] 2 tests from HelpTopicFormattingTest (1 ms total) 36: 36: [----------] 11 tests from HelpWriterContextTest 36: [ RUN ] HelpWriterContextTest.FormatsParagraphs 36: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) 36: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 36: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) 36: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 36: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) 36: [ RUN ] HelpWriterContextTest.FormatsLiteralText 36: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms) 36: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 36: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) 36: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 36: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) 36: [ RUN ] HelpWriterContextTest.FormatsBulletList 36: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) 36: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 36: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) 36: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 36: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms) 36: [ RUN ] HelpWriterContextTest.FormatsGridTable 36: [ OK ] HelpWriterContextTest.FormatsGridTable (1 ms) 36: [ RUN ] HelpWriterContextTest.FormatsTitles 36: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms) 36: [----------] 11 tests from HelpWriterContextTest (12 ms total) 36: 36: [----------] Global test environment tear-down 36: [==========] 22 tests from 4 test suites ran. (31 ms total) 36: [ PASSED ] 22 tests. 36/87 Test #36: OnlineHelpUnitTests ....................... Passed 0.06 sec test 37 Start 37: OptionsUnitTests 37: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/options-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/OptionsUnitTests.xml" 37: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options/tests 37: Test timeout computed to be: 30 37: [==========] Running 111 tests from 18 test suites. 37: [----------] Global test environment set-up. 37: [----------] 5 tests from AbstractOptionStorageTest 37: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 37: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 37: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 37: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) 37: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 37: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 37: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 37: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) 37: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 37: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 37: [----------] 5 tests from AbstractOptionStorageTest (4 ms total) 37: 37: [----------] 10 tests from FileNameOptionTest 37: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 37: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 37: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 37: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 37: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 37: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 37: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 37: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 37: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 37: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 37: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 37: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 37: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 37: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 37: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 37: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 37: [ RUN ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension 37: [ OK ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension (0 ms) 37: [ RUN ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue 37: [ OK ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue (0 ms) 37: [----------] 10 tests from FileNameOptionTest (0 ms total) 37: 37: [----------] 15 tests from FileNameOptionManagerTest 37: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 37: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 37: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 37: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 37: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 37: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) 37: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 37: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 37: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 37: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 37: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 37: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 37: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 37: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 37: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 37: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 37: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 37: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 37: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 37: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 37: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 37: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 37: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 37: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 37: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 37: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 37: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 37: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 37: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 37: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 37: [----------] 15 tests from FileNameOptionManagerTest (0 ms total) 37: 37: [----------] 1 test from OptionsTest 37: [ RUN ] OptionsTest.FailsOnNonsafeStorage 37: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 37: [----------] 1 test from OptionsTest (0 ms total) 37: 37: [----------] 9 tests from OptionsAssignerTest 37: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 37: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 37: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 37: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 37: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 37: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 37: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 37: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 37: [ RUN ] OptionsAssignerTest.HandlesMissingValue 37: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 37: [ RUN ] OptionsAssignerTest.HandlesExtraValue 37: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 37: [ RUN ] OptionsAssignerTest.HandlesGroups 37: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 37: [ RUN ] OptionsAssignerTest.HandlesSections 37: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 37: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 37: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 37: [----------] 9 tests from OptionsAssignerTest (0 ms total) 37: 37: [----------] 4 tests from OptionsAssignerBooleanTest 37: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 37: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 37: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 37: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 37: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 37: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 37: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 37: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 37: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 37: 37: [----------] 13 tests from OptionsAssignerIntegerTest 37: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 37: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 37: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 37: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 37: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 37: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 37: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 37: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 37: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 37: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 37: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 37: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 37: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 37: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 37: [----------] 13 tests from OptionsAssignerIntegerTest (0 ms total) 37: 37: [----------] 5 tests from OptionsAssignerDoubleTest 37: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 37: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 37: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 37: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 37: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 37: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 37: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 37: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 37: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 37: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 37: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) 37: 37: [----------] 9 tests from OptionsAssignerStringTest 37: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 37: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 37: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 37: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 37: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 37: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 37: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 37: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 37: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 37: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 37: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 37: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 37: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 37: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 37: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 37: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 37: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 37: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 37: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) 37: 37: [----------] 6 tests from OptionsAssignerEnumTest 37: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 37: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 37: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 37: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 37: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 37: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 37: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 37: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 37: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 37: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 37: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 37: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 37: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) 37: 37: [----------] 8 tests from RepeatingOptionSectionTest 37: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 37: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 37: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 37: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 37: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 37: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 37: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 37: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 37: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 37: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 37: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 37: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 37: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 37: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 37: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 37: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 37: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) 37: 37: [----------] 1 test from TimeUnitManagerTest 37: [ RUN ] TimeUnitManagerTest.BasicOperations 37: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 37: [----------] 1 test from TimeUnitManagerTest (0 ms total) 37: 37: [----------] 4 tests from TimeUnitBehaviorTest 37: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 37: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 37: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 37: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 37: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 37: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 37: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 37: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 37: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 37: 37: [----------] 2 tests from TreeValueSupportAssignTest 37: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 37: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 37: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 37: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 37: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) 37: 37: [----------] 1 test from TreeValueSupportAssignErrorTest 37: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 37: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 37: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 37: 37: [----------] 5 tests from TreeValueSupportCheckTest 37: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 37: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 37: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 37: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 37: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 37: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 37: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 37: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 37: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 37: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 37: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 37: 37: [----------] 6 tests from TreeValueSupportAdjustTest 37: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 37: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms) 37: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 37: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (1 ms) 37: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 37: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms) 37: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 37: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) 37: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 37: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) 37: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 37: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) 37: [----------] 6 tests from TreeValueSupportAdjustTest (5 ms total) 37: 37: [----------] 7 tests from TreeValueSupportTest 37: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 37: [ OK ] TreeValueSupportTest.SupportsBooleanOption (1 ms) 37: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 37: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms) 37: [ RUN ] TreeValueSupportTest.SupportsInt64Option 37: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms) 37: [ RUN ] TreeValueSupportTest.SupportsStringOption 37: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) 37: [ RUN ] TreeValueSupportTest.SupportsFloatOption 37: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) 37: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 37: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) 37: [ RUN ] TreeValueSupportTest.SupportsEnumOption 37: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) 37: [----------] 7 tests from TreeValueSupportTest (5 ms total) 37: 37: [----------] Global test environment tear-down 37: [==========] 111 tests from 18 test suites ran. (16 ms total) 37: [ PASSED ] 111 tests. 37/87 Test #37: OptionsUnitTests .......................... Passed 0.04 sec test 38 Start 38: PbcutilUnitTest 38: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/pbcutil-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/PbcutilUnitTest.xml" 38: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pbcutil/tests 38: Test timeout computed to be: 30 38: [==========] Running 37 tests from 5 test suites. 38: [----------] Global test environment set-up. 38: [----------] 1 test from ShiftTest 38: [ RUN ] ShiftTest.CoordinateShiftWorks 38: [ OK ] ShiftTest.CoordinateShiftWorks (0 ms) 38: [----------] 1 test from ShiftTest (0 ms total) 38: 38: [----------] 2 tests from MShift 38: [ RUN ] MShift.shiftsAndUnshifts 38: [ OK ] MShift.shiftsAndUnshifts (0 ms) 38: [ RUN ] MShift.shiftsAndUnshiftsSelf 38: [ OK ] MShift.shiftsAndUnshiftsSelf (0 ms) 38: [----------] 2 tests from MShift (0 ms total) 38: 38: [----------] 5 tests from PbcTest 38: [ RUN ] PbcTest.CalcShiftsWorks 38: [ OK ] PbcTest.CalcShiftsWorks (1 ms) 38: [ RUN ] PbcTest.PutAtomsInCubicBoxAlreadyInBox 38: [ OK ] PbcTest.PutAtomsInCubicBoxAlreadyInBox (0 ms) 38: [ RUN ] PbcTest.PutAtomsInCubicBoxFromOutsideBox 38: [ OK ] PbcTest.PutAtomsInCubicBoxFromOutsideBox (0 ms) 38: [ RUN ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox 38: [ OK ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox (0 ms) 38: [ RUN ] PbcTest.PutAtomsInBoxHandlesInf 38: [ OK ] PbcTest.PutAtomsInBoxHandlesInf (0 ms) 38: [----------] 5 tests from PbcTest (1 ms total) 38: 38: [----------] 2 tests from PbcEnumsTest 38: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect 38: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms) 38: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect 38: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms) 38: [----------] 2 tests from PbcEnumsTest (0 ms total) 38: 38: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 (1 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 (2 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 (0 ms) 38: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest (36 ms total) 38: 38: [----------] Global test environment tear-down 38: [==========] 37 tests from 5 test suites ran. (38 ms total) 38: [ PASSED ] 37 tests. 38/87 Test #38: PbcutilUnitTest ........................... Passed 0.07 sec test 39 Start 39: RandomUnitTests 39: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/random-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/RandomUnitTests.xml" 39: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/random/tests 39: Test timeout computed to be: 30 39: [==========] Running 44 tests from 10 test suites. 39: [----------] Global test environment set-up. 39: [----------] 4 tests from ExponentialDistributionTest 39: [ RUN ] ExponentialDistributionTest.Output 39: [ OK ] ExponentialDistributionTest.Output (1 ms) 39: [ RUN ] ExponentialDistributionTest.Logical 39: [ OK ] ExponentialDistributionTest.Logical (0 ms) 39: [ RUN ] ExponentialDistributionTest.Reset 39: [ OK ] ExponentialDistributionTest.Reset (0 ms) 39: [ RUN ] ExponentialDistributionTest.AltParam 39: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 39: [----------] 4 tests from ExponentialDistributionTest (1 ms total) 39: 39: [----------] 4 tests from GammaDistributionTest 39: [ RUN ] GammaDistributionTest.Output 39: [ OK ] GammaDistributionTest.Output (1 ms) 39: [ RUN ] GammaDistributionTest.Logical 39: [ OK ] GammaDistributionTest.Logical (0 ms) 39: [ RUN ] GammaDistributionTest.Reset 39: [ OK ] GammaDistributionTest.Reset (0 ms) 39: [ RUN ] GammaDistributionTest.AltParam 39: [ OK ] GammaDistributionTest.AltParam (0 ms) 39: [----------] 4 tests from GammaDistributionTest (1 ms total) 39: 39: [----------] 4 tests from NormalDistributionTest 39: [ RUN ] NormalDistributionTest.Output 39: [ OK ] NormalDistributionTest.Output (0 ms) 39: [ RUN ] NormalDistributionTest.Logical 39: [ OK ] NormalDistributionTest.Logical (0 ms) 39: [ RUN ] NormalDistributionTest.Reset 39: [ OK ] NormalDistributionTest.Reset (0 ms) 39: [ RUN ] NormalDistributionTest.AltParam 39: [ OK ] NormalDistributionTest.AltParam (0 ms) 39: [----------] 4 tests from NormalDistributionTest (0 ms total) 39: 39: [----------] 1 test from SeedTest 39: [ RUN ] SeedTest.makeRandomSeed 39: [ OK ] SeedTest.makeRandomSeed (0 ms) 39: [----------] 1 test from SeedTest (0 ms total) 39: 39: [----------] 6 tests from TabulatedNormalDistributionTest 39: [ RUN ] TabulatedNormalDistributionTest.Output14 39: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) 39: [ RUN ] TabulatedNormalDistributionTest.Output16 39: [ OK ] TabulatedNormalDistributionTest.Output16 (5 ms) 39: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 39: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (2 ms) 39: [ RUN ] TabulatedNormalDistributionTest.Logical 39: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 39: [ RUN ] TabulatedNormalDistributionTest.Reset 39: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 39: [ RUN ] TabulatedNormalDistributionTest.AltParam 39: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 39: [----------] 6 tests from TabulatedNormalDistributionTest (8 ms total) 39: 39: [----------] 1 test from TabulatedNormalDistributionTableTest 39: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 39: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (0 ms) 39: [----------] 1 test from TabulatedNormalDistributionTableTest (0 ms total) 39: 39: [----------] 6 tests from ThreeFry2x64Test 39: [ RUN ] ThreeFry2x64Test.Logical 39: [ OK ] ThreeFry2x64Test.Logical (0 ms) 39: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 39: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms) 39: [ RUN ] ThreeFry2x64Test.Reseed 39: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 39: [ RUN ] ThreeFry2x64Test.Discard 39: [ OK ] ThreeFry2x64Test.Discard (0 ms) 39: [ RUN ] ThreeFry2x64Test.InvalidCounter 39: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) 39: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 39: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 39: [----------] 6 tests from ThreeFry2x64Test (1 ms total) 39: 39: [----------] 4 tests from UniformIntDistributionTest 39: [ RUN ] UniformIntDistributionTest.Output 39: [ OK ] UniformIntDistributionTest.Output (0 ms) 39: [ RUN ] UniformIntDistributionTest.Logical 39: [ OK ] UniformIntDistributionTest.Logical (0 ms) 39: [ RUN ] UniformIntDistributionTest.Reset 39: [ OK ] UniformIntDistributionTest.Reset (0 ms) 39: [ RUN ] UniformIntDistributionTest.AltParam 39: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 39: [----------] 4 tests from UniformIntDistributionTest (0 ms total) 39: 39: [----------] 5 tests from UniformRealDistributionTest 39: [ RUN ] UniformRealDistributionTest.GenerateCanonical 39: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) 39: [ RUN ] UniformRealDistributionTest.Output 39: [ OK ] UniformRealDistributionTest.Output (1 ms) 39: [ RUN ] UniformRealDistributionTest.Logical 39: [ OK ] UniformRealDistributionTest.Logical (0 ms) 39: [ RUN ] UniformRealDistributionTest.Reset 39: [ OK ] UniformRealDistributionTest.Reset (0 ms) 39: [ RUN ] UniformRealDistributionTest.AltParam 39: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 39: [----------] 5 tests from UniformRealDistributionTest (1 ms total) 39: 39: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 39: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 39: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms) 39: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 39: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) 39: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 39: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) 39: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 39: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 39: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 39: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) 39: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 39: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) 39: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 39: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 39: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 39: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) 39: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 39: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) 39: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (7 ms total) 39: 39: [----------] Global test environment tear-down 39: [==========] 44 tests from 10 test suites ran. (23 ms total) 39: [ PASSED ] 44 tests. 39/87 Test #39: RandomUnitTests ........................... Passed 0.06 sec test 40 Start 40: RestraintTests 40: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/restraintpotential-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/RestraintTests.xml" 40: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/restraint/tests 40: Test timeout computed to be: 30 40: [==========] Running 1 test from 1 test suite. 40: [----------] Global test environment set-up. 40: [----------] 1 test from RestraintManager 40: [ RUN ] RestraintManager.restraintList 40: [ OK ] RestraintManager.restraintList (0 ms) 40: [----------] 1 test from RestraintManager (0 ms total) 40: 40: [----------] Global test environment tear-down 40: [==========] 1 test from 1 test suite ran. (0 ms total) 40: [ PASSED ] 1 test. 40/87 Test #40: RestraintTests ............................ Passed 0.04 sec test 41 Start 41: TableUnitTests 41: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/table-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/TableUnitTests.xml" 41: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tables/tests 41: Test timeout computed to be: 30 41: [==========] Running 20 tests from 2 test suites. 41: [----------] Global test environment set-up. 41: [----------] 10 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 41: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 41: [ OK ] SplineTableTest/0.HandlesIncorrectInput (0 ms) 41: [ RUN ] SplineTableTest/0.Sinc 41: [ OK ] SplineTableTest/0.Sinc (0 ms) 41: [ RUN ] SplineTableTest/0.LJ12 41: [ OK ] SplineTableTest/0.LJ12 (9 ms) 41: [ RUN ] SplineTableTest/0.PmeCorrection 41: [ OK ] SplineTableTest/0.PmeCorrection (0 ms) 41: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 41: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (0 ms) 41: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 41: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (0 ms) 41: [ RUN ] SplineTableTest/0.TwoFunctions 41: [ OK ] SplineTableTest/0.TwoFunctions (18 ms) 41: [ RUN ] SplineTableTest/0.ThreeFunctions 41: [ OK ] SplineTableTest/0.ThreeFunctions (22 ms) 41: [ RUN ] SplineTableTest/0.Simd 41: [ OK ] SplineTableTest/0.Simd (1 ms) 41: [ RUN ] SplineTableTest/0.SimdTwoFunctions 41: [ OK ] SplineTableTest/0.SimdTwoFunctions (7 ms) 41: [----------] 10 tests from SplineTableTest/0 (67 ms total) 41: 41: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 41: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 41: [ OK ] SplineTableTest/1.HandlesIncorrectInput (0 ms) 41: [ RUN ] SplineTableTest/1.Sinc 41: [ OK ] SplineTableTest/1.Sinc (0 ms) 41: [ RUN ] SplineTableTest/1.LJ12 41: [ OK ] SplineTableTest/1.LJ12 (0 ms) 41: [ RUN ] SplineTableTest/1.PmeCorrection 41: [ OK ] SplineTableTest/1.PmeCorrection (0 ms) 41: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 41: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (0 ms) 41: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 41: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (0 ms) 41: [ RUN ] SplineTableTest/1.TwoFunctions 41: [ OK ] SplineTableTest/1.TwoFunctions (1 ms) 41: [ RUN ] SplineTableTest/1.ThreeFunctions 41: [ OK ] SplineTableTest/1.ThreeFunctions (1 ms) 41: [ RUN ] SplineTableTest/1.Simd 41: [ OK ] SplineTableTest/1.Simd (0 ms) 41: [ RUN ] SplineTableTest/1.SimdTwoFunctions 41: [ OK ] SplineTableTest/1.SimdTwoFunctions (1 ms) 41: [----------] 10 tests from SplineTableTest/1 (5 ms total) 41: 41: [----------] Global test environment tear-down 41: [==========] 20 tests from 2 test suites ran. (76 ms total) 41: [ PASSED ] 20 tests. 41/87 Test #41: TableUnitTests ............................ Passed 0.10 sec test 42 Start 42: TaskAssignmentUnitTests 42: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/taskassignment-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/TaskAssignmentUnitTests.xml" 42: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/taskassignment/tests 42: Test timeout computed to be: 30 42: [==========] Running 3 tests from 2 test suites. 42: [----------] Global test environment set-up. 42: [----------] 2 tests from UserTaskAssignmentStringHandlingTest 42: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork 42: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (0 ms) 42: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid 42: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms) 42: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (0 ms total) 42: 42: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest 42: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow 42: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (0 ms) 42: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (0 ms total) 42: 42: [----------] Global test environment tear-down 42: [==========] 3 tests from 2 test suites ran. (0 ms total) 42: [ PASSED ] 3 tests. 42/87 Test #42: TaskAssignmentUnitTests ................... Passed 0.02 sec test 43 Start 43: GmxTimingTests 43: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/timing-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/GmxTimingTests.xml" 43: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/timing/tests 43: Test timeout computed to be: 30 43: [==========] Running 6 tests from 1 test suite. 43: [----------] Global test environment set-up. 43: [----------] 6 tests from TimingTest 43: [ RUN ] TimingTest.ElementCountingWorks 43: [ OK ] TimingTest.ElementCountingWorks (0 ms) 43: [ RUN ] TimingTest.ElementNoCountingWorks 43: [ OK ] TimingTest.ElementNoCountingWorks (0 ms) 43: [ RUN ] TimingTest.SubElementCountingWorks 43: [ OK ] TimingTest.SubElementCountingWorks (0 ms) 43: [ RUN ] TimingTest.SubElementNoCountingWorks 43: [ OK ] TimingTest.SubElementNoCountingWorks (0 ms) 43: [ RUN ] TimingTest.RunWallCycle 43: [ OK ] TimingTest.RunWallCycle (1 ms) 43: [ RUN ] TimingTest.RunWallCycleSub 43: [ OK ] TimingTest.RunWallCycleSub (0 ms) 43: [----------] 6 tests from TimingTest (1 ms total) 43: 43: [----------] Global test environment tear-down 43: [==========] 6 tests from 1 test suite ran. (1 ms total) 43: [ PASSED ] 6 tests. 43/87 Test #43: GmxTimingTests ............................ Passed 0.03 sec test 44 Start 44: TopologyTest 44: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/topology-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/TopologyTest.xml" 44: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/topology/tests 44: Test timeout computed to be: 30 44: [==========] Running 153 tests from 10 test suites. 44: [----------] Global test environment set-up. 44: [----------] 3 tests from PdbAtomEntryTest 44: [ RUN ] PdbAtomEntryTest.CanCreateBasicEntry 44: [ OK ] PdbAtomEntryTest.CanCreateBasicEntry (0 ms) 44: [ RUN ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac 44: [ OK ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac (0 ms) 44: [ RUN ] PdbAtomEntryTest.CanCreateFullEntry 44: [ OK ] PdbAtomEntryTest.CanCreateFullEntry (0 ms) 44: [----------] 3 tests from PdbAtomEntryTest (0 ms total) 44: 44: [----------] 3 tests from ExclusionBlockTest 44: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks 44: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms) 44: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka 44: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms) 44: [ RUN ] ExclusionBlockTest.MergeExclusions 44: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms) 44: [----------] 3 tests from ExclusionBlockTest (0 ms total) 44: 44: [----------] 6 tests from InteractionListTest 44: [ RUN ] InteractionListTest.EmptyWorks 44: [ OK ] InteractionListTest.EmptyWorks (0 ms) 44: [ RUN ] InteractionListTest.CanAddInteractionArray 44: [ OK ] InteractionListTest.CanAddInteractionArray (0 ms) 44: [ RUN ] InteractionListTest.CanAddInteractionArrayMultipleAtoms 44: [ OK ] InteractionListTest.CanAddInteractionArrayMultipleAtoms (0 ms) 44: [ RUN ] InteractionListTest.CanAddInteractionPointer 44: [ OK ] InteractionListTest.CanAddInteractionPointer (0 ms) 44: [ RUN ] InteractionListTest.CanAddListToOtherList 44: [ OK ] InteractionListTest.CanAddListToOtherList (0 ms) 44: [ RUN ] InteractionListTest.ClearingWorks 44: [ OK ] InteractionListTest.ClearingWorks (0 ms) 44: [----------] 6 tests from InteractionListTest (0 ms total) 44: 44: [----------] 3 tests from IndexTest 44: [ RUN ] IndexTest.AnalyseWorksDefaultGroups 44: 44: WARNING: Masses and atomic (Van der Waals) radii will be guessed 44: based on residue and atom names, since they could not be 44: definitively assigned from the information in your input 44: files. These guessed numbers might deviate from the mass 44: and radius of the atom type. Please check the output 44: files if necessary. Note, that this functionality may 44: be removed in a future GROMACS version. Please, consider 44: using another file format for your input. 44: 44: [ OK ] IndexTest.AnalyseWorksDefaultGroups (5 ms) 44: [ RUN ] IndexTest.WriteIndexWorks 44: 44: WARNING: Masses and atomic (Van der Waals) radii will be guessed 44: based on residue and atom names, since they could not be 44: definitively assigned from the information in your input 44: files. These guessed numbers might deviate from the mass 44: and radius of the atom type. Please check the output 44: files if necessary. Note, that this functionality may 44: be removed in a future GROMACS version. Please, consider 44: using another file format for your input. 44: 44: [ OK ] IndexTest.WriteIndexWorks (8 ms) 44: [ RUN ] IndexTest.WriteAndReadIndexWorks 44: 44: WARNING: Masses and atomic (Van der Waals) radii will be guessed 44: based on residue and atom names, since they could not be 44: definitively assigned from the information in your input 44: files. These guessed numbers might deviate from the mass 44: and radius of the atom type. Please check the output 44: files if necessary. Note, that this functionality may 44: be removed in a future GROMACS version. Please, consider 44: using another file format for your input. 44: 44: [ OK ] IndexTest.WriteAndReadIndexWorks (2 ms) 44: [----------] 3 tests from IndexTest (18 ms total) 44: 44: [----------] 4 tests from MtopTest 44: [ RUN ] MtopTest.RangeBasedLoop 44: [ OK ] MtopTest.RangeBasedLoop (0 ms) 44: [ RUN ] MtopTest.Operators 44: [ OK ] MtopTest.Operators (0 ms) 44: [ RUN ] MtopTest.CanFindResidueStartAndEndAtoms 44: [ OK ] MtopTest.CanFindResidueStartAndEndAtoms (0 ms) 44: [ RUN ] MtopTest.CanSortPerturbedInteractionsCorrectly 44: [ OK ] MtopTest.CanSortPerturbedInteractionsCorrectly (0 ms) 44: [----------] 4 tests from MtopTest (0 ms total) 44: 44: [----------] 2 tests from IListRangeTest 44: [ RUN ] IListRangeTest.RangeBasedLoopWorks 44: [ OK ] IListRangeTest.RangeBasedLoopWorks (0 ms) 44: [ RUN ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction 44: [ OK ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction (0 ms) 44: [----------] 2 tests from IListRangeTest (0 ms total) 44: 44: [----------] 13 tests from StringTableTest 44: [ RUN ] StringTableTest.AddSingleEntry 44: [ OK ] StringTableTest.AddSingleEntry (1 ms) 44: [ RUN ] StringTableTest.CanAccessWithAt 44: [ OK ] StringTableTest.CanAccessWithAt (0 ms) 44: [ RUN ] StringTableTest.CanAccessWithBracket 44: [ OK ] StringTableTest.CanAccessWithBracket (0 ms) 44: [ RUN ] StringTableTest.ThrowsOutOfRange 44: [ OK ] StringTableTest.ThrowsOutOfRange (0 ms) 44: [ RUN ] StringTableTest.StringCompareIsCorrect 44: [ OK ] StringTableTest.StringCompareIsCorrect (0 ms) 44: [ RUN ] StringTableTest.AddTwoDistinctEntries 44: [ OK ] StringTableTest.AddTwoDistinctEntries (0 ms) 44: [ RUN ] StringTableTest.TryToAddDuplicates 44: [ OK ] StringTableTest.TryToAddDuplicates (2 ms) 44: [ RUN ] StringTableTest.AddLargeNumberOfEntries 44: [ OK ] StringTableTest.AddLargeNumberOfEntries (0 ms) 44: [ RUN ] StringTableTest.NoDuplicatesInLargeTable 44: [ OK ] StringTableTest.NoDuplicatesInLargeTable (0 ms) 44: [ RUN ] StringTableTest.CanWriteToBuffer 44: [ OK ] StringTableTest.CanWriteToBuffer (1 ms) 44: [ RUN ] StringTableTest.Roundtrip 44: [ OK ] StringTableTest.Roundtrip (0 ms) 44: [ RUN ] StringTableTest.RoundtripWithCorrectStringIndices 44: [ OK ] StringTableTest.RoundtripWithCorrectStringIndices (0 ms) 44: [ RUN ] StringTableTest.CanCopyToLegacyTable 44: [ OK ] StringTableTest.CanCopyToLegacyTable (0 ms) 44: [----------] 13 tests from StringTableTest (12 ms total) 44: 44: [----------] 6 tests from LegacySymtabTest 44: [ RUN ] LegacySymtabTest.EmptyOnOpen 44: [ OK ] LegacySymtabTest.EmptyOnOpen (0 ms) 44: [ RUN ] LegacySymtabTest.AddSingleEntry 44: [ OK ] LegacySymtabTest.AddSingleEntry (0 ms) 44: [ RUN ] LegacySymtabTest.AddTwoDistinctEntries 44: [ OK ] LegacySymtabTest.AddTwoDistinctEntries (0 ms) 44: [ RUN ] LegacySymtabTest.TryToAddDuplicates 44: [ OK ] LegacySymtabTest.TryToAddDuplicates (0 ms) 44: [ RUN ] LegacySymtabTest.AddLargeNumberOfEntries 44: [ OK ] LegacySymtabTest.AddLargeNumberOfEntries (0 ms) 44: [ RUN ] LegacySymtabTest.NoDuplicatesInLargeTable 44: [ OK ] LegacySymtabTest.NoDuplicatesInLargeTable (0 ms) 44: [----------] 6 tests from LegacySymtabTest (2 ms total) 44: 44: [----------] 5 tests from TopSortTest 44: [ RUN ] TopSortTest.WorksOnEmptyIdef 44: [ OK ] TopSortTest.WorksOnEmptyIdef (0 ms) 44: [ RUN ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction 44: [ OK ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction (0 ms) 44: [ RUN ] TopSortTest.WorksOnIdefWithPerturbedInteractions 44: [ OK ] TopSortTest.WorksOnIdefWithPerturbedInteractions (0 ms) 44: [ RUN ] TopSortTest.SortsIdefWithPerturbedInteractions 44: [ OK ] TopSortTest.SortsIdefWithPerturbedInteractions (0 ms) 44: [ RUN ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions 44: [ OK ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions (0 ms) 44: [----------] 5 tests from TopSortTest (0 ms total) 44: 44: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 (4 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 (2 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 (2 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 (1 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 (2 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 (1 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 (4 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 (1 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 (1 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 (2 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 (2 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 (5 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 (1 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 (2 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 (1 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 (1 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 (1 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 (1 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 (2 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 (3 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 (1 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 (1 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 (1 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 (1 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 (4 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 (0 ms) 44: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest (138 ms total) 44: 44: [----------] Global test environment tear-down 44: [==========] 153 tests from 10 test suites ran. (172 ms total) 44: [ PASSED ] 153 tests. 44: 44: YOU HAVE 1 DISABLED TEST 44: 44/87 Test #44: TopologyTest .............................. Passed 0.20 sec test 45 Start 45: PullTest 45: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/pull-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/PullTest.xml" 45: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pulling/tests 45: Test timeout computed to be: 30 45: [==========] Running 10 tests from 1 test suite. 45: [----------] Global test environment set-up. 45: [----------] 10 tests from PullTest 45: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 45: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) 45: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 45: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 45: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 45: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 45: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 45: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 45: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 45: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 45: [ RUN ] PullTest.TransformationCoordSimple 45: [ OK ] PullTest.TransformationCoordSimple (5 ms) 45: [ RUN ] PullTest.TransformationCoordAdvanced 45: [ OK ] PullTest.TransformationCoordAdvanced (0 ms) 45: [ RUN ] PullTest.TransformationCoordTime 45: [ OK ] PullTest.TransformationCoordTime (0 ms) 45: [ RUN ] PullTest.TransformationCoordTimeNotAllowed 45: [ OK ] PullTest.TransformationCoordTimeNotAllowed (0 ms) 45: [ RUN ] PullTest.TransformationCoordDummyExpression 45: [ OK ] PullTest.TransformationCoordDummyExpression (0 ms) 45: [----------] 10 tests from PullTest (6 ms total) 45: 45: [----------] Global test environment tear-down 45: [==========] 10 tests from 1 test suite ran. (6 ms total) 45: [ PASSED ] 10 tests. 45/87 Test #45: PullTest .................................. Passed 0.03 sec test 46 Start 46: SimdUnitTests 46: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/simd-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/SimdUnitTests.xml" 46: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/simd/tests 46: Test timeout computed to be: 30 46: [==========] Running 288 tests from 22 test suites. 46: [----------] Global test environment set-up. 46: [----------] 9 tests from SimdBootstrapTest 46: [ RUN ] SimdBootstrapTest.loadStore 46: [ OK ] SimdBootstrapTest.loadStore (0 ms) 46: [ RUN ] SimdBootstrapTest.loadU 46: [ OK ] SimdBootstrapTest.loadU (0 ms) 46: [ RUN ] SimdBootstrapTest.storeU 46: [ OK ] SimdBootstrapTest.storeU (0 ms) 46: [ RUN ] SimdBootstrapTest.loadStoreI 46: [ OK ] SimdBootstrapTest.loadStoreI (0 ms) 46: [ RUN ] SimdBootstrapTest.loadUI 46: [ OK ] SimdBootstrapTest.loadUI (0 ms) 46: [ RUN ] SimdBootstrapTest.storeUI 46: [ OK ] SimdBootstrapTest.storeUI (0 ms) 46: [ RUN ] SimdBootstrapTest.simd4LoadStore 46: [ OK ] SimdBootstrapTest.simd4LoadStore (0 ms) 46: [ RUN ] SimdBootstrapTest.simd4LoadU 46: [ OK ] SimdBootstrapTest.simd4LoadU (0 ms) 46: [ RUN ] SimdBootstrapTest.simd4StoreU 46: [ OK ] SimdBootstrapTest.simd4StoreU (0 ms) 46: [----------] 9 tests from SimdBootstrapTest (0 ms total) 46: 46: [----------] 41 tests from SimdScalarTest 46: [ RUN ] SimdScalarTest.load 46: [ OK ] SimdScalarTest.load (0 ms) 46: [ RUN ] SimdScalarTest.loadU 46: [ OK ] SimdScalarTest.loadU (0 ms) 46: [ RUN ] SimdScalarTest.store 46: [ OK ] SimdScalarTest.store (0 ms) 46: [ RUN ] SimdScalarTest.storeU 46: [ OK ] SimdScalarTest.storeU (0 ms) 46: [ RUN ] SimdScalarTest.setZero 46: [ OK ] SimdScalarTest.setZero (0 ms) 46: [ RUN ] SimdScalarTest.andNot 46: [ OK ] SimdScalarTest.andNot (0 ms) 46: [ RUN ] SimdScalarTest.fma 46: [ OK ] SimdScalarTest.fma (0 ms) 46: [ RUN ] SimdScalarTest.fms 46: [ OK ] SimdScalarTest.fms (0 ms) 46: [ RUN ] SimdScalarTest.fnma 46: [ OK ] SimdScalarTest.fnma (0 ms) 46: [ RUN ] SimdScalarTest.fnms 46: [ OK ] SimdScalarTest.fnms (0 ms) 46: [ RUN ] SimdScalarTest.maskAdd 46: [ OK ] SimdScalarTest.maskAdd (0 ms) 46: [ RUN ] SimdScalarTest.maskzMul 46: [ OK ] SimdScalarTest.maskzMul (0 ms) 46: [ RUN ] SimdScalarTest.maskzFma 46: [ OK ] SimdScalarTest.maskzFma (0 ms) 46: [ RUN ] SimdScalarTest.abs 46: [ OK ] SimdScalarTest.abs (0 ms) 46: [ RUN ] SimdScalarTest.max 46: [ OK ] SimdScalarTest.max (0 ms) 46: [ RUN ] SimdScalarTest.min 46: [ OK ] SimdScalarTest.min (0 ms) 46: [ RUN ] SimdScalarTest.round 46: [ OK ] SimdScalarTest.round (0 ms) 46: [ RUN ] SimdScalarTest.trunc 46: [ OK ] SimdScalarTest.trunc (0 ms) 46: [ RUN ] SimdScalarTest.reduce 46: [ OK ] SimdScalarTest.reduce (0 ms) 46: [ RUN ] SimdScalarTest.testBits 46: [ OK ] SimdScalarTest.testBits (0 ms) 46: [ RUN ] SimdScalarTest.anyTrue 46: [ OK ] SimdScalarTest.anyTrue (0 ms) 46: [ RUN ] SimdScalarTest.selectByMask 46: [ OK ] SimdScalarTest.selectByMask (0 ms) 46: [ RUN ] SimdScalarTest.selectByNotMask 46: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 46: [ RUN ] SimdScalarTest.blend 46: [ OK ] SimdScalarTest.blend (0 ms) 46: [ RUN ] SimdScalarTest.cvtR2I 46: [ OK ] SimdScalarTest.cvtR2I (0 ms) 46: [ RUN ] SimdScalarTest.cvttR2I 46: [ OK ] SimdScalarTest.cvttR2I (0 ms) 46: [ RUN ] SimdScalarTest.cvtI2R 46: [ OK ] SimdScalarTest.cvtI2R (0 ms) 46: [ RUN ] SimdScalarTest.cvtF2D 46: [ OK ] SimdScalarTest.cvtF2D (0 ms) 46: [ RUN ] SimdScalarTest.cvtD2D 46: [ OK ] SimdScalarTest.cvtD2D (0 ms) 46: [ RUN ] SimdScalarTest.loadI 46: [ OK ] SimdScalarTest.loadI (0 ms) 46: [ RUN ] SimdScalarTest.loadUI 46: [ OK ] SimdScalarTest.loadUI (0 ms) 46: [ RUN ] SimdScalarTest.storeI 46: [ OK ] SimdScalarTest.storeI (0 ms) 46: [ RUN ] SimdScalarTest.storeUI 46: [ OK ] SimdScalarTest.storeUI (0 ms) 46: [ RUN ] SimdScalarTest.andNotI 46: [ OK ] SimdScalarTest.andNotI (0 ms) 46: [ RUN ] SimdScalarTest.testBitsI 46: [ OK ] SimdScalarTest.testBitsI (0 ms) 46: [ RUN ] SimdScalarTest.selectByMaskI 46: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 46: [ RUN ] SimdScalarTest.selectByNotMaskI 46: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 46: [ RUN ] SimdScalarTest.blendI 46: [ OK ] SimdScalarTest.blendI (0 ms) 46: [ RUN ] SimdScalarTest.cvtB2IB 46: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 46: [ RUN ] SimdScalarTest.cvtIB2B 46: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 46: [ RUN ] SimdScalarTest.expandScalarsToTriplets 46: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 46: [----------] 41 tests from SimdScalarTest (0 ms total) 46: 46: [----------] 8 tests from SimdScalarUtilTest 46: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 46: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 46: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 46: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 46: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 46: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 46: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 46: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 46: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 46: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 46: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 46: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 46: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 46: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 46: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 46: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 46: [----------] 8 tests from SimdScalarUtilTest (0 ms total) 46: 46: [----------] 37 tests from SimdScalarMathTest 46: [ RUN ] SimdScalarMathTest.copysign 46: [ OK ] SimdScalarMathTest.copysign (0 ms) 46: [ RUN ] SimdScalarMathTest.invsqrtPair 46: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 46: [ RUN ] SimdScalarMathTest.inv 46: [ OK ] SimdScalarMathTest.inv (0 ms) 46: [ RUN ] SimdScalarMathTest.maskzInvsqrt 46: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 46: [ RUN ] SimdScalarMathTest.log 46: [ OK ] SimdScalarMathTest.log (0 ms) 46: [ RUN ] SimdScalarMathTest.exp2 46: [ OK ] SimdScalarMathTest.exp2 (0 ms) 46: [ RUN ] SimdScalarMathTest.exp 46: [ OK ] SimdScalarMathTest.exp (0 ms) 46: [ RUN ] SimdScalarMathTest.erf 46: [ OK ] SimdScalarMathTest.erf (0 ms) 46: [ RUN ] SimdScalarMathTest.erfc 46: [ OK ] SimdScalarMathTest.erfc (0 ms) 46: [ RUN ] SimdScalarMathTest.sincos 46: [ OK ] SimdScalarMathTest.sincos (0 ms) 46: [ RUN ] SimdScalarMathTest.sin 46: [ OK ] SimdScalarMathTest.sin (0 ms) 46: [ RUN ] SimdScalarMathTest.cos 46: [ OK ] SimdScalarMathTest.cos (0 ms) 46: [ RUN ] SimdScalarMathTest.tan 46: [ OK ] SimdScalarMathTest.tan (0 ms) 46: [ RUN ] SimdScalarMathTest.asin 46: [ OK ] SimdScalarMathTest.asin (0 ms) 46: [ RUN ] SimdScalarMathTest.acos 46: [ OK ] SimdScalarMathTest.acos (0 ms) 46: [ RUN ] SimdScalarMathTest.atan 46: [ OK ] SimdScalarMathTest.atan (0 ms) 46: [ RUN ] SimdScalarMathTest.atan2 46: [ OK ] SimdScalarMathTest.atan2 (0 ms) 46: [ RUN ] SimdScalarMathTest.pmeForceCorrection 46: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 46: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 46: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 46: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 46: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.invSingleAccuracy 46: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 46: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.logSingleAccuracy 46: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 46: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.expSingleAccuracy 46: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 46: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 46: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 46: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 46: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 46: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 46: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 46: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 46: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 46: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 46: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 46: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 46: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 46: [----------] 37 tests from SimdScalarMathTest (0 ms total) 46: 46: [----------] 1 test from SimdTest 46: [ RUN ] SimdTest.GmxAligned 46: [ OK ] SimdTest.GmxAligned (0 ms) 46: [----------] 1 test from SimdTest (0 ms total) 46: 46: [----------] 42 tests from SimdFloatingpointTest 46: [ RUN ] SimdFloatingpointTest.setZero 46: [ OK ] SimdFloatingpointTest.setZero (0 ms) 46: [ RUN ] SimdFloatingpointTest.set 46: [ OK ] SimdFloatingpointTest.set (0 ms) 46: [ RUN ] SimdFloatingpointTest.add 46: [ OK ] SimdFloatingpointTest.add (0 ms) 46: [ RUN ] SimdFloatingpointTest.maskAdd 46: [ OK ] SimdFloatingpointTest.maskAdd (0 ms) 46: [ RUN ] SimdFloatingpointTest.sub 46: [ OK ] SimdFloatingpointTest.sub (0 ms) 46: [ RUN ] SimdFloatingpointTest.mul 46: [ OK ] SimdFloatingpointTest.mul (0 ms) 46: [ RUN ] SimdFloatingpointTest.maskzMul 46: [ OK ] SimdFloatingpointTest.maskzMul (0 ms) 46: [ RUN ] SimdFloatingpointTest.fma 46: [ OK ] SimdFloatingpointTest.fma (0 ms) 46: [ RUN ] SimdFloatingpointTest.maskzFma 46: [ OK ] SimdFloatingpointTest.maskzFma (0 ms) 46: [ RUN ] SimdFloatingpointTest.fms 46: [ OK ] SimdFloatingpointTest.fms (0 ms) 46: [ RUN ] SimdFloatingpointTest.fnma 46: [ OK ] SimdFloatingpointTest.fnma (0 ms) 46: [ RUN ] SimdFloatingpointTest.fnms 46: [ OK ] SimdFloatingpointTest.fnms (0 ms) 46: [ RUN ] SimdFloatingpointTest.abs 46: [ OK ] SimdFloatingpointTest.abs (0 ms) 46: [ RUN ] SimdFloatingpointTest.neg 46: [ OK ] SimdFloatingpointTest.neg (0 ms) 46: [ RUN ] SimdFloatingpointTest.and 46: [ OK ] SimdFloatingpointTest.and (0 ms) 46: [ RUN ] SimdFloatingpointTest.or 46: [ OK ] SimdFloatingpointTest.or (0 ms) 46: [ RUN ] SimdFloatingpointTest.xor 46: [ OK ] SimdFloatingpointTest.xor (0 ms) 46: [ RUN ] SimdFloatingpointTest.andNot 46: [ OK ] SimdFloatingpointTest.andNot (0 ms) 46: [ RUN ] SimdFloatingpointTest.max 46: [ OK ] SimdFloatingpointTest.max (0 ms) 46: [ RUN ] SimdFloatingpointTest.min 46: [ OK ] SimdFloatingpointTest.min (0 ms) 46: [ RUN ] SimdFloatingpointTest.round 46: [ OK ] SimdFloatingpointTest.round (0 ms) 46: [ RUN ] SimdFloatingpointTest.roundMode 46: [ OK ] SimdFloatingpointTest.roundMode (0 ms) 46: [ RUN ] SimdFloatingpointTest.trunc 46: [ OK ] SimdFloatingpointTest.trunc (0 ms) 46: [ RUN ] SimdFloatingpointTest.frexp 46: [ OK ] SimdFloatingpointTest.frexp (0 ms) 46: [ RUN ] SimdFloatingpointTest.ldexp 46: [ OK ] SimdFloatingpointTest.ldexp (0 ms) 46: [ RUN ] SimdFloatingpointTest.rsqrt 46: [ OK ] SimdFloatingpointTest.rsqrt (0 ms) 46: [ RUN ] SimdFloatingpointTest.maskzRsqrt 46: [ OK ] SimdFloatingpointTest.maskzRsqrt (0 ms) 46: [ RUN ] SimdFloatingpointTest.rcp 46: [ OK ] SimdFloatingpointTest.rcp (0 ms) 46: [ RUN ] SimdFloatingpointTest.maskzRcp 46: [ OK ] SimdFloatingpointTest.maskzRcp (0 ms) 46: [ RUN ] SimdFloatingpointTest.cmpEqAndSelectByMask 46: [ OK ] SimdFloatingpointTest.cmpEqAndSelectByMask (0 ms) 46: [ RUN ] SimdFloatingpointTest.selectByNotMask 46: [ OK ] SimdFloatingpointTest.selectByNotMask (0 ms) 46: [ RUN ] SimdFloatingpointTest.cmpNe 46: [ OK ] SimdFloatingpointTest.cmpNe (0 ms) 46: [ RUN ] SimdFloatingpointTest.cmpLe 46: [ OK ] SimdFloatingpointTest.cmpLe (0 ms) 46: [ RUN ] SimdFloatingpointTest.cmpLt 46: [ OK ] SimdFloatingpointTest.cmpLt (0 ms) 46: [ RUN ] SimdFloatingpointTest.testBits 46: [ OK ] SimdFloatingpointTest.testBits (0 ms) 46: [ RUN ] SimdFloatingpointTest.andB 46: [ OK ] SimdFloatingpointTest.andB (0 ms) 46: [ RUN ] SimdFloatingpointTest.orB 46: [ OK ] SimdFloatingpointTest.orB (0 ms) 46: [ RUN ] SimdFloatingpointTest.anyTrueB 46: [ OK ] SimdFloatingpointTest.anyTrueB (0 ms) 46: [ RUN ] SimdFloatingpointTest.blend 46: [ OK ] SimdFloatingpointTest.blend (0 ms) 46: [ RUN ] SimdFloatingpointTest.reduce 46: [ OK ] SimdFloatingpointTest.reduce (0 ms) 46: [ RUN ] SimdFloatingpointTest.cvtFloat2Double 46: [ OK ] SimdFloatingpointTest.cvtFloat2Double (0 ms) 46: [ RUN ] SimdFloatingpointTest.cvtDouble2Float 46: [ OK ] SimdFloatingpointTest.cvtDouble2Float (0 ms) 46: [----------] 42 tests from SimdFloatingpointTest (0 ms total) 46: 46: [----------] 16 tests from SimdFloatingpointUtilTest 46: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose4 46: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose4 (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose2 46: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose2 (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 46: [ OK ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.transposeScatterStoreU3 46: [ OK ] SimdFloatingpointUtilTest.transposeScatterStoreU3 (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3 46: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3 (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping 46: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3 46: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3 (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping 46: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.expandScalarsToTriplets 46: [ OK ] SimdFloatingpointUtilTest.expandScalarsToTriplets (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 46: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 46: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 46: [ OK ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.reduceIncr4Sum 46: [ OK ] SimdFloatingpointUtilTest.reduceIncr4Sum (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.loadUNDuplicate4 46: [ OK ] SimdFloatingpointUtilTest.loadUNDuplicate4 (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.load4DuplicateN 46: [ OK ] SimdFloatingpointUtilTest.load4DuplicateN (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.loadU4NOffset 46: [ OK ] SimdFloatingpointUtilTest.loadU4NOffset (0 ms) 46: [----------] 16 tests from SimdFloatingpointUtilTest (0 ms total) 46: 46: [----------] 23 tests from SimdIntegerTest 46: [ RUN ] SimdIntegerTest.setZero 46: [ OK ] SimdIntegerTest.setZero (0 ms) 46: [ RUN ] SimdIntegerTest.set 46: [ OK ] SimdIntegerTest.set (0 ms) 46: [ RUN ] SimdIntegerTest.add 46: [ OK ] SimdIntegerTest.add (0 ms) 46: [ RUN ] SimdIntegerTest.sub 46: [ OK ] SimdIntegerTest.sub (0 ms) 46: [ RUN ] SimdIntegerTest.mul 46: [ OK ] SimdIntegerTest.mul (0 ms) 46: [ RUN ] SimdIntegerTest.and 46: [ OK ] SimdIntegerTest.and (0 ms) 46: [ RUN ] SimdIntegerTest.andNot 46: [ OK ] SimdIntegerTest.andNot (0 ms) 46: [ RUN ] SimdIntegerTest.or 46: [ OK ] SimdIntegerTest.or (0 ms) 46: [ RUN ] SimdIntegerTest.xor 46: [ OK ] SimdIntegerTest.xor (0 ms) 46: [ RUN ] SimdIntegerTest.extract 46: [ OK ] SimdIntegerTest.extract (0 ms) 46: [ RUN ] SimdIntegerTest.cvtR2I 46: [ OK ] SimdIntegerTest.cvtR2I (0 ms) 46: [ RUN ] SimdIntegerTest.cvttR2I 46: [ OK ] SimdIntegerTest.cvttR2I (0 ms) 46: [ RUN ] SimdIntegerTest.cvtI2R 46: [ OK ] SimdIntegerTest.cvtI2R (0 ms) 46: [ RUN ] SimdIntegerTest.cmpEqAndSelectMask 46: [ OK ] SimdIntegerTest.cmpEqAndSelectMask (0 ms) 46: [ RUN ] SimdIntegerTest.cmpEqAndSelectNotMask 46: [ OK ] SimdIntegerTest.cmpEqAndSelectNotMask (0 ms) 46: [ RUN ] SimdIntegerTest.cmpLt 46: [ OK ] SimdIntegerTest.cmpLt (0 ms) 46: [ RUN ] SimdIntegerTest.testBits 46: [ OK ] SimdIntegerTest.testBits (0 ms) 46: [ RUN ] SimdIntegerTest.andB 46: [ OK ] SimdIntegerTest.andB (0 ms) 46: [ RUN ] SimdIntegerTest.orB 46: [ OK ] SimdIntegerTest.orB (0 ms) 46: [ RUN ] SimdIntegerTest.anyTrue 46: [ OK ] SimdIntegerTest.anyTrue (0 ms) 46: [ RUN ] SimdIntegerTest.blend 46: [ OK ] SimdIntegerTest.blend (0 ms) 46: [ RUN ] SimdIntegerTest.cvtB2IB 46: [ OK ] SimdIntegerTest.cvtB2IB (0 ms) 46: [ RUN ] SimdIntegerTest.cvtIB2B 46: [ OK ] SimdIntegerTest.cvtIB2B (0 ms) 46: [----------] 23 tests from SimdIntegerTest (0 ms total) 46: 46: [----------] 56 tests from SimdMathTest 46: [ RUN ] SimdMathTest.generateTestPointsFloat 46: [ OK ] SimdMathTest.generateTestPointsFloat (3 ms) 46: [ RUN ] SimdMathTest.copysign 46: [ OK ] SimdMathTest.copysign (0 ms) 46: [ RUN ] SimdMathTest.invsqrt 46: [ OK ] SimdMathTest.invsqrt (0 ms) 46: [ RUN ] SimdMathTest.maskzInvsqrt 46: [ OK ] SimdMathTest.maskzInvsqrt (0 ms) 46: [ RUN ] SimdMathTest.invsqrtPair 46: [ OK ] SimdMathTest.invsqrtPair (0 ms) 46: [ RUN ] SimdMathTest.sqrt 46: [ OK ] SimdMathTest.sqrt (0 ms) 46: [ RUN ] SimdMathTest.sqrtUnsafe 46: [ OK ] SimdMathTest.sqrtUnsafe (0 ms) 46: [ RUN ] SimdMathTest.inv 46: [ OK ] SimdMathTest.inv (0 ms) 46: [ RUN ] SimdMathTest.maskzInv 46: [ OK ] SimdMathTest.maskzInv (0 ms) 46: [ RUN ] SimdMathTest.cbrt 46: [ OK ] SimdMathTest.cbrt (0 ms) 46: [ RUN ] SimdMathTest.invcbrt 46: [ OK ] SimdMathTest.invcbrt (0 ms) 46: [ RUN ] SimdMathTest.log2 46: [ OK ] SimdMathTest.log2 (0 ms) 46: [ RUN ] SimdMathTest.log 46: [ OK ] SimdMathTest.log (0 ms) 46: [ RUN ] SimdMathTest.exp2 46: [ OK ] SimdMathTest.exp2 (0 ms) 46: [ RUN ] SimdMathTest.exp2Unsafe 46: [ OK ] SimdMathTest.exp2Unsafe (0 ms) 46: [ RUN ] SimdMathTest.exp 46: [ OK ] SimdMathTest.exp (4 ms) 46: [ RUN ] SimdMathTest.expUnsafe 46: [ OK ] SimdMathTest.expUnsafe (0 ms) 46: [ RUN ] SimdMathTest.pow 46: [ OK ] SimdMathTest.pow (0 ms) 46: [ RUN ] SimdMathTest.powUnsafe 46: [ OK ] SimdMathTest.powUnsafe (0 ms) 46: [ RUN ] SimdMathTest.erf 46: [ OK ] SimdMathTest.erf (0 ms) 46: [ RUN ] SimdMathTest.erfc 46: [ OK ] SimdMathTest.erfc (0 ms) 46: [ RUN ] SimdMathTest.sin 46: [ OK ] SimdMathTest.sin (0 ms) 46: [ RUN ] SimdMathTest.cos 46: [ OK ] SimdMathTest.cos (0 ms) 46: [ RUN ] SimdMathTest.tan 46: [ OK ] SimdMathTest.tan (0 ms) 46: [ RUN ] SimdMathTest.asin 46: [ OK ] SimdMathTest.asin (0 ms) 46: [ RUN ] SimdMathTest.acos 46: [ OK ] SimdMathTest.acos (0 ms) 46: [ RUN ] SimdMathTest.atan 46: [ OK ] SimdMathTest.atan (0 ms) 46: [ RUN ] SimdMathTest.atan2 46: [ OK ] SimdMathTest.atan2 (0 ms) 46: [ RUN ] SimdMathTest.pmeForceCorrection 46: [ OK ] SimdMathTest.pmeForceCorrection (0 ms) 46: [ RUN ] SimdMathTest.pmePotentialCorrection 46: [ OK ] SimdMathTest.pmePotentialCorrection (4 ms) 46: [ RUN ] SimdMathTest.invsqrtSingleAccuracy 46: [ OK ] SimdMathTest.invsqrtSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.invsqrtPairSingleAccuracy 46: [ OK ] SimdMathTest.invsqrtPairSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.sqrtSingleAccuracy 46: [ OK ] SimdMathTest.sqrtSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.sqrtSingleAccuracyUnsafe 46: [ OK ] SimdMathTest.sqrtSingleAccuracyUnsafe (0 ms) 46: [ RUN ] SimdMathTest.invSingleAccuracy 46: [ OK ] SimdMathTest.invSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.cbrtSingleAccuracy 46: [ OK ] SimdMathTest.cbrtSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.invcbrtSingleAccuracy 46: [ OK ] SimdMathTest.invcbrtSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.log2SingleAccuracy 46: [ OK ] SimdMathTest.log2SingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.logSingleAccuracy 46: [ OK ] SimdMathTest.logSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.exp2SingleAccuracy 46: [ OK ] SimdMathTest.exp2SingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe 46: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (0 ms) 46: [ RUN ] SimdMathTest.expSingleAccuracy 46: [ OK ] SimdMathTest.expSingleAccuracy (4 ms) 46: [ RUN ] SimdMathTest.expSingleAccuracyUnsafe 46: [ OK ] SimdMathTest.expSingleAccuracyUnsafe (0 ms) 46: [ RUN ] SimdMathTest.powSingleAccuracy 46: [ OK ] SimdMathTest.powSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.powSingleAccuracyUnsafe 46: [ OK ] SimdMathTest.powSingleAccuracyUnsafe (0 ms) 46: [ RUN ] SimdMathTest.erfSingleAccuracy 46: [ OK ] SimdMathTest.erfSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.erfcSingleAccuracy 46: [ OK ] SimdMathTest.erfcSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.sinSingleAccuracy 46: [ OK ] SimdMathTest.sinSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.cosSingleAccuracy 46: [ OK ] SimdMathTest.cosSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.tanSingleAccuracy 46: [ OK ] SimdMathTest.tanSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.asinSingleAccuracy 46: [ OK ] SimdMathTest.asinSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.acosSingleAccuracy 46: [ OK ] SimdMathTest.acosSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.atanSingleAccuracy 46: [ OK ] SimdMathTest.atanSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.atan2SingleAccuracy 46: [ OK ] SimdMathTest.atan2SingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.pmeForceCorrectionSingleAccuracy 46: [ OK ] SimdMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy 46: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 46: [----------] 56 tests from SimdMathTest (34 ms total) 46: 46: [----------] 1 test from EmptyArrayRefTest 46: [ RUN ] EmptyArrayRefTest.IsEmpty 46: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 46: [----------] 1 test from EmptyArrayRefTest (0 ms total) 46: 46: [----------] 3 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 46: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 46: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 46: [ RUN ] ArrayRefTest/0.ConstructFromArrayRefWorks 46: [ OK ] ArrayRefTest/0.ConstructFromArrayRefWorks (0 ms) 46: [ RUN ] ArrayRefTest/0.ConstructFromArrayWorks 46: [ OK ] ArrayRefTest/0.ConstructFromArrayWorks (0 ms) 46: [----------] 3 tests from ArrayRefTest/0 (0 ms total) 46: 46: [----------] 3 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 46: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 46: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 46: [ RUN ] ArrayRefTest/1.ConstructFromArrayRefWorks 46: [ OK ] ArrayRefTest/1.ConstructFromArrayRefWorks (0 ms) 46: [ RUN ] ArrayRefTest/1.ConstructFromArrayWorks 46: [ OK ] ArrayRefTest/1.ConstructFromArrayWorks (0 ms) 46: [----------] 3 tests from ArrayRefTest/1 (0 ms total) 46: 46: [----------] 3 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 46: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 46: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 46: [ RUN ] ArrayRefTest/2.ConstructFromArrayRefWorks 46: [ OK ] ArrayRefTest/2.ConstructFromArrayRefWorks (0 ms) 46: [ RUN ] ArrayRefTest/2.ConstructFromArrayWorks 46: [ OK ] ArrayRefTest/2.ConstructFromArrayWorks (0 ms) 46: [----------] 3 tests from ArrayRefTest/2 (0 ms total) 46: 46: [----------] 3 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 46: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 46: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 46: [ RUN ] ArrayRefTest/3.ConstructFromArrayRefWorks 46: [ OK ] ArrayRefTest/3.ConstructFromArrayRefWorks (0 ms) 46: [ RUN ] ArrayRefTest/3.ConstructFromArrayWorks 46: [ OK ] ArrayRefTest/3.ConstructFromArrayWorks (0 ms) 46: [----------] 3 tests from ArrayRefTest/3 (0 ms total) 46: 46: [----------] 1 test from ArrayRefReadWriteTest/0, where TypeParam = gmx::ArrayRef 46: [ RUN ] ArrayRefReadWriteTest/0.Assignment 46: [ OK ] ArrayRefReadWriteTest/0.Assignment (0 ms) 46: [----------] 1 test from ArrayRefReadWriteTest/0 (0 ms total) 46: 46: [----------] 1 test from ArrayRefReadWriteTest/1, where TypeParam = gmx::ArrayRef 46: [ RUN ] ArrayRefReadWriteTest/1.Assignment 46: [ OK ] ArrayRefReadWriteTest/1.Assignment (0 ms) 46: [----------] 1 test from ArrayRefReadWriteTest/1 (0 ms total) 46: 46: [----------] 1 test from ArrayRefArithmeticTest/0, where TypeParam = gmx::ArrayRef 46: [ RUN ] ArrayRefArithmeticTest/0.Basic 46: [ OK ] ArrayRefArithmeticTest/0.Basic (0 ms) 46: [----------] 1 test from ArrayRefArithmeticTest/0 (0 ms total) 46: 46: [----------] 1 test from ArrayRefArithmeticTest/1, where TypeParam = gmx::ArrayRef 46: [ RUN ] ArrayRefArithmeticTest/1.Basic 46: [ OK ] ArrayRefArithmeticTest/1.Basic (0 ms) 46: [----------] 1 test from ArrayRefArithmeticTest/1 (0 ms total) 46: 46: [----------] 3 tests from SimdVectorOperationsTest 46: [ RUN ] SimdVectorOperationsTest.iprod 46: [ OK ] SimdVectorOperationsTest.iprod (0 ms) 46: [ RUN ] SimdVectorOperationsTest.norm2 46: [ OK ] SimdVectorOperationsTest.norm2 (0 ms) 46: [ RUN ] SimdVectorOperationsTest.cprod 46: [ OK ] SimdVectorOperationsTest.cprod (0 ms) 46: [----------] 3 tests from SimdVectorOperationsTest (0 ms total) 46: 46: [----------] 32 tests from Simd4FloatingpointTest 46: [ RUN ] Simd4FloatingpointTest.setZero 46: [ OK ] Simd4FloatingpointTest.setZero (0 ms) 46: [ RUN ] Simd4FloatingpointTest.set 46: [ OK ] Simd4FloatingpointTest.set (0 ms) 46: [ RUN ] Simd4FloatingpointTest.add 46: [ OK ] Simd4FloatingpointTest.add (0 ms) 46: [ RUN ] Simd4FloatingpointTest.sub 46: [ OK ] Simd4FloatingpointTest.sub (0 ms) 46: [ RUN ] Simd4FloatingpointTest.mul 46: [ OK ] Simd4FloatingpointTest.mul (0 ms) 46: [ RUN ] Simd4FloatingpointTest.fma 46: [ OK ] Simd4FloatingpointTest.fma (0 ms) 46: [ RUN ] Simd4FloatingpointTest.fms 46: [ OK ] Simd4FloatingpointTest.fms (0 ms) 46: [ RUN ] Simd4FloatingpointTest.fnma 46: [ OK ] Simd4FloatingpointTest.fnma (0 ms) 46: [ RUN ] Simd4FloatingpointTest.fnms 46: [ OK ] Simd4FloatingpointTest.fnms (0 ms) 46: [ RUN ] Simd4FloatingpointTest.abs 46: [ OK ] Simd4FloatingpointTest.abs (0 ms) 46: [ RUN ] Simd4FloatingpointTest.neg 46: [ OK ] Simd4FloatingpointTest.neg (0 ms) 46: [ RUN ] Simd4FloatingpointTest.and 46: [ OK ] Simd4FloatingpointTest.and (0 ms) 46: [ RUN ] Simd4FloatingpointTest.or 46: [ OK ] Simd4FloatingpointTest.or (0 ms) 46: [ RUN ] Simd4FloatingpointTest.xor 46: [ OK ] Simd4FloatingpointTest.xor (0 ms) 46: [ RUN ] Simd4FloatingpointTest.andNot 46: [ OK ] Simd4FloatingpointTest.andNot (0 ms) 46: [ RUN ] Simd4FloatingpointTest.max 46: [ OK ] Simd4FloatingpointTest.max (0 ms) 46: [ RUN ] Simd4FloatingpointTest.min 46: [ OK ] Simd4FloatingpointTest.min (0 ms) 46: [ RUN ] Simd4FloatingpointTest.round 46: [ OK ] Simd4FloatingpointTest.round (0 ms) 46: [ RUN ] Simd4FloatingpointTest.trunc 46: [ OK ] Simd4FloatingpointTest.trunc (0 ms) 46: [ RUN ] Simd4FloatingpointTest.gmxSimd4RsqrtR 46: [ OK ] Simd4FloatingpointTest.gmxSimd4RsqrtR (0 ms) 46: [ RUN ] Simd4FloatingpointTest.cmpEqAndSelectByMask 46: [ OK ] Simd4FloatingpointTest.cmpEqAndSelectByMask (0 ms) 46: [ RUN ] Simd4FloatingpointTest.selectByNotMask 46: [ OK ] Simd4FloatingpointTest.selectByNotMask (0 ms) 46: [ RUN ] Simd4FloatingpointTest.cmpNe 46: [ OK ] Simd4FloatingpointTest.cmpNe (0 ms) 46: [ RUN ] Simd4FloatingpointTest.cmpLe 46: [ OK ] Simd4FloatingpointTest.cmpLe (0 ms) 46: [ RUN ] Simd4FloatingpointTest.cmpLt 46: [ OK ] Simd4FloatingpointTest.cmpLt (0 ms) 46: [ RUN ] Simd4FloatingpointTest.andB 46: [ OK ] Simd4FloatingpointTest.andB (0 ms) 46: [ RUN ] Simd4FloatingpointTest.orB 46: [ OK ] Simd4FloatingpointTest.orB (0 ms) 46: [ RUN ] Simd4FloatingpointTest.anyTrue 46: [ OK ] Simd4FloatingpointTest.anyTrue (0 ms) 46: [ RUN ] Simd4FloatingpointTest.blend 46: [ OK ] Simd4FloatingpointTest.blend (0 ms) 46: [ RUN ] Simd4FloatingpointTest.reduce 46: [ OK ] Simd4FloatingpointTest.reduce (0 ms) 46: [ RUN ] Simd4FloatingpointTest.dotProduct 46: [ OK ] Simd4FloatingpointTest.dotProduct (0 ms) 46: [ RUN ] Simd4FloatingpointTest.transpose 46: [ OK ] Simd4FloatingpointTest.transpose (0 ms) 46: [----------] 32 tests from Simd4FloatingpointTest (0 ms total) 46: 46: [----------] 2 tests from Simd4MathTest 46: [ RUN ] Simd4MathTest.invsqrt 46: [ OK ] Simd4MathTest.invsqrt (0 ms) 46: [ RUN ] Simd4MathTest.invsqrtSingleAccuracy 46: [ OK ] Simd4MathTest.invsqrtSingleAccuracy (0 ms) 46: [----------] 2 tests from Simd4MathTest (0 ms total) 46: 46: [----------] 1 test from Simd4VectorOperationsTest 46: [ RUN ] Simd4VectorOperationsTest.norm2 46: [ OK ] Simd4VectorOperationsTest.norm2 (0 ms) 46: [----------] 1 test from Simd4VectorOperationsTest (0 ms total) 46: 46: [----------] Global test environment tear-down 46: [==========] 288 tests from 22 test suites ran. (35 ms total) 46: [ PASSED ] 288 tests. 46/87 Test #46: SimdUnitTests ............................. Passed 0.07 sec test 47 Start 47: CompatibilityHelpersTests 47: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/compat-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/CompatibilityHelpersTests.xml" 47: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/compat/tests 47: Test timeout computed to be: 30 47: [==========] Running 9 tests from 6 test suites. 47: [----------] Global test environment set-up. 47: [----------] 4 tests from TemplateMPTest 47: [ RUN ] TemplateMPTest.MpWithIndexInt 47: [ OK ] TemplateMPTest.MpWithIndexInt (0 ms) 47: [ RUN ] TemplateMPTest.MpWithIndexIntBad 47: [ OK ] TemplateMPTest.MpWithIndexIntBad (0 ms) 47: [ RUN ] TemplateMPTest.MpWithIndexBool 47: [ OK ] TemplateMPTest.MpWithIndexBool (0 ms) 47: [ RUN ] TemplateMPTest.MpWithIndexEnum 47: [ OK ] TemplateMPTest.MpWithIndexEnum (0 ms) 47: [----------] 4 tests from TemplateMPTest (0 ms total) 47: 47: [----------] 1 test from NotNullConstruction 47: [ RUN ] NotNullConstruction.Works 47: [ OK ] NotNullConstruction.Works (0 ms) 47: [----------] 1 test from NotNullConstruction (0 ms total) 47: 47: [----------] 1 test from NotNullCasting 47: [ RUN ] NotNullCasting.Works 47: [ OK ] NotNullCasting.Works (0 ms) 47: [----------] 1 test from NotNullCasting (0 ms total) 47: 47: [----------] 1 test from NotNullAssignment 47: [ RUN ] NotNullAssignment.Works 47: [ OK ] NotNullAssignment.Works (0 ms) 47: [----------] 1 test from NotNullAssignment (0 ms total) 47: 47: [----------] 1 test from MakeNotNull 47: [ RUN ] MakeNotNull.Works 47: [ OK ] MakeNotNull.Works (0 ms) 47: [----------] 1 test from MakeNotNull (0 ms total) 47: 47: [----------] 1 test from NotNull 47: [ RUN ] NotNull.WorksInContainers 47: [ OK ] NotNull.WorksInContainers (0 ms) 47: [----------] 1 test from NotNull (0 ms total) 47: 47: [----------] Global test environment tear-down 47: [==========] 9 tests from 6 test suites ran. (0 ms total) 47: [ PASSED ] 9 tests. 47/87 Test #47: CompatibilityHelpersTests ................. Passed 0.03 sec test 48 Start 48: GmxAnaTest 48: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/gmxana-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/GmxAnaTest.xml" 48: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxana/tests 48: Test timeout computed to be: 600 48: [==========] Running 31 tests from 4 test suites. 48: [----------] Global test environment set-up. 48: [----------] 7 tests from Entropy 48: [ RUN ] Entropy.Schlitter_300_NoLinear 48: [ OK ] Entropy.Schlitter_300_NoLinear (0 ms) 48: [ RUN ] Entropy.Schlitter_300_Linear 48: [ OK ] Entropy.Schlitter_300_Linear (0 ms) 48: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear 48: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms) 48: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear 48: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms) 48: [ RUN ] Entropy.QuasiHarmonic_200_Linear 48: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms) 48: [ RUN ] Entropy.EntropyCompare_200_Linear 48: [ OK ] Entropy.EntropyCompare_200_Linear (0 ms) 48: [ RUN ] Entropy.EntropyCompare_300_Linear 48: [ OK ] Entropy.EntropyCompare_300_Linear (0 ms) 48: [----------] 7 tests from Entropy (4 ms total) 48: 48: [----------] 2 tests from GmxChiTest 48: [ RUN ] GmxChiTest.gmxchiWorksWithAll 48: Analyzing from residue 1 to residue 11 48: 10 residues with dihedrals found 48: 46 dihedrals found 48: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 48: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 48: j after resetting (nr. active dihedrals) = 46 48: Printing phiLYS1.xvg Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing phiGLU7.xvg Printing phiLEU8.xvg Printing phiALA9.xvg Printing phiALA10.xvg Printing psiLYS1.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing psiGLU7.xvg Printing psiLEU8.xvg Printing psiALA9.xvg Printing psiALA10.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing omegaGLU7.xvg Printing omegaLEU8.xvg Printing omegaALA9.xvg Printing omegaALA10.xvg Printing chi1LYS1.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi1GLU7.xvg Printing chi1LEU8.xvg Printing chi2LYS1.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi2GLU7.xvg Printing chi2LEU8.xvg Printing chi3LYS1.xvg Printing chi3ARG5.xvg Printing chi3GLU7.xvg Printing chi4LYS1.xvg Printing chi4ARG5.xvg 48: Now calculating transitions... 48: Total number of transitions: 0 48: Now printing out transitions and OPs... 48: Now printing out rotamer occupancies... 48: Now calculating Chi product trajectories... 48: Printing chiproductLYS1.xvg and histo-chiprodLYS1.xvg Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg Printing chiproductGLU7.xvg and histo-chiprodGLU7.xvg Printing chiproductLEU8.xvg and histo-chiprodLEU8.xvg 48: [ OK ] GmxChiTest.gmxchiWorksWithAll (705 ms) 48: [ RUN ] GmxChiTest.gmxchiWorksWithr0AndrN 48: Analyzing from residue 2 to residue 6 48: 5 residues with dihedrals found 48: 23 dihedrals found 48: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 48: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 48: j after resetting (nr. active dihedrals) = 23 48: Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi3ARG5.xvg Printing chi4ARG5.xvg 48: Now calculating transitions... 48: Total number of transitions: 0 48: Now printing out transitions and OPs... 48: Now printing out rotamer occupancies... 48: Now calculating Chi product trajectories... 48: Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg 48: [ OK ] GmxChiTest.gmxchiWorksWithr0AndrN (346 ms) 48: [----------] 2 tests from GmxChiTest (1143 ms total) 48: 48: [----------] 10 tests from MindistTest 48: [ RUN ] MindistTest.mindistWorksWithSingleAtoms 48: Group 0 ( atom1) has 1 elements 48: Group 1 ( atom2) has 1 elements 48: Group 2 ( atom3) has 1 elements 48: Group 3 ( atoms12) has 2 elements 48: Group 4 ( atoms23) has 2 elements 48: Group 5 ( atoms123) has 3 elements 48: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: Selected 0: 'atom1' 48: Selected 1: 'atom2' 48: [ OK ] MindistTest.mindistWorksWithSingleAtoms (8 ms) 48: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms 48: Group 0 ( atom1) has 1 elements 48: Group 1 ( atom2) has 1 elements 48: Group 2 ( atom3) has 1 elements 48: Group 3 ( atoms12) has 2 elements 48: Group 4 ( atoms23) has 2 elements 48: Group 5 ( atoms123) has 3 elements 48: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: Selected 2: 'atom3' 48: Selected 3: 'atoms12' 48: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (3 ms) 48: [ RUN ] MindistTest.mindistDoesNotPickUpContacts 48: Group 0 ( atom1) has 1 elements 48: Group 1 ( atom2) has 1 elements 48: Group 2 ( atom3) has 1 elements 48: Group 3 ( atoms12) has 2 elements 48: Group 4 ( atoms23) has 2 elements 48: Group 5 ( atoms123) has 3 elements 48: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: Selected 0: 'atom1' 48: Selected 1: 'atom2' 48: [ OK ] MindistTest.mindistDoesNotPickUpContacts (1 ms) 48: [ RUN ] MindistTest.mindistPicksUpContacts 48: Group 0 ( atom1) has 1 elements 48: Group 1 ( atom2) has 1 elements 48: Group 2 ( atom3) has 1 elements 48: Group 3 ( atoms12) has 2 elements 48: Group 4 ( atoms23) has 2 elements 48: Group 5 ( atoms123) has 3 elements 48: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: Selected 0: 'atom1' 48: Selected 1: 'atom2' 48: [ OK ] MindistTest.mindistPicksUpContacts (1 ms) 48: [ RUN ] MindistTest.ngWorks 48: Group 0 ( atom1) has 1 elements 48: Group 1 ( atom2) has 1 elements 48: Group 2 ( atom3) has 1 elements 48: Group 3 ( atoms12) has 2 elements 48: Group 4 ( atoms23) has 2 elements 48: Group 5 ( atoms123) has 3 elements 48: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: Selected 0: 'atom1' 48: Selected 1: 'atom2' 48: Selected 2: 'atom3' 48: [ OK ] MindistTest.ngWorks (39 ms) 48: [ RUN ] MindistTest.groupWorks 48: Group 0 ( atom1) has 1 elements 48: Group 1 ( atom2) has 1 elements 48: Group 2 ( atom3) has 1 elements 48: Group 3 ( atoms12) has 2 elements 48: Group 4 ( atoms23) has 2 elements 48: Group 5 ( atoms123) has 3 elements 48: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: Selected 3: 'atoms12' 48: Selected 2: 'atom3' 48: [ OK ] MindistTest.groupWorks (11 ms) 48: [ RUN ] MindistTest.maxDistWorks 48: Group 0 ( atom1) has 1 elements 48: Group 1 ( atom2) has 1 elements 48: Group 2 ( atom3) has 1 elements 48: Group 3 ( atoms12) has 2 elements 48: Group 4 ( atoms23) has 2 elements 48: Group 5 ( atoms123) has 3 elements 48: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: Selected 2: 'atom3' 48: Selected 3: 'atoms12' 48: [ OK ] MindistTest.maxDistWorks (3 ms) 48: [ RUN ] MindistTest.noPbcWorks 48: Group 0 ( atom1) has 1 elements 48: Group 1 ( atom2) has 1 elements 48: Group 2 ( atom3) has 1 elements 48: Group 3 ( atoms12) has 2 elements 48: Group 4 ( atoms23) has 2 elements 48: Group 5 ( atoms123) has 3 elements 48: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: Selected 0: 'atom1' 48: Selected 1: 'atom2' 48: [ OK ] MindistTest.noPbcWorks (5 ms) 48: [ RUN ] MindistTest.resPerTimeWorks 48: Group 0 ( atom1) has 1 elements 48: Group 1 ( atom2) has 1 elements 48: Group 2 ( atom3) has 1 elements 48: Group 3 ( atoms12) has 2 elements 48: Group 4 ( atoms23) has 2 elements 48: Group 5 ( atoms123) has 3 elements 48: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: Selected 3: 'atoms12' 48: Selected 2: 'atom3' 48: [ OK ] MindistTest.resPerTimeWorks (1 ms) 48: [ RUN ] MindistTest.matrixWorks 48: Group 0 ( atom1) has 1 elements 48: Group 1 ( atom2) has 1 elements 48: Group 2 ( atom3) has 1 elements 48: Group 3 ( atoms12) has 2 elements 48: Group 4 ( atoms23) has 2 elements 48: Group 5 ( atoms123) has 3 elements 48: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: Selected 5: 'atoms123' 48: Special case: making distance matrix between all atoms in group atoms123 48: [ OK ] MindistTest.matrixWorks (1 ms) 48: [----------] 10 tests from MindistTest (78 ms total) 48: 48: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: trr version: GMX_trn_file (single precision) 48: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (5 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (6 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 48: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (7 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 48: Reading frame 1 time 1.000 Last frame 1 time 1.000 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (2 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (7 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (8 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frame 0 time 0.000 48: WARNING: If there are molecules in the input trajectory file 48: that are broken across periodic boundaries, they 48: cannot be made whole (or treated as whole) without 48: you providing a run input file. 48: 48: Reading frame 1 time 1.000 Last frame 1 time 1.000 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 (7 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frame 0 time 0.000 48: WARNING: If there are molecules in the input trajectory file 48: that are broken across periodic boundaries, they 48: cannot be made whole (or treated as whole) without 48: you providing a run input file. 48: 48: Reading frame 1 time 1.000 Last frame 1 time 1.000 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 (2 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 48: Reading frame 0 time 0.000 48: WARNING: If there are molecules in the input trajectory file 48: that are broken across periodic boundaries, they 48: cannot be made whole (or treated as whole) without 48: you providing a run input file. 48: 48: Reading frame 1 time 1.000 Last frame 1 time 1.000 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 (4 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 48: WARNING: If there are molecules in the input trajectory file 48: that are broken across periodic boundaries, they 48: cannot be made whole (or treated as whole) without 48: you providing a run input file. 48: 48: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 48: Reading frame 1 time 1.000 Last frame 1 time 1.000 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 (5 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frame 0 time 0.000 48: WARNING: If there are molecules in the input trajectory file 48: that are broken across periodic boundaries, they 48: cannot be made whole (or treated as whole) without 48: you providing a run input file. 48: 48: Reading frame 1 time 1.000 Last frame 1 time 1.000 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 (6 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frame 0 time 0.000 48: WARNING: If there are molecules in the input trajectory file 48: that are broken across periodic boundaries, they 48: cannot be made whole (or treated as whole) without 48: you providing a run input file. 48: 48: Reading frame 1 time 1.000 Last frame 1 time 1.000 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 (2 ms) 48: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj (76 ms total) 48: 48: [----------] Global test environment tear-down 48: [==========] 31 tests from 4 test suites ran. (1302 ms total) 48: [ PASSED ] 31 tests. 48/87 Test #48: GmxAnaTest ................................ Passed 1.35 sec test 49 Start 49: GmxPreprocessTests 49: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/gmxpreprocess-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/GmxPreprocessTests.xml" 49: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests 49: Test timeout computed to be: 1920 49: [==========] Running 138 tests from 13 test suites. 49: [----------] Global test environment set-up. 49: [----------] 4 tests from GenconfTest 49: [ RUN ] GenconfTest.nbox_Works 49: [ OK ] GenconfTest.nbox_Works (6 ms) 49: [ RUN ] GenconfTest.nbox_norenumber_Works 49: [ OK ] GenconfTest.nbox_norenumber_Works (1 ms) 49: [ RUN ] GenconfTest.nbox_dist_Works 49: [ OK ] GenconfTest.nbox_dist_Works (1 ms) 49: [ RUN ] GenconfTest.nbox_rot_Works 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: [ OK ] GenconfTest.nbox_rot_Works (2 ms) 49: [----------] 4 tests from GenconfTest (12 ms total) 49: 49: [----------] 2 tests from GenionTest 49: [ RUN ] GenionTest.HighConcentrationIonPlacement 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 49: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 49: buffer. The cluster pair list does have a buffering effect, but choosing 49: a larger rlist might be necessary for good energy conservation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 49: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 49: < 0 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: Generating 1-4 interactions: fudge = 0.5 49: Number of degrees of freedom in T-Coupling group rest is 1308.00 49: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 NOTEs 49: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 49: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 49: Group 0 ( System) has 653 elements 49: Group 1 ( Water) has 648 elements 49: Group 2 ( SOL) has 648 elements 49: Group 3 ( non-Water) has 5 elements 49: Group 4 ( Other) has 5 elements 49: Group 5 ( METH) has 5 elements 49: Select a group: Number of (3-atomic) solvent molecules: 216 49: Using random seed 1997. 49: Replacing solvent molecule 56 (atom 168) with NA 49: Replacing solvent molecule 120 (atom 360) with NA 49: Replacing solvent molecule 182 (atom 546) with NA 49: Replacing solvent molecule 71 (atom 213) with NA 49: Replacing solvent molecule 189 (atom 567) with CL 49: Replacing solvent molecule 54 (atom 162) with CL 49: Replacing solvent molecule 155 (atom 465) with CL 49: Replacing solvent molecule 99 (atom 297) with CL 49: 49: Setting the LD random seed to 1610477420 49: 49: Generated 331705 of the 331705 non-bonded parameter combinations 49: 49: Generated 331705 of the 331705 1-4 parameter combinations 49: 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: 49: Excluding 3 bonded neighbours molecule type 'methane' 49: Analysing residue names: 49: There are: 216 Water residues 49: There are: 1 Other residues 49: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 49: 49: This run will generate roughly 0 Mb of data 49: Will try to add 4 NA ions and 4 CL ions. 49: Select a continuous group of solvent molecules 49: Selected 1: 'Water' 49: [ OK ] GenionTest.HighConcentrationIonPlacement (410 ms) 49: [ RUN ] GenionTest.NoIonPlacement 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 49: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 49: buffer. The cluster pair list does have a buffering effect, but choosing 49: a larger rlist might be necessary for good energy conservation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 49: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 49: < 0 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: Generating 1-4 interactions: fudge = 0.5 49: Number of degrees of freedom in T-Coupling group rest is 1308.00 49: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 NOTEs 49: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 49: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 49: No ions to add, will just copy input configuration. 49: Setting the LD random seed to -1242710342 49: 49: Generated 331705 of the 331705 non-bonded parameter combinations 49: 49: Generated 331705 of the 331705 1-4 parameter combinations 49: 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: 49: Excluding 3 bonded neighbours molecule type 'methane' 49: Analysing residue names: 49: There are: 216 Water residues 49: There are: 1 Other residues 49: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 49: 49: This run will generate roughly 0 Mb of data 49: [ OK ] GenionTest.NoIonPlacement (315 ms) 49: [----------] 2 tests from GenionTest (726 ms total) 49: 49: [----------] 1 test from GenRestrTest 49: [ RUN ] GenRestrTest.SimpleRestraintsGenerated 49: 49: Reading structure file 49: Group 0 ( System) has 156 elements 49: Group 1 ( Protein) has 156 elements 49: Group 2 ( Protein-H) has 75 elements 49: Group 3 ( C-alpha) has 10 elements 49: Group 4 ( Backbone) has 30 elements 49: Group 5 ( MainChain) has 40 elements 49: Group 6 ( MainChain+Cb) has 49 elements 49: Group 7 ( MainChain+H) has 52 elements 49: Group 8 ( SideChain) has 104 elements 49: Group 9 ( SideChain-H) has 35 elements 49: Select a group: Select group to position restrain 49: Selected 3: 'C-alpha' 49: [ OK ] GenRestrTest.SimpleRestraintsGenerated (4 ms) 49: [----------] 1 test from GenRestrTest (4 ms total) 49: 49: [----------] 9 tests from PreprocessingAtomTypesTest 49: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate 49: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms) 49: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid 49: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms) 49: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks 49: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms) 49: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks 49: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms) 49: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry 49: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms) 49: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound 49: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms) 49: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound 49: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms) 49: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber 49: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms) 49: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber 49: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms) 49: [----------] 9 tests from PreprocessingAtomTypesTest (0 ms total) 49: 49: [----------] 10 tests from PreprocessingBondAtomTypeTest 49: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate 49: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms) 49: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid 49: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms) 49: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks 49: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms) 49: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks 49: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms) 49: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry 49: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms) 49: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType 49: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms) 49: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound 49: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms) 49: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound 49: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms) 49: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber 49: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms) 49: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber 49: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms) 49: [----------] 10 tests from PreprocessingBondAtomTypeTest (0 ms total) 49: 49: [----------] 1 test from GromppDirectiveTest 49: [ RUN ] GromppDirectiveTest.edgeCaseAtomTypeNames 49: Ignoring obsolete mdp entry 'title' 49: Generating 1-4 interactions: fudge = 0.5 49: 49: NOTE 1 [file directives.top, line 44]: 49: In moleculetype 'A' 2 atoms are not bound by a potential or constraint to 49: any other atom in the same moleculetype. Although technically this might 49: not cause issues in a simulation, this often means that the user forgot 49: to add a bond/potential/constraint or put multiple molecules in the same 49: moleculetype definition by mistake. Run with -v to get information for 49: each atom. 49: 49: Number of degrees of freedom in T-Coupling group rest is 9.00 49: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.mdp]: 49: NVE simulation: will use the initial temperature of 300.000 K for 49: determining the Verlet buffer size 49: 49: 49: There were 2 NOTEs 49: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 49: Setting the LD random seed to -844236675 49: 49: Generated 10 of the 10 non-bonded parameter combinations 49: 49: Generated 10 of the 10 1-4 parameter combinations 49: 49: Excluding 0 bonded neighbours molecule type 'A' 49: 49: Setting gen_seed to 1983102445 49: 49: Velocities were taken from a Maxwell distribution at 300 K 49: Analysing residue names: 49: There are: 1 Other residues 49: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 49: 49: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 49: 49: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 49: 49: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 49: 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: 49: This run will generate roughly 0 Mb of data 49: [ OK ] GromppDirectiveTest.edgeCaseAtomTypeNames (11 ms) 49: [----------] 1 test from GromppDirectiveTest (11 ms total) 49: 49: [----------] 5 tests from InsertMoleculesTest 49: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration 49: Reading solute configuration 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Using random seed 1997 49: Try 1 success (now 8 atoms)! 49: 49: Added 1 molecules (out of 1 requested) 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro 49: 49: Output configuration contains 8 atoms in 4 residues 49: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (6 ms) 49: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Using random seed 1997 49: Try 1 success (now 2 atoms)! 49: Try 2 success (now 4 atoms)! 49: Try 3 success (now 6 atoms)! 49: Try 4 success (now 8 atoms)! 49: Try 5 success (now 10 atoms)! 49: 49: Added 5 molecules (out of 5 requested) 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro 49: 49: Output configuration contains 10 atoms in 10 residues 49: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (1 ms) 49: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox 49: Reading solute configuration 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Using random seed 1997 49: Try 1 success (now 8 atoms)! 49: Try 2 success (now 10 atoms)! 49: 49: Added 2 molecules (out of 2 requested) 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro 49: 49: Output configuration contains 10 atoms in 4 residues 49: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (6 ms) 49: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement 49: Reading solute configuration 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Using random seed 1997 49: Try 1 success (now 650 atoms)! 49: Try 2 success (now 652 atoms)! 49: Try 3 success (now 654 atoms)! 49: Try 4 success (now 656 atoms)! 49: 49: Added 4 molecules (out of 4 requested) 49: Replaced 8 residues (24 atoms) 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro 49: 49: Output configuration contains 632 atoms in 212 residues 49: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (12 ms) 49: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Using random seed 1997 49: Read 4 positions from file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat 49: 49: Try 1 success (now 2 atoms)! 49: Try 2 success (now 4 atoms)! 49: Try 3 Try 4 Try 5 Try 6 Try 7 Try 8 Try 9 Try 10 Try 11 Try 12 skipped position (0.990, 2.010, 3.000) 49: Try 13 success (now 6 atoms)! 49: 49: Added 3 molecules (out of 4 requested) 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro 49: 49: Output configuration contains 6 atoms in 3 residues 49: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (4 ms) 49: [----------] 5 tests from InsertMoleculesTest (31 ms total) 49: 49: [----------] 3 tests from MassRepartitioning 49: [ RUN ] MassRepartitioning.ValidCaseWorks 49: The smallest mass in the system is 2, setting the minimum mass to 6 49: [ OK ] MassRepartitioning.ValidCaseWorks (0 ms) 49: [ RUN ] MassRepartitioning.UnboundGivesWarning 49: 49: WARNING 1 [file unknown]: 49: The are 1 atoms that have a mass below the mass repartitioning limit but 49: are not bound. These masses cannot be repartitioned. 49: 49: The smallest mass in the system is 2, setting the minimum mass to 6 49: [ OK ] MassRepartitioning.UnboundGivesWarning (0 ms) 49: [ RUN ] MassRepartitioning.LightPartnerGivesError 49: 49: ERROR 1 [file unknown]: 49: Light atoms are bound to at least one atom that has a too low mass for 49: repartioning 49: 49: The smallest mass in the system is 2, setting the minimum mass to 6 49: [ OK ] MassRepartitioning.LightPartnerGivesError (0 ms) 49: [----------] 3 tests from MassRepartitioning (0 ms total) 49: 49: [----------] 35 tests from GetIrTest 49: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines 49: Ignoring obsolete mdp entry 'title' 49: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps' 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (6 ms) 49: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals 49: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (13 ms) 49: [ RUN ] GetIrTest.AcceptsKeyWithoutValue 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.AcceptsKeyWithoutValue (6 ms) 49: [ RUN ] GetIrTest.RejectsValueWithoutKey 49: [ OK ] GetIrTest.RejectsValueWithoutKey (7 ms) 49: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue 49: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (12 ms) 49: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (2 ms) 49: [ RUN ] GetIrTest.AcceptsEmptyLines 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.AcceptsEmptyLines (6 ms) 49: [ RUN ] GetIrTest.MtsCheckNstcalcenergy 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 49: With MTS, nstcalcenergy = 5 should be a multiple of mts-factor = 2 49: 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.MtsCheckNstcalcenergy (5 ms) 49: [ RUN ] GetIrTest.MtsCheckNstenergy 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 49: With MTS, nstenergy = 5 should be a multiple of mts-factor = 2 49: 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (5) 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.MtsCheckNstenergy (9 ms) 49: [ RUN ] GetIrTest.MtsCheckNstpcouple 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 49: Pressure coupling incorrect number of values (I need exactly 1) 49: 49: 49: ERROR 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 49: Pressure coupling incorrect number of values (I need exactly 1) 49: 49: 49: ERROR 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 49: With multiple time stepping, nstpcouple should be a multiple of 49: mts-factor 49: 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: 49: ERROR 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 49: The Berendsen barostat does not generate any strictly correct ensemble, 49: and should not be used for new production simulations (in our opinion). 49: We recommend using the C-rescale barostat instead. 49: 49: 49: ERROR 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 49: compressibility must be > 0 when using pressure coupling Berendsen 49: 49: 49: [ OK ] GetIrTest.MtsCheckNstpcouple (1 ms) 49: [ RUN ] GetIrTest.MtsCheckNstdhdl 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 49: With MTS, nstdhdl = 5 should be a multiple of mts-factor = 2 49: 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstdhdl (5) 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: 49: ERROR 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 49: Lambda state must be set, either with init-lambda-state or with 49: init-lambda 49: 49: [ OK ] GetIrTest.MtsCheckNstdhdl (1 ms) 49: [ RUN ] GetIrTest.MtsCheckSDNotSupported 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 49: Multiple time stepping is only supported with integrator md 49: 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.MtsCheckSDNotSupported (1 ms) 49: [ RUN ] GetIrTest.AcceptsElectricField 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.AcceptsElectricField (10 ms) 49: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (2 ms) 49: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (4 ms) 49: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys 49: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (11 ms) 49: [ RUN ] GetIrTest.AcceptsImplicitSolventNo 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.AcceptsImplicitSolventNo (7 ms) 49: [ RUN ] GetIrTest.RejectsImplicitSolventYes 49: [ OK ] GetIrTest.RejectsImplicitSolventYes (13 ms) 49: [ RUN ] GetIrTest.AcceptsMimic 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.AcceptsMimic (3 ms) 49: [ RUN ] GetIrTest.AcceptsTransformationCoord 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp, line 11]: 49: pull-coord2 has a non-zero force constant and is also referenced in 49: pull-coord1-expression. Make sure that this is intended. In most use 49: cases, the pull coordinates referenced by a transformation coordinate 49: should have their force constant set to zero. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.AcceptsTransformationCoord (3 ms) 49: [ RUN ] GetIrTest.InvalidTransformationCoordWithConstraint 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp, line 7]: 49: pull-coord1 cannot have type 'constraint' and geometry 'transformation' 49: 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.InvalidTransformationCoordWithConstraint (4 ms) 49: [ RUN ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp, line 10]: 49: pull-coord2 can not use pull-coord1 in the transformation since this is a 49: constraint 49: 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression (1 ms) 49: [ RUN ] GetIrTest.InvalidTransformationCoordDxValue 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp, line 7]: 49: pull-coord1-dx cannot be set to zero for pull coordinate of geometry 49: 'transformation' 49: 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.InvalidTransformationCoordDxValue (5 ms) 49: [ RUN ] GetIrTest.MissingTransformationCoordExpression 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp, line 5]: 49: pull-coord1-expression not set for pull coordinate of geometry 49: 'transformation' 49: 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.MissingTransformationCoordExpression (2 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep 49: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep (1 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta 49: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta (1 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep 49: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep (1 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta 49: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta (1 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_input.mdp]: 49: With init-lambda = 0 and delta_lambda = 1e-05 and no explicit input, 49: coul-lambdas and vdw-lambdas will be greater than 1 after step 100000 of 49: in total 100001 steps. This is not compatible with using soft-core 49: potentials. 49: 49: 49: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch (5 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta_input.mdp]: 49: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 49: won't change anymore after step 100000 until the end of the simulation 49: after 100001 steps. 49: 49: 49: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta (1 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta_input.mdp]: 49: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 49: won't change anymore after step 100000 until the end of the simulation 49: after 100001 steps. 49: 49: 49: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta (7 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_input.mdp]: 49: With init-lambda-state = 0 and delta_lambda = 1e-05, the lambda 49: components won't change anymore after step 100000 until the end of the 49: simulation after 100001 steps. 49: 49: 49: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch (2 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta_input.mdp]: 49: With init-lambda-state = 2 and delta_lambda = -1e-05, the lambda 49: components won't change anymore after step 100000 until the end of the 49: simulation after 100001 steps. 49: 49: 49: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta (1 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep 49: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep (1 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta 49: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta (5 ms) 49: [----------] 35 tests from GetIrTest (187 ms total) 49: 49: [----------] 6 tests from SolvateTest 49: [ RUN ] SolvateTest.cs_box_Works 49: Reading solvent configuration 49: 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Generating solvent configuration 49: Will generate new solvent configuration of 1x1x1 boxes 49: Solvent box contains 270 atoms in 90 residues 49: Removed 129 solvent atoms due to solvent-solvent overlap 49: Sorting configuration 49: Found 1 molecule type: 49: SOL ( 3 atoms): 47 residues 49: Generated solvent containing 141 atoms in 47 residues 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro 49: 49: Output configuration contains 141 atoms in 47 residues 49: Volume : 1.331 (nm^3) 49: Density : 1056.36 (g/l) 49: Number of solvent molecules: 47 49: 49: [ OK ] SolvateTest.cs_box_Works (12 ms) 49: [ RUN ] SolvateTest.cs_cp_Works 49: Reading solute configuration 49: Reading solvent configuration 49: 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Generating solvent configuration 49: Will generate new solvent configuration of 2x2x2 boxes 49: Solvent box contains 3660 atoms in 1220 residues 49: Removed 987 solvent atoms due to solvent-solvent overlap 49: Removed 15 solvent atoms due to solute-solvent overlap 49: Sorting configuration 49: Found 1 molecule type: 49: SOL ( 3 atoms): 886 residues 49: Generated solvent containing 2658 atoms in 886 residues 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro 49: 49: Output configuration contains 2664 atoms in 888 residues 49: Volume : 27.2709 (nm^3) 49: Density : 974.777 (g/l) 49: Number of solvent molecules: 886 49: 49: [ OK ] SolvateTest.cs_cp_Works (25 ms) 49: [ RUN ] SolvateTest.cs_cp_p_Works 49: Reading solute configuration 49: Reading solvent configuration 49: 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Generating solvent configuration 49: Will generate new solvent configuration of 2x2x2 boxes 49: Solvent box contains 3660 atoms in 1220 residues 49: Removed 987 solvent atoms due to solvent-solvent overlap 49: Removed 15 solvent atoms due to solute-solvent overlap 49: Sorting configuration 49: Found 1 molecule type: 49: SOL ( 3 atoms): 886 residues 49: Generated solvent containing 2658 atoms in 886 residues 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro 49: 49: Output configuration contains 2664 atoms in 888 residues 49: Volume : 27.2709 (nm^3) 49: Density : 974.777 (g/l) 49: Number of solvent molecules: 886 49: 49: Processing topology 49: Adding line for 886 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top) 49: [ OK ] SolvateTest.cs_cp_p_Works (32 ms) 49: [ RUN ] SolvateTest.shell_Works 49: Reading solute configuration 49: Reading solvent configuration 49: 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Generating solvent configuration 49: Will generate new solvent configuration of 2x2x2 boxes 49: Solvent box contains 3660 atoms in 1220 residues 49: Removed 987 solvent atoms due to solvent-solvent overlap 49: Removed 1902 solvent atoms more than 1.000000 nm from solute. 49: Removed 15 solvent atoms due to solute-solvent overlap 49: Sorting configuration 49: Found 1 molecule type: 49: SOL ( 3 atoms): 252 residues 49: Generated solvent containing 756 atoms in 252 residues 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro 49: 49: Output configuration contains 762 atoms in 254 residues 49: Volume : 27.2709 (nm^3) 49: Density : 279.3 (g/l) 49: Number of solvent molecules: 252 49: 49: [ OK ] SolvateTest.shell_Works (13 ms) 49: [ RUN ] SolvateTest.update_Topology_Works 49: Reading solute configuration 49: Reading solvent configuration 49: 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Generating solvent configuration 49: Will generate new solvent configuration of 3x3x3 boxes 49: Solvent box contains 14952 atoms in 4984 residues 49: Removed 2787 solvent atoms due to solvent-solvent overlap 49: Removed 30 solvent atoms due to solute-solvent overlap 49: Sorting configuration 49: Found 2 different molecule types: 49: HOH ( 3 atoms): 1876 residues 49: SOL ( 3 atoms): 2169 residues 49: Generated solvent containing 0 atoms in 0 residues 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro 49: 49: Output configuration contains 12141 atoms in 4047 residues 49: Volume : 125 (nm^3) 49: Density : 968.963 (g/l) 49: Number of solvent molecules: 4045 49: 49: Processing topology 49: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 49: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 49: [ OK ] SolvateTest.update_Topology_Works (85 ms) 49: [ RUN ] SolvateTest.cs_pdb_big_box_Works 49: Reading solvent configuration 49: 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Generating solvent configuration 49: Will generate new solvent configuration of 2x2x2 boxes 49: Solvent box contains 1218 atoms in 406 residues 49: Removed 555 solvent atoms due to solvent-solvent overlap 49: Sorting configuration 49: Found 1 molecule type: 49: SOL ( 3 atoms): 221 residues 49: Generated solvent containing 663 atoms in 221 residues 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_pdb_big_box_Works_out.gro 49: 49: Output configuration contains 663 atoms in 221 residues 49: Volume : 8 (nm^3) 49: Density : 826.409 (g/l) 49: Number of solvent molecules: 221 49: 49: [ OK ] SolvateTest.cs_pdb_big_box_Works (6 ms) 49: [----------] 6 tests from SolvateTest (176 ms total) 49: 49: [----------] 1 test from TopDirTests 49: [ RUN ] TopDirTests.NamesArrayHasCorrectSize 49: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms) 49: [----------] 1 test from TopDirTests (0 ms total) 49: 49: [----------] 45 tests from SinglePeptideFragments/EditconfTest 49: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 (11 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 (2 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 (2 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 (4 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 (2 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 (2 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 (8 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 (1 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 (2 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 49: 49: Select a group for output: 49: Group 0 ( two_residues) has 23 elements 49: There is one group in the index 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 (6 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 49: 49: Select a group for output: 49: Group 0 ( two_residues) has 23 elements 49: There is one group in the index 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 (2 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 49: 49: Select a group for output: 49: Group 0 ( two_residues) has 23 elements 49: There is one group in the index 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 (2 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 49: 49: Select a group for output: 49: Group 0 ( two_residues) has 23 elements 49: There is one group in the index 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 (1 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 49: 49: Select a group for output: 49: Group 0 ( two_residues) has 23 elements 49: There is one group in the index 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 (3 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 49: 49: Select a group for output: 49: Group 0 ( two_residues) has 23 elements 49: There is one group in the index 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 (1 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 49: 49: Select a group for output: 49: Group 0 ( two_residues) has 23 elements 49: There is one group in the index 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 (6 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 49: 49: Select a group for output: 49: Group 0 ( two_residues) has 23 elements 49: There is one group in the index 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 (1 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 49: 49: Select a group for output: 49: Group 0 ( two_residues) has 23 elements 49: There is one group in the index 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 (1 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/0 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: shift : 0.212 1.187 3.527 (nm) 49: new center : 4.028 2.819 3.723 (nm) 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/0 (2 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/1 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: shift : 0.212 1.187 3.527 (nm) 49: new center : 4.028 2.819 3.723 (nm) 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/1 (2 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/2 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: shift : 0.212 1.187 3.527 (nm) 49: new center : 4.028 2.819 3.723 (nm) 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/2 (8 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/3 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: shift : 0.212 1.187 3.527 (nm) 49: new center : 4.028 2.819 3.723 (nm) 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/3 (2 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/4 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: shift : 0.212 1.187 3.527 (nm) 49: new center : 4.028 2.819 3.723 (nm) 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/4 (1 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/5 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: shift : 0.212 1.187 3.527 (nm) 49: new center : 4.028 2.819 3.723 (nm) 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/5 (3 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/6 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: shift : 0.212 1.187 3.527 (nm) 49: new center : 4.028 2.819 3.723 (nm) 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/6 (4 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/7 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: shift : 0.212 1.187 3.527 (nm) 49: new center : 4.028 2.819 3.723 (nm) 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/7 (1 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/8 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: shift : 0.212 1.187 3.527 (nm) 49: new center : 4.028 2.819 3.723 (nm) 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/8 (8 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/0 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: shift : -0.814 1.104 2.657 (nm) 49: new center : 3.002 2.736 2.852 (nm) 49: new box vectors : 6.004 5.472 5.704 (nm) 49: new box angles : 90.00 90.00 90.00 (degrees) 49: new box volume : 187.42 (nm^3) 49: 49: WARNING: No boxtype specified - distance condition applied in each dimension. 49: If the molecule rotates the actual distance will be smaller. You might want 49: to use a cubic box instead, or why not try a dodecahedron today? 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/0 (4 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/1 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: shift : -0.814 1.104 2.657 (nm) 49: new center : 3.002 2.736 2.852 (nm) 49: new box vectors : 6.004 5.472 5.704 (nm) 49: new box angles : 90.00 90.00 90.00 (degrees) 49: new box volume : 187.42 (nm^3) 49: 49: WARNING: No boxtype specified - distance condition applied in each dimension. 49: If the molecule rotates the actual distance will be smaller. You might want 49: to use a cubic box instead, or why not try a dodecahedron today? 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/1 (5 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/2 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: shift : -0.814 1.104 2.657 (nm) 49: new center : 3.002 2.736 2.852 (nm) 49: new box vectors : 6.004 5.472 5.704 (nm) 49: new box angles : 90.00 90.00 90.00 (degrees) 49: new box volume : 187.42 (nm^3) 49: 49: WARNING: No boxtype specified - distance condition applied in each dimension. 49: If the molecule rotates the actual distance will be smaller. You might want 49: to use a cubic box instead, or why not try a dodecahedron today? 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/2 (3 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/3 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: shift : -0.814 1.104 2.657 (nm) 49: new center : 3.002 2.736 2.852 (nm) 49: new box vectors : 6.004 5.472 5.704 (nm) 49: new box angles : 90.00 90.00 90.00 (degrees) 49: new box volume : 187.40 (nm^3) 49: 49: WARNING: No boxtype specified - distance condition applied in each dimension. 49: If the molecule rotates the actual distance will be smaller. You might want 49: to use a cubic box instead, or why not try a dodecahedron today? 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/3 (8 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/4 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: shift : -0.814 1.104 2.657 (nm) 49: new center : 3.002 2.736 2.852 (nm) 49: new box vectors : 6.004 5.472 5.704 (nm) 49: new box angles : 90.00 90.00 90.00 (degrees) 49: new box volume : 187.40 (nm^3) 49: 49: WARNING: No boxtype specified - distance condition applied in each dimension. 49: If the molecule rotates the actual distance will be smaller. You might want 49: to use a cubic box instead, or why not try a dodecahedron today? 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/4 (1 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/5 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: shift : -0.814 1.104 2.657 (nm) 49: new center : 3.002 2.736 2.852 (nm) 49: new box vectors : 6.004 5.472 5.704 (nm) 49: new box angles : 90.00 90.00 90.00 (degrees) 49: new box volume : 187.40 (nm^3) 49: 49: WARNING: No boxtype specified - distance condition applied in each dimension. 49: If the molecule rotates the actual distance will be smaller. You might want 49: to use a cubic box instead, or why not try a dodecahedron today? 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/5 (2 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/6 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: shift : -0.814 1.104 2.657 (nm) 49: new center : 3.002 2.736 2.852 (nm) 49: new box vectors : 6.004 5.472 5.704 (nm) 49: new box angles : 90.00 90.00 90.00 (degrees) 49: new box volume : 187.40 (nm^3) 49: 49: WARNING: No boxtype specified - distance condition applied in each dimension. 49: If the molecule rotates the actual distance will be smaller. You might want 49: to use a cubic box instead, or why not try a dodecahedron today? 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/6 (3 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/7 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: shift : -0.814 1.104 2.657 (nm) 49: new center : 3.002 2.736 2.852 (nm) 49: new box vectors : 6.004 5.472 5.704 (nm) 49: new box angles : 90.00 90.00 90.00 (degrees) 49: new box volume : 187.40 (nm^3) 49: 49: WARNING: No boxtype specified - distance condition applied in each dimension. 49: If the molecule rotates the actual distance will be smaller. You might want 49: to use a cubic box instead, or why not try a dodecahedron today? 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/7 (4 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/8 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: shift : -0.814 1.104 2.657 (nm) 49: new center : 3.002 2.736 2.852 (nm) 49: new box vectors : 6.004 5.472 5.704 (nm) 49: new box angles : 90.00 90.00 90.00 (degrees) 49: new box volume : 187.40 (nm^3) 49: 49: WARNING: No boxtype specified - distance condition applied in each dimension. 49: If the molecule rotates the actual distance will be smaller. You might want 49: to use a cubic box instead, or why not try a dodecahedron today? 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/8 (7 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/0 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: new center : 3.816 1.632 0.195 (nm) 49: new box vectors : 5.004 4.472 4.704 (nm) 49: new box angles : 90.00 90.00 90.00 (degrees) 49: new box volume : 105.28 (nm^3) 49: 49: WARNING: No boxtype specified - distance condition applied in each dimension. 49: If the molecule rotates the actual distance will be smaller. You might want 49: to use a cubic box instead, or why not try a dodecahedron today? 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/0 (4 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/1 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: new center : 3.816 1.632 0.195 (nm) 49: new box vectors : 5.004 4.472 4.704 (nm) 49: new box angles : 90.00 90.00 90.00 (degrees) 49: new box volume : 105.28 (nm^3) 49: 49: WARNING: No boxtype specified - distance condition applied in each dimension. 49: If the molecule rotates the actual distance will be smaller. You might want 49: to use a cubic box instead, or why not try a dodecahedron today? 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/1 (2 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/2 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: new center : 3.816 1.632 0.195 (nm) 49: new box vectors : 5.004 4.472 4.704 (nm) 49: new box angles : 90.00 90.00 90.00 (degrees) 49: new box volume : 105.28 (nm^3) 49: 49: WARNING: No boxtype specified - distance condition applied in each dimension. 49: If the molecule rotates the actual distance will be smaller. You might want 49: to use a cubic box instead, or why not try a dodecahedron today? 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/2 (5 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/3 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: new center : 3.816 1.632 0.195 (nm) 49: new box vectors : 5.004 4.472 4.704 (nm) 49: new box angles : 90.00 90.00 90.00 (degrees) 49: new box volume : 105.27 (nm^3) 49: 49: WARNING: No boxtype specified - distance condition applied in each dimension. 49: If the molecule rotates the actual distance will be smaller. You might want 49: to use a cubic box instead, or why not try a dodecahedron today? 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/3 (3 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/4 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: new center : 3.816 1.632 0.195 (nm) 49: new box vectors : 5.004 4.472 4.704 (nm) 49: new box angles : 90.00 90.00 90.00 (degrees) 49: new box volume : 105.27 (nm^3) 49: 49: WARNING: No boxtype specified - distance condition applied in each dimension. 49: If the molecule rotates the actual distance will be smaller. You might want 49: to use a cubic box instead, or why not try a dodecahedron today? 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/4 (1 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/5 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: new center : 3.816 1.632 0.195 (nm) 49: new box vectors : 5.004 4.472 4.704 (nm) 49: new box angles : 90.00 90.00 90.00 (degrees) 49: new box volume : 105.27 (nm^3) 49: 49: WARNING: No boxtype specified - distance condition applied in each dimension. 49: If the molecule rotates the actual distance will be smaller. You might want 49: to use a cubic box instead, or why not try a dodecahedron today? 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/5 (7 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/6 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: new center : 3.816 1.632 0.195 (nm) 49: new box vectors : 5.004 4.472 4.704 (nm) 49: new box angles : 90.00 90.00 90.00 (degrees) 49: new box volume : 105.27 (nm^3) 49: 49: WARNING: No boxtype specified - distance condition applied in each dimension. 49: If the molecule rotates the actual distance will be smaller. You might want 49: to use a cubic box instead, or why not try a dodecahedron today? 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/6 (3 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/7 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: new center : 3.816 1.632 0.195 (nm) 49: new box vectors : 5.004 4.472 4.704 (nm) 49: new box angles : 90.00 90.00 90.00 (degrees) 49: new box volume : 105.27 (nm^3) 49: 49: WARNING: No boxtype specified - distance condition applied in each dimension. 49: If the molecule rotates the actual distance will be smaller. You might want 49: to use a cubic box instead, or why not try a dodecahedron today? 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/7 (2 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/8 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: new center : 3.816 1.632 0.195 (nm) 49: new box vectors : 5.004 4.472 4.704 (nm) 49: new box angles : 90.00 90.00 90.00 (degrees) 49: new box volume : 105.27 (nm^3) 49: 49: WARNING: No boxtype specified - distance condition applied in each dimension. 49: If the molecule rotates the actual distance will be smaller. You might want 49: to use a cubic box instead, or why not try a dodecahedron today? 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/8 (5 ms) 49: [----------] 45 tests from SinglePeptideFragments/EditconfTest (203 ms total) 49: 49: [----------] 16 tests from CorrectVelocity/MaxwellTest 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/0 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/0 (1 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/1 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/1 (3 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/2 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/2 (1 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/3 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/3 (2 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/4 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/4 (1 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/5 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/5 (5 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/6 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/6 (1 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/7 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/7 (2 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/8 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/8 (1 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/9 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/9 (2 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/10 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/10 (0 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/11 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/11 (7 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/12 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/12 (2 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/13 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/13 (2 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/14 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/14 (1 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/15 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/15 (2 ms) 49: [----------] 16 tests from CorrectVelocity/MaxwellTest (41 ms total) 49: 49: [----------] Global test environment tear-down 49: [==========] 138 tests from 13 test suites ran. (1396 ms total) 49: [ PASSED ] 138 tests. 49/87 Test #49: GmxPreprocessTests ........................ Passed 1.42 sec test 50 Start 50: Pdb2gmx1Test 50: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/pdb2gmx1-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/Pdb2gmx1Test.xml" 50: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests 50: Test timeout computed to be: 1920 50: [==========] Running 30 tests from 1 test suite. 50: [----------] Global test environment set-up. 50: [----------] 30 tests from Oplsaa/Pdb2gmxTest 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 25 donors and 23 acceptors were found. 50: There are 41 hydrogen bonds 50: Will use HISE for residue 8 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS3 HIS8 50: SG9 NE251 50: HIS8 NE251 1.055 50: MET12 SD83 0.763 0.990 50: Before cleaning: 653 pairs 50: Before cleaning: 663 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 50: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 128 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (128 atoms, 16 residues) 50: 50: Identified residue ALA2 as a starting terminus. 50: 50: Identified residue SER17 as a ending terminus. 50: Start terminus ALA-2: NH3+ 50: End terminus SER-17: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 252 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 254, now 254 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 663 dihedrals, 51 impropers, 457 angles 50: 650 pairs, 254 bonds and 0 virtual sites 50: 50: Total mass 1846.112 a.m.u. 50: 50: Total charge -0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 50: 50: The Oplsaa force field and the tip3p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (43 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 30 donors and 22 acceptors were found. 50: There are 36 hydrogen bonds 50: Will use HISE for residue 29 50: Will use HISE for residue 32 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS27 HIS29 50: SG90 NE2111 50: HIS29 NE2111 0.987 50: HIS32 NE2135 1.590 1.155 50: Before cleaning: 748 pairs 50: Before cleaning: 778 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 50: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 149 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (149 atoms, 16 residues) 50: 50: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue THR18 as a starting terminus. 50: 50: Identified residue PHE33 as a ending terminus. 50: Start terminus THR-18: NH3+ 50: End terminus PHE-33: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 281 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 290, now 290 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 778 dihedrals, 72 impropers, 516 angles 50: 736 pairs, 290 bonds and 0 virtual sites 50: 50: Total mass 2088.357 a.m.u. 50: 50: Total charge 1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 50: 50: The Oplsaa force field and the tip3p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (45 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 22 acceptors were found. 50: There are 26 hydrogen bonds 50: Will use HISE for residue 45 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS45 50: NE295 50: MET46 SD102 1.078 50: Before cleaning: 676 pairs 50: Before cleaning: 696 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 50: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 132 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (132 atoms, 16 residues) 50: 50: Identified residue ALA34 as a starting terminus. 50: 50: Identified residue ALA49 as a ending terminus. 50: Start terminus ALA-34: NH3+ 50: End terminus ALA-49: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 255 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 261, now 261 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 696 dihedrals, 56 impropers, 472 angles 50: 667 pairs, 261 bonds and 0 virtual sites 50: 50: Total mass 1861.128 a.m.u. 50: 50: Total charge -1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 50: 50: The Oplsaa force field and the tip3p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (29 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 21 acceptors were found. 50: There are 30 hydrogen bonds 50: Will use HISE for residue 60 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS60 50: NE285 50: CYS62 SG98 0.803 50: Before cleaning: 603 pairs 50: Before cleaning: 618 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 50: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 117 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (117 atoms, 16 residues) 50: 50: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue LYS50 as a starting terminus. 50: 50: Identified residue PRO65 as a ending terminus. 50: Start terminus LYS-50: NH3+ 50: End terminus PRO-65: PRO-COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 228 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 232, now 232 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 618 dihedrals, 48 impropers, 419 angles 50: 597 pairs, 232 bonds and 0 virtual sites 50: 50: Total mass 1662.883 a.m.u. 50: 50: Total charge -0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 50: 50: The Oplsaa force field and the tip3p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (29 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 89 donors and 98 acceptors were found. 50: There are 129 hydrogen bonds 50: Will use HISE for residue 31 50: Will use HISE for residue 51 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS25 HIS31 HIS51 50: SG14 NE264 NE2226 50: HIS31 NE264 1.921 50: HIS51 NE2226 1.498 2.650 50: CYS80 SG477 0.207 1.984 1.570 50: Linking CYS-25 SG-14 and CYS-80 SG-477... 50: Before cleaning: 2499 pairs 50: Before cleaning: 2524 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 50: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 50: 50: chain #res #atoms 50: 50: 1 'A' 58 488 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 'A' (488 atoms, 58 residues) 50: 50: Identified residue ASN24 as a starting terminus. 50: 50: Identified residue ARG81 as a ending terminus. 50: Start terminus ASN-24: NH3+ 50: End terminus ARG-81: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 58 residues with 936 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 951, now 951 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 2524 dihedrals, 208 impropers, 1704 angles 50: 2469 pairs, 951 bonds and 0 virtual sites 50: 50: Total mass 6908.578 a.m.u. 50: 50: Total charge -6.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 50: 50: The Oplsaa force field and the tip3p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (81 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 25 donors and 23 acceptors were found. 50: There are 41 hydrogen bonds 50: Will use HISE for residue 8 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS3 HIS8 50: SG9 NE251 50: HIS8 NE251 1.055 50: MET12 SD83 0.763 0.990 50: Marked 124 virtual sites 50: Added 16 dummy masses 50: Added 26 new constraints 50: Before cleaning: 653 pairs 50: Before cleaning: 663 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 50: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 128 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (128 atoms, 16 residues) 50: 50: Identified residue ALA2 as a starting terminus. 50: 50: Identified residue SER17 as a ending terminus. 50: Start terminus ALA-2: NH3+ 50: End terminus SER-17: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 252 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 254, now 254 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 663 dihedrals, 51 impropers, 457 angles 50: 650 pairs, 254 bonds and 130 virtual sites 50: 50: Total mass 1846.112 a.m.u. 50: 50: Total charge -0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 50: 50: The Oplsaa force field and the tip3p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (42 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 30 donors and 22 acceptors were found. 50: There are 36 hydrogen bonds 50: Will use HISE for residue 29 50: Will use HISE for residue 32 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS27 HIS29 50: SG90 NE2111 50: HIS29 NE2111 0.987 50: HIS32 NE2135 1.590 1.155 50: Marked 132 virtual sites 50: Added 10 dummy masses 50: Added 19 new constraints 50: Before cleaning: 748 pairs 50: Before cleaning: 778 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 50: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 149 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (149 atoms, 16 residues) 50: 50: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue THR18 as a starting terminus. 50: 50: Identified residue PHE33 as a ending terminus. 50: Start terminus THR-18: NH3+ 50: End terminus PHE-33: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 281 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 290, now 290 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 778 dihedrals, 72 impropers, 516 angles 50: 736 pairs, 290 bonds and 133 virtual sites 50: 50: Total mass 2088.357 a.m.u. 50: 50: Total charge 1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 50: 50: The Oplsaa force field and the tip3p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (101 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 22 acceptors were found. 50: There are 26 hydrogen bonds 50: Will use HISE for residue 45 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS45 50: NE295 50: MET46 SD102 1.078 50: Marked 123 virtual sites 50: Added 22 dummy masses 50: Added 35 new constraints 50: Before cleaning: 676 pairs 50: Before cleaning: 696 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 50: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 132 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (132 atoms, 16 residues) 50: 50: Identified residue ALA34 as a starting terminus. 50: 50: Identified residue ALA49 as a ending terminus. 50: Start terminus ALA-34: NH3+ 50: End terminus ALA-49: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 255 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 261, now 261 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 696 dihedrals, 56 impropers, 472 angles 50: 667 pairs, 261 bonds and 132 virtual sites 50: 50: Total mass 1861.128 a.m.u. 50: 50: Total charge -1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 50: 50: The Oplsaa force field and the tip3p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (104 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 21 acceptors were found. 50: There are 30 hydrogen bonds 50: Will use HISE for residue 60 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS60 50: NE285 50: CYS62 SG98 0.803 50: Marked 111 virtual sites 50: Added 18 dummy masses 50: Added 31 new constraints 50: Before cleaning: 603 pairs 50: Before cleaning: 618 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 50: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 117 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (117 atoms, 16 residues) 50: 50: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue LYS50 as a starting terminus. 50: 50: Identified residue PRO65 as a ending terminus. 50: Start terminus LYS-50: NH3+ 50: End terminus PRO-65: PRO-COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 228 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 232, now 232 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 618 dihedrals, 48 impropers, 419 angles 50: 597 pairs, 232 bonds and 116 virtual sites 50: 50: Total mass 1662.883 a.m.u. 50: 50: Total charge -0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 50: 50: The Oplsaa force field and the tip3p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (202 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 89 donors and 98 acceptors were found. 50: There are 129 hydrogen bonds 50: Will use HISE for residue 31 50: Will use HISE for residue 51 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS25 HIS31 HIS51 50: SG14 NE264 NE2226 50: HIS31 NE264 1.921 50: HIS51 NE2226 1.498 2.650 50: CYS80 SG477 0.207 1.984 1.570 50: Linking CYS-25 SG-14 and CYS-80 SG-477... 50: Marked 447 virtual sites 50: Added 58 dummy masses 50: Added 101 new constraints 50: Before cleaning: 2499 pairs 50: Before cleaning: 2524 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 50: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 50: 50: chain #res #atoms 50: 50: 1 'A' 58 488 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 'A' (488 atoms, 58 residues) 50: 50: Identified residue ASN24 as a starting terminus. 50: 50: Identified residue ARG81 as a ending terminus. 50: Start terminus ASN-24: NH3+ 50: End terminus ARG-81: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 58 residues with 936 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 951, now 951 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 2524 dihedrals, 208 impropers, 1704 angles 50: 2469 pairs, 951 bonds and 462 virtual sites 50: 50: Total mass 6908.578 a.m.u. 50: 50: Total charge -6.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 50: 50: The Oplsaa force field and the tip3p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (57 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 25 donors and 23 acceptors were found. 50: There are 41 hydrogen bonds 50: Will use HISE for residue 8 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS3 HIS8 50: SG9 NE251 50: HIS8 NE251 1.055 50: MET12 SD83 0.763 0.990 50: Before cleaning: 653 pairs 50: Before cleaning: 663 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 50: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 128 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (128 atoms, 16 residues) 50: 50: Identified residue ALA2 as a starting terminus. 50: 50: Identified residue SER17 as a ending terminus. 50: Start terminus ALA-2: NH3+ 50: End terminus SER-17: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 252 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 254, now 254 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 663 dihedrals, 51 impropers, 457 angles 50: 650 pairs, 254 bonds and 0 virtual sites 50: 50: Total mass 1846.112 a.m.u. 50: 50: Total charge -0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 50: 50: The Oplsaa force field and the tip4p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (37 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 30 donors and 22 acceptors were found. 50: There are 36 hydrogen bonds 50: Will use HISE for residue 29 50: Will use HISE for residue 32 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS27 HIS29 50: SG90 NE2111 50: HIS29 NE2111 0.987 50: HIS32 NE2135 1.590 1.155 50: Before cleaning: 748 pairs 50: Before cleaning: 778 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 50: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 149 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (149 atoms, 16 residues) 50: 50: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue THR18 as a starting terminus. 50: 50: Identified residue PHE33 as a ending terminus. 50: Start terminus THR-18: NH3+ 50: End terminus PHE-33: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 281 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 290, now 290 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 778 dihedrals, 72 impropers, 516 angles 50: 736 pairs, 290 bonds and 0 virtual sites 50: 50: Total mass 2088.357 a.m.u. 50: 50: Total charge 1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 50: 50: The Oplsaa force field and the tip4p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (36 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 22 acceptors were found. 50: There are 26 hydrogen bonds 50: Will use HISE for residue 45 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS45 50: NE295 50: MET46 SD102 1.078 50: Before cleaning: 676 pairs 50: Before cleaning: 696 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 50: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 132 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (132 atoms, 16 residues) 50: 50: Identified residue ALA34 as a starting terminus. 50: 50: Identified residue ALA49 as a ending terminus. 50: Start terminus ALA-34: NH3+ 50: End terminus ALA-49: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 255 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 261, now 261 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 696 dihedrals, 56 impropers, 472 angles 50: 667 pairs, 261 bonds and 0 virtual sites 50: 50: Total mass 1861.128 a.m.u. 50: 50: Total charge -1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 50: 50: The Oplsaa force field and the tip4p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (42 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 21 acceptors were found. 50: There are 30 hydrogen bonds 50: Will use HISE for residue 60 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS60 50: NE285 50: CYS62 SG98 0.803 50: Before cleaning: 603 pairs 50: Before cleaning: 618 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 50: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 117 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (117 atoms, 16 residues) 50: 50: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue LYS50 as a starting terminus. 50: 50: Identified residue PRO65 as a ending terminus. 50: Start terminus LYS-50: NH3+ 50: End terminus PRO-65: PRO-COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 228 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 232, now 232 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 618 dihedrals, 48 impropers, 419 angles 50: 597 pairs, 232 bonds and 0 virtual sites 50: 50: Total mass 1662.883 a.m.u. 50: 50: Total charge -0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 50: 50: The Oplsaa force field and the tip4p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (24 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 89 donors and 98 acceptors were found. 50: There are 129 hydrogen bonds 50: Will use HISE for residue 31 50: Will use HISE for residue 51 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS25 HIS31 HIS51 50: SG14 NE264 NE2226 50: HIS31 NE264 1.921 50: HIS51 NE2226 1.498 2.650 50: CYS80 SG477 0.207 1.984 1.570 50: Linking CYS-25 SG-14 and CYS-80 SG-477... 50: Before cleaning: 2499 pairs 50: Before cleaning: 2524 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 50: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 50: 50: chain #res #atoms 50: 50: 1 'A' 58 488 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 'A' (488 atoms, 58 residues) 50: 50: Identified residue ASN24 as a starting terminus. 50: 50: Identified residue ARG81 as a ending terminus. 50: Start terminus ASN-24: NH3+ 50: End terminus ARG-81: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 58 residues with 936 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 951, now 951 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 2524 dihedrals, 208 impropers, 1704 angles 50: 2469 pairs, 951 bonds and 0 virtual sites 50: 50: Total mass 6908.578 a.m.u. 50: 50: Total charge -6.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 50: 50: The Oplsaa force field and the tip4p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (64 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 25 donors and 23 acceptors were found. 50: There are 41 hydrogen bonds 50: Will use HISE for residue 8 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS3 HIS8 50: SG9 NE251 50: HIS8 NE251 1.055 50: MET12 SD83 0.763 0.990 50: Marked 124 virtual sites 50: Added 16 dummy masses 50: Added 26 new constraints 50: Before cleaning: 653 pairs 50: Before cleaning: 663 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 50: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 128 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (128 atoms, 16 residues) 50: 50: Identified residue ALA2 as a starting terminus. 50: 50: Identified residue SER17 as a ending terminus. 50: Start terminus ALA-2: NH3+ 50: End terminus SER-17: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 252 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 254, now 254 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 663 dihedrals, 51 impropers, 457 angles 50: 650 pairs, 254 bonds and 130 virtual sites 50: 50: Total mass 1846.112 a.m.u. 50: 50: Total charge -0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 50: 50: The Oplsaa force field and the tip4p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (35 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 30 donors and 22 acceptors were found. 50: There are 36 hydrogen bonds 50: Will use HISE for residue 29 50: Will use HISE for residue 32 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS27 HIS29 50: SG90 NE2111 50: HIS29 NE2111 0.987 50: HIS32 NE2135 1.590 1.155 50: Marked 132 virtual sites 50: Added 10 dummy masses 50: Added 19 new constraints 50: Before cleaning: 748 pairs 50: Before cleaning: 778 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 50: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 149 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (149 atoms, 16 residues) 50: 50: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue THR18 as a starting terminus. 50: 50: Identified residue PHE33 as a ending terminus. 50: Start terminus THR-18: NH3+ 50: End terminus PHE-33: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 281 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 290, now 290 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 778 dihedrals, 72 impropers, 516 angles 50: 736 pairs, 290 bonds and 133 virtual sites 50: 50: Total mass 2088.357 a.m.u. 50: 50: Total charge 1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 50: 50: The Oplsaa force field and the tip4p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (26 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 22 acceptors were found. 50: There are 26 hydrogen bonds 50: Will use HISE for residue 45 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS45 50: NE295 50: MET46 SD102 1.078 50: Marked 123 virtual sites 50: Added 22 dummy masses 50: Added 35 new constraints 50: Before cleaning: 676 pairs 50: Before cleaning: 696 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 50: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 132 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (132 atoms, 16 residues) 50: 50: Identified residue ALA34 as a starting terminus. 50: 50: Identified residue ALA49 as a ending terminus. 50: Start terminus ALA-34: NH3+ 50: End terminus ALA-49: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 255 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 261, now 261 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 696 dihedrals, 56 impropers, 472 angles 50: 667 pairs, 261 bonds and 132 virtual sites 50: 50: Total mass 1861.128 a.m.u. 50: 50: Total charge -1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 50: 50: The Oplsaa force field and the tip4p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (39 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 21 acceptors were found. 50: There are 30 hydrogen bonds 50: Will use HISE for residue 60 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS60 50: NE285 50: CYS62 SG98 0.803 50: Marked 111 virtual sites 50: Added 18 dummy masses 50: Added 31 new constraints 50: Before cleaning: 603 pairs 50: Before cleaning: 618 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 50: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 117 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (117 atoms, 16 residues) 50: 50: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue LYS50 as a starting terminus. 50: 50: Identified residue PRO65 as a ending terminus. 50: Start terminus LYS-50: NH3+ 50: End terminus PRO-65: PRO-COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 228 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 232, now 232 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 618 dihedrals, 48 impropers, 419 angles 50: 597 pairs, 232 bonds and 116 virtual sites 50: 50: Total mass 1662.883 a.m.u. 50: 50: Total charge -0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 50: 50: The Oplsaa force field and the tip4p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (31 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 89 donors and 98 acceptors were found. 50: There are 129 hydrogen bonds 50: Will use HISE for residue 31 50: Will use HISE for residue 51 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS25 HIS31 HIS51 50: SG14 NE264 NE2226 50: HIS31 NE264 1.921 50: HIS51 NE2226 1.498 2.650 50: CYS80 SG477 0.207 1.984 1.570 50: Linking CYS-25 SG-14 and CYS-80 SG-477... 50: Marked 447 virtual sites 50: Added 58 dummy masses 50: Added 101 new constraints 50: Before cleaning: 2499 pairs 50: Before cleaning: 2524 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 50: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 50: 50: chain #res #atoms 50: 50: 1 'A' 58 488 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 'A' (488 atoms, 58 residues) 50: 50: Identified residue ASN24 as a starting terminus. 50: 50: Identified residue ARG81 as a ending terminus. 50: Start terminus ASN-24: NH3+ 50: End terminus ARG-81: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 58 residues with 936 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 951, now 951 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 2524 dihedrals, 208 impropers, 1704 angles 50: 2469 pairs, 951 bonds and 462 virtual sites 50: 50: Total mass 6908.578 a.m.u. 50: 50: Total charge -6.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 50: 50: The Oplsaa force field and the tip4p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (63 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 25 donors and 23 acceptors were found. 50: There are 41 hydrogen bonds 50: Will use HISE for residue 8 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS3 HIS8 50: SG9 NE251 50: HIS8 NE251 1.055 50: MET12 SD83 0.763 0.990 50: Before cleaning: 653 pairs 50: Before cleaning: 663 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 50: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 128 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (128 atoms, 16 residues) 50: 50: Identified residue ALA2 as a starting terminus. 50: 50: Identified residue SER17 as a ending terminus. 50: Start terminus ALA-2: NH3+ 50: End terminus SER-17: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 252 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 254, now 254 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 663 dihedrals, 51 impropers, 457 angles 50: 650 pairs, 254 bonds and 0 virtual sites 50: 50: Total mass 1846.112 a.m.u. 50: 50: Total charge -0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 50: 50: The Oplsaa force field and the tip5p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (44 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 30 donors and 22 acceptors were found. 50: There are 36 hydrogen bonds 50: Will use HISE for residue 29 50: Will use HISE for residue 32 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS27 HIS29 50: SG90 NE2111 50: HIS29 NE2111 0.987 50: HIS32 NE2135 1.590 1.155 50: Before cleaning: 748 pairs 50: Before cleaning: 778 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 50: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 149 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (149 atoms, 16 residues) 50: 50: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue THR18 as a starting terminus. 50: 50: Identified residue PHE33 as a ending terminus. 50: Start terminus THR-18: NH3+ 50: End terminus PHE-33: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 281 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 290, now 290 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 778 dihedrals, 72 impropers, 516 angles 50: 736 pairs, 290 bonds and 0 virtual sites 50: 50: Total mass 2088.357 a.m.u. 50: 50: Total charge 1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 50: 50: The Oplsaa force field and the tip5p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (34 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 22 acceptors were found. 50: There are 26 hydrogen bonds 50: Will use HISE for residue 45 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS45 50: NE295 50: MET46 SD102 1.078 50: Before cleaning: 676 pairs 50: Before cleaning: 696 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 50: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 132 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (132 atoms, 16 residues) 50: 50: Identified residue ALA34 as a starting terminus. 50: 50: Identified residue ALA49 as a ending terminus. 50: Start terminus ALA-34: NH3+ 50: End terminus ALA-49: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 255 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 261, now 261 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 696 dihedrals, 56 impropers, 472 angles 50: 667 pairs, 261 bonds and 0 virtual sites 50: 50: Total mass 1861.128 a.m.u. 50: 50: Total charge -1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 50: 50: The Oplsaa force field and the tip5p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (24 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 21 acceptors were found. 50: There are 30 hydrogen bonds 50: Will use HISE for residue 60 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS60 50: NE285 50: CYS62 SG98 0.803 50: Before cleaning: 603 pairs 50: Before cleaning: 618 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 50: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 117 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (117 atoms, 16 residues) 50: 50: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue LYS50 as a starting terminus. 50: 50: Identified residue PRO65 as a ending terminus. 50: Start terminus LYS-50: NH3+ 50: End terminus PRO-65: PRO-COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 228 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 232, now 232 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 618 dihedrals, 48 impropers, 419 angles 50: 597 pairs, 232 bonds and 0 virtual sites 50: 50: Total mass 1662.883 a.m.u. 50: 50: Total charge -0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 50: 50: The Oplsaa force field and the tip5p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (22 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 89 donors and 98 acceptors were found. 50: There are 129 hydrogen bonds 50: Will use HISE for residue 31 50: Will use HISE for residue 51 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS25 HIS31 HIS51 50: SG14 NE264 NE2226 50: HIS31 NE264 1.921 50: HIS51 NE2226 1.498 2.650 50: CYS80 SG477 0.207 1.984 1.570 50: Linking CYS-25 SG-14 and CYS-80 SG-477... 50: Before cleaning: 2499 pairs 50: Before cleaning: 2524 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 50: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 50: 50: chain #res #atoms 50: 50: 1 'A' 58 488 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 'A' (488 atoms, 58 residues) 50: 50: Identified residue ASN24 as a starting terminus. 50: 50: Identified residue ARG81 as a ending terminus. 50: Start terminus ASN-24: NH3+ 50: End terminus ARG-81: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 58 residues with 936 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 951, now 951 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 2524 dihedrals, 208 impropers, 1704 angles 50: 2469 pairs, 951 bonds and 0 virtual sites 50: 50: Total mass 6908.578 a.m.u. 50: 50: Total charge -6.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 50: 50: The Oplsaa force field and the tip5p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (65 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 25 donors and 23 acceptors were found. 50: There are 41 hydrogen bonds 50: Will use HISE for residue 8 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS3 HIS8 50: SG9 NE251 50: HIS8 NE251 1.055 50: MET12 SD83 0.763 0.990 50: Marked 124 virtual sites 50: Added 16 dummy masses 50: Added 26 new constraints 50: Before cleaning: 653 pairs 50: Before cleaning: 663 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 50: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 128 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (128 atoms, 16 residues) 50: 50: Identified residue ALA2 as a starting terminus. 50: 50: Identified residue SER17 as a ending terminus. 50: Start terminus ALA-2: NH3+ 50: End terminus SER-17: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 252 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 254, now 254 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 663 dihedrals, 51 impropers, 457 angles 50: 650 pairs, 254 bonds and 130 virtual sites 50: 50: Total mass 1846.112 a.m.u. 50: 50: Total charge -0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 50: 50: The Oplsaa force field and the tip5p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (36 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 30 donors and 22 acceptors were found. 50: There are 36 hydrogen bonds 50: Will use HISE for residue 29 50: Will use HISE for residue 32 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS27 HIS29 50: SG90 NE2111 50: HIS29 NE2111 0.987 50: HIS32 NE2135 1.590 1.155 50: Marked 132 virtual sites 50: Added 10 dummy masses 50: Added 19 new constraints 50: Before cleaning: 748 pairs 50: Before cleaning: 778 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 50: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 149 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (149 atoms, 16 residues) 50: 50: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue THR18 as a starting terminus. 50: 50: Identified residue PHE33 as a ending terminus. 50: Start terminus THR-18: NH3+ 50: End terminus PHE-33: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 281 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 290, now 290 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 778 dihedrals, 72 impropers, 516 angles 50: 736 pairs, 290 bonds and 133 virtual sites 50: 50: Total mass 2088.357 a.m.u. 50: 50: Total charge 1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 50: 50: The Oplsaa force field and the tip5p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (43 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 22 acceptors were found. 50: There are 26 hydrogen bonds 50: Will use HISE for residue 45 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS45 50: NE295 50: MET46 SD102 1.078 50: Marked 123 virtual sites 50: Added 22 dummy masses 50: Added 35 new constraints 50: Before cleaning: 676 pairs 50: Before cleaning: 696 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 50: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 132 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (132 atoms, 16 residues) 50: 50: Identified residue ALA34 as a starting terminus. 50: 50: Identified residue ALA49 as a ending terminus. 50: Start terminus ALA-34: NH3+ 50: End terminus ALA-49: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 255 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 261, now 261 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 696 dihedrals, 56 impropers, 472 angles 50: 667 pairs, 261 bonds and 132 virtual sites 50: 50: Total mass 1861.128 a.m.u. 50: 50: Total charge -1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 50: 50: The Oplsaa force field and the tip5p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (45 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 21 acceptors were found. 50: There are 30 hydrogen bonds 50: Will use HISE for residue 60 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS60 50: NE285 50: CYS62 SG98 0.803 50: Marked 111 virtual sites 50: Added 18 dummy masses 50: Added 31 new constraints 50: Before cleaning: 603 pairs 50: Before cleaning: 618 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 50: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 117 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (117 atoms, 16 residues) 50: 50: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue LYS50 as a starting terminus. 50: 50: Identified residue PRO65 as a ending terminus. 50: Start terminus LYS-50: NH3+ 50: End terminus PRO-65: PRO-COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 228 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 232, now 232 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 618 dihedrals, 48 impropers, 419 angles 50: 597 pairs, 232 bonds and 116 virtual sites 50: 50: Total mass 1662.883 a.m.u. 50: 50: Total charge -0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 50: 50: The Oplsaa force field and the tip5p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (23 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 89 donors and 98 acceptors were found. 50: There are 129 hydrogen bonds 50: Will use HISE for residue 31 50: Will use HISE for residue 51 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS25 HIS31 HIS51 50: SG14 NE264 NE2226 50: HIS31 NE264 1.921 50: HIS51 NE2226 1.498 2.650 50: CYS80 SG477 0.207 1.984 1.570 50: Linking CYS-25 SG-14 and CYS-80 SG-477... 50: Marked 447 virtual sites 50: Added 58 dummy masses 50: Added 101 new constraints 50: Before cleaning: 2499 pairs 50: Before cleaning: 2524 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 50: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 50: 50: chain #res #atoms 50: 50: 1 'A' 58 488 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 'A' (488 atoms, 58 residues) 50: 50: Identified residue ASN24 as a starting terminus. 50: 50: Identified residue ARG81 as a ending terminus. 50: Start terminus ASN-24: NH3+ 50: End terminus ARG-81: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 58 residues with 936 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 951, now 951 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 2524 dihedrals, 208 impropers, 1704 angles 50: 2469 pairs, 951 bonds and 462 virtual sites 50: 50: Total mass 6908.578 a.m.u. 50: 50: Total charge -6.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 50: 50: The Oplsaa force field and the tip5p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (82 ms) 50: [----------] 30 tests from Oplsaa/Pdb2gmxTest (1616 ms total) 50: 50: [----------] Global test environment tear-down 50: [==========] 30 tests from 1 test suite ran. (1616 ms total) 50: [ PASSED ] 30 tests. 50/87 Test #50: Pdb2gmx1Test .............................. Passed 1.63 sec test 51 Start 51: Pdb2gmx2Test 51: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/pdb2gmx2-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/Pdb2gmx2Test.xml" 51: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests 51: Test timeout computed to be: 1920 51: [==========] Running 40 tests from 2 test suites. 51: [----------] Global test environment set-up. 51: [----------] 20 tests from G43a1/Pdb2gmxTest 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 25 donors and 23 acceptors were found. 51: There are 41 hydrogen bonds 51: Will use HISE for residue 8 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS3 HIS8 51: SG9 NE251 51: HIS8 NE251 1.055 51: MET12 SD83 0.763 0.990 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 267 pairs 51: Before cleaning: 305 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 51: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 128 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (128 atoms, 16 residues) 51: 51: Identified residue ALA2 as a starting terminus. 51: 51: Identified residue SER17 as a ending terminus. 51: Start terminus ALA-2: NH3+ 51: End terminus SER-17: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 165 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 172, now 167 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 90 dihedrals, 77 impropers, 241 angles 51: 267 pairs, 167 bonds and 0 virtual sites 51: 51: Total mass 1846.116 a.m.u. 51: 51: Total charge 0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 51: 51: The Gromos43a1 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (64 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 30 donors and 22 acceptors were found. 51: There are 36 hydrogen bonds 51: Will use HISE for residue 29 51: Will use HISE for residue 32 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS27 HIS29 51: SG90 NE2111 51: HIS29 NE2111 0.987 51: HIS32 NE2135 1.590 1.155 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 273 pairs 51: Before cleaning: 429 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 51: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 149 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (149 atoms, 16 residues) 51: 51: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue THR18 as a starting terminus. 51: 51: Identified residue PHE33 as a ending terminus. 51: Start terminus THR-18: NH3+ 51: End terminus PHE-33: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 202 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 216, now 211 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 93 dihedrals, 134 impropers, 316 angles 51: 273 pairs, 211 bonds and 0 virtual sites 51: 51: Total mass 2088.361 a.m.u. 51: 51: Total charge 1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 51: 51: The Gromos43a1 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (27 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 22 acceptors were found. 51: There are 26 hydrogen bonds 51: Will use HISE for residue 45 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS45 51: NE295 51: MET46 SD102 1.078 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 242 pairs 51: Before cleaning: 349 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 51: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 132 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (132 atoms, 16 residues) 51: 51: Identified residue ALA34 as a starting terminus. 51: 51: Identified residue ALA49 as a ending terminus. 51: Start terminus ALA-34: NH3+ 51: End terminus ALA-49: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 168 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 179, now 174 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 81 dihedrals, 102 impropers, 260 angles 51: 242 pairs, 174 bonds and 0 virtual sites 51: 51: Total mass 1861.132 a.m.u. 51: 51: Total charge -1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 51: 51: The Gromos43a1 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (52 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 21 acceptors were found. 51: There are 30 hydrogen bonds 51: Will use HISE for residue 60 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS60 51: NE285 51: CYS62 SG98 0.803 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 232 pairs 51: Before cleaning: 299 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 51: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 117 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (117 atoms, 16 residues) 51: 51: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue LYS50 as a starting terminus. 51: 51: Identified residue PRO65 as a ending terminus. 51: Start terminus LYS-50: NH3+ 51: End terminus PRO-65: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 150 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 159, now 154 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 78 dihedrals, 80 impropers, 227 angles 51: 232 pairs, 154 bonds and 0 virtual sites 51: 51: Total mass 1662.887 a.m.u. 51: 51: Total charge 0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 51: 51: The Gromos43a1 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (43 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 89 donors and 98 acceptors were found. 51: There are 129 hydrogen bonds 51: Will use HISE for residue 31 51: Will use HISE for residue 51 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS25 HIS31 HIS51 51: SG14 NE264 NE2226 51: HIS31 NE264 1.921 51: HIS51 NE2226 1.498 2.650 51: CYS80 SG477 0.207 1.984 1.570 51: Linking CYS-25 SG-14 and CYS-80 SG-477... 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 972 pairs 51: Before cleaning: 1256 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 51: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 51: 51: chain #res #atoms 51: 51: 1 'A' 58 488 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 'A' (488 atoms, 58 residues) 51: 51: Identified residue ASN24 as a starting terminus. 51: 51: Identified residue ARG81 as a ending terminus. 51: Start terminus ASN-24: NH3+ 51: End terminus ARG-81: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 58 residues with 635 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 655, now 650 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 321 dihedrals, 350 impropers, 955 angles 51: 972 pairs, 650 bonds and 0 virtual sites 51: 51: Total mass 6908.582 a.m.u. 51: 51: Total charge -6.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 51: 51: The Gromos43a1 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (62 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 25 donors and 23 acceptors were found. 51: There are 41 hydrogen bonds 51: Will use HISE for residue 8 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS3 HIS8 51: SG9 NE251 51: HIS8 NE251 1.055 51: MET12 SD83 0.763 0.990 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 37 virtual sites 51: Added 4 dummy masses 51: Added 8 new constraints 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 267 pairs 51: Before cleaning: 305 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 51: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 128 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (128 atoms, 16 residues) 51: 51: Identified residue ALA2 as a starting terminus. 51: 51: Identified residue SER17 as a ending terminus. 51: Start terminus ALA-2: NH3+ 51: End terminus SER-17: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 165 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 172, now 167 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 90 dihedrals, 77 impropers, 241 angles 51: 267 pairs, 167 bonds and 37 virtual sites 51: 51: Total mass 1846.116 a.m.u. 51: 51: Total charge 0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 51: 51: The Gromos43a1 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (41 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 30 donors and 22 acceptors were found. 51: There are 36 hydrogen bonds 51: Will use HISE for residue 29 51: Will use HISE for residue 32 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS27 HIS29 51: SG90 NE2111 51: HIS29 NE2111 0.987 51: HIS32 NE2135 1.590 1.155 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 53 virtual sites 51: Added 4 dummy masses 51: Added 10 new constraints 51: 51: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 273 pairs 51: Before cleaning: 429 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 51: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 149 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (149 atoms, 16 residues) 51: 51: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue THR18 as a starting terminus. 51: 51: Identified residue PHE33 as a ending terminus. 51: Start terminus THR-18: NH3+ 51: End terminus PHE-33: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 202 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 216, now 211 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 93 dihedrals, 134 impropers, 316 angles 51: 273 pairs, 211 bonds and 51 virtual sites 51: 51: Total mass 2088.361 a.m.u. 51: 51: Total charge 1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 51: 51: The Gromos43a1 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (100 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 22 acceptors were found. 51: There are 26 hydrogen bonds 51: Will use HISE for residue 45 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS45 51: NE295 51: MET46 SD102 1.078 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 36 virtual sites 51: Added 4 dummy masses 51: Added 8 new constraints 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 242 pairs 51: Before cleaning: 349 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 51: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 132 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (132 atoms, 16 residues) 51: 51: Identified residue ALA34 as a starting terminus. 51: 51: Identified residue ALA49 as a ending terminus. 51: Start terminus ALA-34: NH3+ 51: End terminus ALA-49: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 168 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 179, now 174 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 81 dihedrals, 102 impropers, 260 angles 51: 242 pairs, 174 bonds and 36 virtual sites 51: 51: Total mass 1861.132 a.m.u. 51: 51: Total charge -1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 51: 51: The Gromos43a1 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (36 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 21 acceptors were found. 51: There are 30 hydrogen bonds 51: Will use HISE for residue 60 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS60 51: NE285 51: CYS62 SG98 0.803 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 33 virtual sites 51: Added 4 dummy masses 51: Added 10 new constraints 51: 51: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 232 pairs 51: Before cleaning: 299 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 51: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 117 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (117 atoms, 16 residues) 51: 51: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue LYS50 as a starting terminus. 51: 51: Identified residue PRO65 as a ending terminus. 51: Start terminus LYS-50: NH3+ 51: End terminus PRO-65: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 150 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 159, now 154 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 78 dihedrals, 80 impropers, 227 angles 51: 232 pairs, 154 bonds and 31 virtual sites 51: 51: Total mass 1662.887 a.m.u. 51: 51: Total charge 0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 51: 51: The Gromos43a1 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (41 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 89 donors and 98 acceptors were found. 51: There are 129 hydrogen bonds 51: Will use HISE for residue 31 51: Will use HISE for residue 51 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS25 HIS31 HIS51 51: SG14 NE264 NE2226 51: HIS31 NE264 1.921 51: HIS51 NE2226 1.498 2.650 51: CYS80 SG477 0.207 1.984 1.570 51: Linking CYS-25 SG-14 and CYS-80 SG-477... 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 146 virtual sites 51: Added 10 dummy masses 51: Added 29 new constraints 51: 51: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 972 pairs 51: Before cleaning: 1256 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 51: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 51: 51: chain #res #atoms 51: 51: 1 'A' 58 488 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 'A' (488 atoms, 58 residues) 51: 51: Identified residue ASN24 as a starting terminus. 51: 51: Identified residue ARG81 as a ending terminus. 51: Start terminus ASN-24: NH3+ 51: End terminus ARG-81: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 58 residues with 635 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 655, now 650 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 321 dihedrals, 350 impropers, 955 angles 51: 972 pairs, 650 bonds and 137 virtual sites 51: 51: Total mass 6908.582 a.m.u. 51: 51: Total charge -6.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 51: 51: The Gromos43a1 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (52 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 25 donors and 23 acceptors were found. 51: There are 41 hydrogen bonds 51: Will use HISE for residue 8 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS3 HIS8 51: SG9 NE251 51: HIS8 NE251 1.055 51: MET12 SD83 0.763 0.990 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 267 pairs 51: Before cleaning: 305 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 51: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 128 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (128 atoms, 16 residues) 51: 51: Identified residue ALA2 as a starting terminus. 51: 51: Identified residue SER17 as a ending terminus. 51: Start terminus ALA-2: NH3+ 51: End terminus SER-17: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 165 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 172, now 167 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 90 dihedrals, 77 impropers, 241 angles 51: 267 pairs, 167 bonds and 0 virtual sites 51: 51: Total mass 1846.116 a.m.u. 51: 51: Total charge 0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 51: 51: The Gromos43a1 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (37 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 30 donors and 22 acceptors were found. 51: There are 36 hydrogen bonds 51: Will use HISE for residue 29 51: Will use HISE for residue 32 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS27 HIS29 51: SG90 NE2111 51: HIS29 NE2111 0.987 51: HIS32 NE2135 1.590 1.155 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 273 pairs 51: Before cleaning: 429 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 51: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 149 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (149 atoms, 16 residues) 51: 51: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue THR18 as a starting terminus. 51: 51: Identified residue PHE33 as a ending terminus. 51: Start terminus THR-18: NH3+ 51: End terminus PHE-33: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 202 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 216, now 211 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 93 dihedrals, 134 impropers, 316 angles 51: 273 pairs, 211 bonds and 0 virtual sites 51: 51: Total mass 2088.361 a.m.u. 51: 51: Total charge 1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 51: 51: The Gromos43a1 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (37 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 22 acceptors were found. 51: There are 26 hydrogen bonds 51: Will use HISE for residue 45 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS45 51: NE295 51: MET46 SD102 1.078 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 242 pairs 51: Before cleaning: 349 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 51: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 132 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (132 atoms, 16 residues) 51: 51: Identified residue ALA34 as a starting terminus. 51: 51: Identified residue ALA49 as a ending terminus. 51: Start terminus ALA-34: NH3+ 51: End terminus ALA-49: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 168 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 179, now 174 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 81 dihedrals, 102 impropers, 260 angles 51: 242 pairs, 174 bonds and 0 virtual sites 51: 51: Total mass 1861.132 a.m.u. 51: 51: Total charge -1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 51: 51: The Gromos43a1 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (35 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 21 acceptors were found. 51: There are 30 hydrogen bonds 51: Will use HISE for residue 60 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS60 51: NE285 51: CYS62 SG98 0.803 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 232 pairs 51: Before cleaning: 299 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 51: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 117 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (117 atoms, 16 residues) 51: 51: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue LYS50 as a starting terminus. 51: 51: Identified residue PRO65 as a ending terminus. 51: Start terminus LYS-50: NH3+ 51: End terminus PRO-65: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 150 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 159, now 154 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 78 dihedrals, 80 impropers, 227 angles 51: 232 pairs, 154 bonds and 0 virtual sites 51: 51: Total mass 1662.887 a.m.u. 51: 51: Total charge 0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 51: 51: The Gromos43a1 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (36 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 89 donors and 98 acceptors were found. 51: There are 129 hydrogen bonds 51: Will use HISE for residue 31 51: Will use HISE for residue 51 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS25 HIS31 HIS51 51: SG14 NE264 NE2226 51: HIS31 NE264 1.921 51: HIS51 NE2226 1.498 2.650 51: CYS80 SG477 0.207 1.984 1.570 51: Linking CYS-25 SG-14 and CYS-80 SG-477... 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 972 pairs 51: Before cleaning: 1256 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 51: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 51: 51: chain #res #atoms 51: 51: 1 'A' 58 488 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 'A' (488 atoms, 58 residues) 51: 51: Identified residue ASN24 as a starting terminus. 51: 51: Identified residue ARG81 as a ending terminus. 51: Start terminus ASN-24: NH3+ 51: End terminus ARG-81: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 58 residues with 635 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 655, now 650 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 321 dihedrals, 350 impropers, 955 angles 51: 972 pairs, 650 bonds and 0 virtual sites 51: 51: Total mass 6908.582 a.m.u. 51: 51: Total charge -6.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 51: 51: The Gromos43a1 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (46 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 25 donors and 23 acceptors were found. 51: There are 41 hydrogen bonds 51: Will use HISE for residue 8 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS3 HIS8 51: SG9 NE251 51: HIS8 NE251 1.055 51: MET12 SD83 0.763 0.990 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 37 virtual sites 51: Added 4 dummy masses 51: Added 8 new constraints 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 267 pairs 51: Before cleaning: 305 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 51: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 128 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (128 atoms, 16 residues) 51: 51: Identified residue ALA2 as a starting terminus. 51: 51: Identified residue SER17 as a ending terminus. 51: Start terminus ALA-2: NH3+ 51: End terminus SER-17: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 165 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 172, now 167 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 90 dihedrals, 77 impropers, 241 angles 51: 267 pairs, 167 bonds and 37 virtual sites 51: 51: Total mass 1846.116 a.m.u. 51: 51: Total charge 0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 51: 51: The Gromos43a1 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (36 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 30 donors and 22 acceptors were found. 51: There are 36 hydrogen bonds 51: Will use HISE for residue 29 51: Will use HISE for residue 32 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS27 HIS29 51: SG90 NE2111 51: HIS29 NE2111 0.987 51: HIS32 NE2135 1.590 1.155 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 53 virtual sites 51: Added 4 dummy masses 51: Added 10 new constraints 51: 51: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 273 pairs 51: Before cleaning: 429 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 51: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 149 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (149 atoms, 16 residues) 51: 51: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue THR18 as a starting terminus. 51: 51: Identified residue PHE33 as a ending terminus. 51: Start terminus THR-18: NH3+ 51: End terminus PHE-33: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 202 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 216, now 211 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 93 dihedrals, 134 impropers, 316 angles 51: 273 pairs, 211 bonds and 51 virtual sites 51: 51: Total mass 2088.361 a.m.u. 51: 51: Total charge 1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 51: 51: The Gromos43a1 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (37 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 22 acceptors were found. 51: There are 26 hydrogen bonds 51: Will use HISE for residue 45 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS45 51: NE295 51: MET46 SD102 1.078 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 36 virtual sites 51: Added 4 dummy masses 51: Added 8 new constraints 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 242 pairs 51: Before cleaning: 349 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 51: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 132 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (132 atoms, 16 residues) 51: 51: Identified residue ALA34 as a starting terminus. 51: 51: Identified residue ALA49 as a ending terminus. 51: Start terminus ALA-34: NH3+ 51: End terminus ALA-49: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 168 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 179, now 174 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 81 dihedrals, 102 impropers, 260 angles 51: 242 pairs, 174 bonds and 36 virtual sites 51: 51: Total mass 1861.132 a.m.u. 51: 51: Total charge -1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 51: 51: The Gromos43a1 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (46 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 21 acceptors were found. 51: There are 30 hydrogen bonds 51: Will use HISE for residue 60 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS60 51: NE285 51: CYS62 SG98 0.803 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 33 virtual sites 51: Added 4 dummy masses 51: Added 10 new constraints 51: 51: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 232 pairs 51: Before cleaning: 299 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 51: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 117 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (117 atoms, 16 residues) 51: 51: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue LYS50 as a starting terminus. 51: 51: Identified residue PRO65 as a ending terminus. 51: Start terminus LYS-50: NH3+ 51: End terminus PRO-65: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 150 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 159, now 154 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 78 dihedrals, 80 impropers, 227 angles 51: 232 pairs, 154 bonds and 31 virtual sites 51: 51: Total mass 1662.887 a.m.u. 51: 51: Total charge 0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 51: 51: The Gromos43a1 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (45 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 89 donors and 98 acceptors were found. 51: There are 129 hydrogen bonds 51: Will use HISE for residue 31 51: Will use HISE for residue 51 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS25 HIS31 HIS51 51: SG14 NE264 NE2226 51: HIS31 NE264 1.921 51: HIS51 NE2226 1.498 2.650 51: CYS80 SG477 0.207 1.984 1.570 51: Linking CYS-25 SG-14 and CYS-80 SG-477... 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 146 virtual sites 51: Added 10 dummy masses 51: Added 29 new constraints 51: 51: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 972 pairs 51: Before cleaning: 1256 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 51: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 51: 51: chain #res #atoms 51: 51: 1 'A' 58 488 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 'A' (488 atoms, 58 residues) 51: 51: Identified residue ASN24 as a starting terminus. 51: 51: Identified residue ARG81 as a ending terminus. 51: Start terminus ASN-24: NH3+ 51: End terminus ARG-81: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 58 residues with 635 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 655, now 650 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 321 dihedrals, 350 impropers, 955 angles 51: 972 pairs, 650 bonds and 137 virtual sites 51: 51: Total mass 6908.582 a.m.u. 51: 51: Total charge -6.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 51: 51: The Gromos43a1 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (85 ms) 51: [----------] 20 tests from G43a1/Pdb2gmxTest (989 ms total) 51: 51: [----------] 20 tests from G53a6/Pdb2gmxTest 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 25 donors and 23 acceptors were found. 51: There are 41 hydrogen bonds 51: Will use HISE for residue 8 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS3 HIS8 51: SG9 NE251 51: HIS8 NE251 1.055 51: MET12 SD83 0.763 0.990 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 267 pairs 51: Before cleaning: 312 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 51: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 128 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (128 atoms, 16 residues) 51: 51: Identified residue ALA2 as a starting terminus. 51: 51: Identified residue SER17 as a ending terminus. 51: Start terminus ALA-2: NH3+ 51: End terminus SER-17: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 167 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 174, now 169 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 90 dihedrals, 79 impropers, 245 angles 51: 267 pairs, 169 bonds and 0 virtual sites 51: 51: Total mass 1846.116 a.m.u. 51: 51: Total charge -0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 51: 51: The Gromos53a6 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (58 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 30 donors and 22 acceptors were found. 51: There are 36 hydrogen bonds 51: Will use HISE for residue 29 51: Will use HISE for residue 32 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS27 HIS29 51: SG90 NE2111 51: HIS29 NE2111 0.987 51: HIS32 NE2135 1.590 1.155 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 273 pairs 51: Before cleaning: 443 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 51: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 149 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (149 atoms, 16 residues) 51: 51: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue THR18 as a starting terminus. 51: 51: Identified residue PHE33 as a ending terminus. 51: Start terminus THR-18: NH3+ 51: End terminus PHE-33: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 206 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 220, now 215 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 93 dihedrals, 138 impropers, 324 angles 51: 273 pairs, 215 bonds and 0 virtual sites 51: 51: Total mass 2088.361 a.m.u. 51: 51: Total charge 1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 51: 51: The Gromos53a6 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (44 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 22 acceptors were found. 51: There are 26 hydrogen bonds 51: Will use HISE for residue 45 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS45 51: NE295 51: MET46 SD102 1.078 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 242 pairs 51: Before cleaning: 356 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 51: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 132 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (132 atoms, 16 residues) 51: 51: Identified residue ALA34 as a starting terminus. 51: 51: Identified residue ALA49 as a ending terminus. 51: Start terminus ALA-34: NH3+ 51: End terminus ALA-49: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 170 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 181, now 176 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 81 dihedrals, 104 impropers, 264 angles 51: 242 pairs, 176 bonds and 0 virtual sites 51: 51: Total mass 1861.132 a.m.u. 51: 51: Total charge -1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 51: 51: The Gromos53a6 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (52 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 21 acceptors were found. 51: There are 30 hydrogen bonds 51: Will use HISE for residue 60 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS60 51: NE285 51: CYS62 SG98 0.803 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 232 pairs 51: Before cleaning: 306 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 51: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 117 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (117 atoms, 16 residues) 51: 51: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue LYS50 as a starting terminus. 51: 51: Identified residue PRO65 as a ending terminus. 51: Start terminus LYS-50: NH3+ 51: End terminus PRO-65: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 152 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 161, now 156 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 78 dihedrals, 82 impropers, 231 angles 51: 232 pairs, 156 bonds and 0 virtual sites 51: 51: Total mass 1662.887 a.m.u. 51: 51: Total charge -0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 51: 51: The Gromos53a6 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (49 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 89 donors and 98 acceptors were found. 51: There are 129 hydrogen bonds 51: Will use HISE for residue 31 51: Will use HISE for residue 51 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS25 HIS31 HIS51 51: SG14 NE264 NE2226 51: HIS31 NE264 1.921 51: HIS51 NE2226 1.498 2.650 51: CYS80 SG477 0.207 1.984 1.570 51: Linking CYS-25 SG-14 and CYS-80 SG-477... 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 972 pairs 51: Before cleaning: 1270 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 51: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 51: 51: chain #res #atoms 51: 51: 1 'A' 58 488 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 'A' (488 atoms, 58 residues) 51: 51: Identified residue ASN24 as a starting terminus. 51: 51: Identified residue ARG81 as a ending terminus. 51: Start terminus ASN-24: NH3+ 51: End terminus ARG-81: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 58 residues with 639 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 659, now 654 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 321 dihedrals, 354 impropers, 963 angles 51: 972 pairs, 654 bonds and 0 virtual sites 51: 51: Total mass 6908.582 a.m.u. 51: 51: Total charge -6.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 51: 51: The Gromos53a6 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (83 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 25 donors and 23 acceptors were found. 51: There are 41 hydrogen bonds 51: Will use HISE for residue 8 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS3 HIS8 51: SG9 NE251 51: HIS8 NE251 1.055 51: MET12 SD83 0.763 0.990 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 39 virtual sites 51: Added 4 dummy masses 51: Added 8 new constraints 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 267 pairs 51: Before cleaning: 312 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 51: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 128 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (128 atoms, 16 residues) 51: 51: Identified residue ALA2 as a starting terminus. 51: 51: Identified residue SER17 as a ending terminus. 51: Start terminus ALA-2: NH3+ 51: End terminus SER-17: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 167 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 174, now 169 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 90 dihedrals, 79 impropers, 245 angles 51: 267 pairs, 169 bonds and 39 virtual sites 51: 51: Total mass 1846.116 a.m.u. 51: 51: Total charge -0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 51: 51: The Gromos53a6 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (56 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 30 donors and 22 acceptors were found. 51: There are 36 hydrogen bonds 51: Will use HISE for residue 29 51: Will use HISE for residue 32 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS27 HIS29 51: SG90 NE2111 51: HIS29 NE2111 0.987 51: HIS32 NE2135 1.590 1.155 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 57 virtual sites 51: Added 4 dummy masses 51: Added 10 new constraints 51: 51: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 273 pairs 51: Before cleaning: 443 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 51: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 149 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (149 atoms, 16 residues) 51: 51: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue THR18 as a starting terminus. 51: 51: Identified residue PHE33 as a ending terminus. 51: Start terminus THR-18: NH3+ 51: End terminus PHE-33: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 206 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 220, now 215 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 93 dihedrals, 138 impropers, 324 angles 51: 273 pairs, 215 bonds and 55 virtual sites 51: 51: Total mass 2088.361 a.m.u. 51: 51: Total charge 1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 51: 51: The Gromos53a6 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (47 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 22 acceptors were found. 51: There are 26 hydrogen bonds 51: Will use HISE for residue 45 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS45 51: NE295 51: MET46 SD102 1.078 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 38 virtual sites 51: Added 4 dummy masses 51: Added 8 new constraints 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 242 pairs 51: Before cleaning: 356 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 51: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 132 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (132 atoms, 16 residues) 51: 51: Identified residue ALA34 as a starting terminus. 51: 51: Identified residue ALA49 as a ending terminus. 51: Start terminus ALA-34: NH3+ 51: End terminus ALA-49: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 170 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 181, now 176 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 81 dihedrals, 104 impropers, 264 angles 51: 242 pairs, 176 bonds and 38 virtual sites 51: 51: Total mass 1861.132 a.m.u. 51: 51: Total charge -1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 51: 51: The Gromos53a6 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (42 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 21 acceptors were found. 51: There are 30 hydrogen bonds 51: Will use HISE for residue 60 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS60 51: NE285 51: CYS62 SG98 0.803 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 35 virtual sites 51: Added 4 dummy masses 51: Added 10 new constraints 51: 51: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 232 pairs 51: Before cleaning: 306 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 51: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 117 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (117 atoms, 16 residues) 51: 51: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue LYS50 as a starting terminus. 51: 51: Identified residue PRO65 as a ending terminus. 51: Start terminus LYS-50: NH3+ 51: End terminus PRO-65: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 152 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 161, now 156 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 78 dihedrals, 82 impropers, 231 angles 51: 232 pairs, 156 bonds and 33 virtual sites 51: 51: Total mass 1662.887 a.m.u. 51: 51: Total charge -0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 51: 51: The Gromos53a6 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (46 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 89 donors and 98 acceptors were found. 51: There are 129 hydrogen bonds 51: Will use HISE for residue 31 51: Will use HISE for residue 51 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS25 HIS31 HIS51 51: SG14 NE264 NE2226 51: HIS31 NE264 1.921 51: HIS51 NE2226 1.498 2.650 51: CYS80 SG477 0.207 1.984 1.570 51: Linking CYS-25 SG-14 and CYS-80 SG-477... 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 150 virtual sites 51: Added 10 dummy masses 51: Added 29 new constraints 51: 51: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 972 pairs 51: Before cleaning: 1270 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 51: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 51: 51: chain #res #atoms 51: 51: 1 'A' 58 488 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 'A' (488 atoms, 58 residues) 51: 51: Identified residue ASN24 as a starting terminus. 51: 51: Identified residue ARG81 as a ending terminus. 51: Start terminus ASN-24: NH3+ 51: End terminus ARG-81: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 58 residues with 639 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 659, now 654 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 321 dihedrals, 354 impropers, 963 angles 51: 972 pairs, 654 bonds and 141 virtual sites 51: 51: Total mass 6908.582 a.m.u. 51: 51: Total charge -6.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 51: 51: The Gromos53a6 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (88 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 25 donors and 23 acceptors were found. 51: There are 41 hydrogen bonds 51: Will use HISE for residue 8 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS3 HIS8 51: SG9 NE251 51: HIS8 NE251 1.055 51: MET12 SD83 0.763 0.990 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 267 pairs 51: Before cleaning: 312 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 51: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 128 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (128 atoms, 16 residues) 51: 51: Identified residue ALA2 as a starting terminus. 51: 51: Identified residue SER17 as a ending terminus. 51: Start terminus ALA-2: NH3+ 51: End terminus SER-17: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 167 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 174, now 169 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 90 dihedrals, 79 impropers, 245 angles 51: 267 pairs, 169 bonds and 0 virtual sites 51: 51: Total mass 1846.116 a.m.u. 51: 51: Total charge -0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 51: 51: The Gromos53a6 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (37 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 30 donors and 22 acceptors were found. 51: There are 36 hydrogen bonds 51: Will use HISE for residue 29 51: Will use HISE for residue 32 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS27 HIS29 51: SG90 NE2111 51: HIS29 NE2111 0.987 51: HIS32 NE2135 1.590 1.155 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 273 pairs 51: Before cleaning: 443 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 51: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 149 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (149 atoms, 16 residues) 51: 51: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue THR18 as a starting terminus. 51: 51: Identified residue PHE33 as a ending terminus. 51: Start terminus THR-18: NH3+ 51: End terminus PHE-33: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 206 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 220, now 215 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 93 dihedrals, 138 impropers, 324 angles 51: 273 pairs, 215 bonds and 0 virtual sites 51: 51: Total mass 2088.361 a.m.u. 51: 51: Total charge 1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 51: 51: The Gromos53a6 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (45 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 22 acceptors were found. 51: There are 26 hydrogen bonds 51: Will use HISE for residue 45 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS45 51: NE295 51: MET46 SD102 1.078 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 242 pairs 51: Before cleaning: 356 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 51: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 132 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (132 atoms, 16 residues) 51: 51: Identified residue ALA34 as a starting terminus. 51: 51: Identified residue ALA49 as a ending terminus. 51: Start terminus ALA-34: NH3+ 51: End terminus ALA-49: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 170 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 181, now 176 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 81 dihedrals, 104 impropers, 264 angles 51: 242 pairs, 176 bonds and 0 virtual sites 51: 51: Total mass 1861.132 a.m.u. 51: 51: Total charge -1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 51: 51: The Gromos53a6 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (37 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 21 acceptors were found. 51: There are 30 hydrogen bonds 51: Will use HISE for residue 60 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS60 51: NE285 51: CYS62 SG98 0.803 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 232 pairs 51: Before cleaning: 306 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 51: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 117 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (117 atoms, 16 residues) 51: 51: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue LYS50 as a starting terminus. 51: 51: Identified residue PRO65 as a ending terminus. 51: Start terminus LYS-50: NH3+ 51: End terminus PRO-65: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 152 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 161, now 156 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 78 dihedrals, 82 impropers, 231 angles 51: 232 pairs, 156 bonds and 0 virtual sites 51: 51: Total mass 1662.887 a.m.u. 51: 51: Total charge -0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 51: 51: The Gromos53a6 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (41 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 89 donors and 98 acceptors were found. 51: There are 129 hydrogen bonds 51: Will use HISE for residue 31 51: Will use HISE for residue 51 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS25 HIS31 HIS51 51: SG14 NE264 NE2226 51: HIS31 NE264 1.921 51: HIS51 NE2226 1.498 2.650 51: CYS80 SG477 0.207 1.984 1.570 51: Linking CYS-25 SG-14 and CYS-80 SG-477... 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 972 pairs 51: Before cleaning: 1270 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 51: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 51: 51: chain #res #atoms 51: 51: 1 'A' 58 488 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 'A' (488 atoms, 58 residues) 51: 51: Identified residue ASN24 as a starting terminus. 51: 51: Identified residue ARG81 as a ending terminus. 51: Start terminus ASN-24: NH3+ 51: End terminus ARG-81: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 58 residues with 639 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 659, now 654 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 321 dihedrals, 354 impropers, 963 angles 51: 972 pairs, 654 bonds and 0 virtual sites 51: 51: Total mass 6908.582 a.m.u. 51: 51: Total charge -6.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 51: 51: The Gromos53a6 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (68 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 25 donors and 23 acceptors were found. 51: There are 41 hydrogen bonds 51: Will use HISE for residue 8 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS3 HIS8 51: SG9 NE251 51: HIS8 NE251 1.055 51: MET12 SD83 0.763 0.990 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 39 virtual sites 51: Added 4 dummy masses 51: Added 8 new constraints 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 267 pairs 51: Before cleaning: 312 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 51: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 128 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (128 atoms, 16 residues) 51: 51: Identified residue ALA2 as a starting terminus. 51: 51: Identified residue SER17 as a ending terminus. 51: Start terminus ALA-2: NH3+ 51: End terminus SER-17: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 167 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 174, now 169 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 90 dihedrals, 79 impropers, 245 angles 51: 267 pairs, 169 bonds and 39 virtual sites 51: 51: Total mass 1846.116 a.m.u. 51: 51: Total charge -0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 51: 51: The Gromos53a6 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (37 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 30 donors and 22 acceptors were found. 51: There are 36 hydrogen bonds 51: Will use HISE for residue 29 51: Will use HISE for residue 32 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS27 HIS29 51: SG90 NE2111 51: HIS29 NE2111 0.987 51: HIS32 NE2135 1.590 1.155 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 57 virtual sites 51: Added 4 dummy masses 51: Added 10 new constraints 51: 51: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 273 pairs 51: Before cleaning: 443 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 51: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 149 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (149 atoms, 16 residues) 51: 51: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue THR18 as a starting terminus. 51: 51: Identified residue PHE33 as a ending terminus. 51: Start terminus THR-18: NH3+ 51: End terminus PHE-33: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 206 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 220, now 215 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 93 dihedrals, 138 impropers, 324 angles 51: 273 pairs, 215 bonds and 55 virtual sites 51: 51: Total mass 2088.361 a.m.u. 51: 51: Total charge 1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 51: 51: The Gromos53a6 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (44 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 22 acceptors were found. 51: There are 26 hydrogen bonds 51: Will use HISE for residue 45 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS45 51: NE295 51: MET46 SD102 1.078 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 38 virtual sites 51: Added 4 dummy masses 51: Added 8 new constraints 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 242 pairs 51: Before cleaning: 356 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 51: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 132 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (132 atoms, 16 residues) 51: 51: Identified residue ALA34 as a starting terminus. 51: 51: Identified residue ALA49 as a ending terminus. 51: Start terminus ALA-34: NH3+ 51: End terminus ALA-49: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 170 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 181, now 176 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 81 dihedrals, 104 impropers, 264 angles 51: 242 pairs, 176 bonds and 38 virtual sites 51: 51: Total mass 1861.132 a.m.u. 51: 51: Total charge -1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 51: 51: The Gromos53a6 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (50 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 21 acceptors were found. 51: There are 30 hydrogen bonds 51: Will use HISE for residue 60 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS60 51: NE285 51: CYS62 SG98 0.803 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 35 virtual sites 51: Added 4 dummy masses 51: Added 10 new constraints 51: 51: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 232 pairs 51: Before cleaning: 306 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 51: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 117 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (117 atoms, 16 residues) 51: 51: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue LYS50 as a starting terminus. 51: 51: Identified residue PRO65 as a ending terminus. 51: Start terminus LYS-50: NH3+ 51: End terminus PRO-65: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 152 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 161, now 156 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 78 dihedrals, 82 impropers, 231 angles 51: 232 pairs, 156 bonds and 33 virtual sites 51: 51: Total mass 1662.887 a.m.u. 51: 51: Total charge -0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 51: 51: The Gromos53a6 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (66 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 89 donors and 98 acceptors were found. 51: There are 129 hydrogen bonds 51: Will use HISE for residue 31 51: Will use HISE for residue 51 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS25 HIS31 HIS51 51: SG14 NE264 NE2226 51: HIS31 NE264 1.921 51: HIS51 NE2226 1.498 2.650 51: CYS80 SG477 0.207 1.984 1.570 51: Linking CYS-25 SG-14 and CYS-80 SG-477... 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 150 virtual sites 51: Added 10 dummy masses 51: Added 29 new constraints 51: 51: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 972 pairs 51: Before cleaning: 1270 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 51: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 51: 51: chain #res #atoms 51: 51: 1 'A' 58 488 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 'A' (488 atoms, 58 residues) 51: 51: Identified residue ASN24 as a starting terminus. 51: 51: Identified residue ARG81 as a ending terminus. 51: Start terminus ASN-24: NH3+ 51: End terminus ARG-81: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 58 residues with 639 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 659, now 654 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 321 dihedrals, 354 impropers, 963 angles 51: 972 pairs, 654 bonds and 141 virtual sites 51: 51: Total mass 6908.582 a.m.u. 51: 51: Total charge -6.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 51: 51: The Gromos53a6 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (83 ms) 51: [----------] 20 tests from G53a6/Pdb2gmxTest (1103 ms total) 51: 51: [----------] Global test environment tear-down 51: [==========] 40 tests from 2 test suites ran. (2093 ms total) 51: [ PASSED ] 40 tests. 51/87 Test #51: Pdb2gmx2Test .............................. Passed 2.11 sec test 52 Start 52: Pdb2gmx3Test 52: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/pdb2gmx3-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/Pdb2gmx3Test.xml" 52: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests 52: Test timeout computed to be: 1920 52: [==========] Running 39 tests from 6 test suites. 52: [----------] Global test environment set-up. 52: [----------] 10 tests from Amber/Pdb2gmxTest 52: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Before cleaning: 653 pairs 52: Before cleaning: 691 dihedrals 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 255, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 691 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 0 virtual sites 52: 52: Total mass 1846.132 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Amber99sb-ildn force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (115 ms) 52: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Before cleaning: 748 pairs 52: Before cleaning: 788 dihedrals 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 291, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 788 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 0 virtual sites 52: 52: Total mass 2088.366 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Amber99sb-ildn force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (48 ms) 52: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Before cleaning: 676 pairs 52: Before cleaning: 727 dihedrals 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 262, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 727 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 0 virtual sites 52: 52: Total mass 1861.124 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Amber99sb-ildn force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (47 ms) 52: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Before cleaning: 603 pairs 52: Before cleaning: 634 dihedrals 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 233, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 634 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 0 virtual sites 52: 52: Total mass 1662.888 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Amber99sb-ildn force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (36 ms) 52: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Before cleaning: 2499 pairs 52: Before cleaning: 2631 dihedrals 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 952, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2631 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 0 virtual sites 52: 52: Total mass 6908.576 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Amber99sb-ildn force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (80 ms) 52: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Marked 124 virtual sites 52: Added 16 dummy masses 52: Added 26 new constraints 52: Before cleaning: 653 pairs 52: Before cleaning: 691 dihedrals 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 255, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 691 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 130 virtual sites 52: 52: Total mass 1846.132 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Amber99sb-ildn force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (44 ms) 52: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Marked 132 virtual sites 52: Added 10 dummy masses 52: Added 19 new constraints 52: Before cleaning: 748 pairs 52: Before cleaning: 788 dihedrals 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 291, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 788 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 133 virtual sites 52: 52: Total mass 2088.366 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Amber99sb-ildn force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (38 ms) 52: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Marked 123 virtual sites 52: Added 22 dummy masses 52: Added 35 new constraints 52: Before cleaning: 676 pairs 52: Before cleaning: 727 dihedrals 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 262, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 727 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 132 virtual sites 52: 52: Total mass 1861.124 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Amber99sb-ildn force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (35 ms) 52: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Marked 111 virtual sites 52: Added 18 dummy masses 52: Added 31 new constraints 52: Before cleaning: 603 pairs 52: Before cleaning: 634 dihedrals 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 233, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 634 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 116 virtual sites 52: 52: Total mass 1662.888 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Amber99sb-ildn force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (33 ms) 52: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Marked 447 virtual sites 52: Added 58 dummy masses 52: Added 101 new constraints 52: Before cleaning: 2499 pairs 52: Before cleaning: 2631 dihedrals 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 952, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2631 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 462 virtual sites 52: 52: Total mass 6908.576 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Amber99sb-ildn force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (118 ms) 52: [----------] 10 tests from Amber/Pdb2gmxTest (609 ms total) 52: 52: [----------] 1 test from AmberTip4p/Pdb2gmxTest 52: [ RUN ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/tip4p.pdb... 52: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 2 4 (only water) 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 (4 atoms, 2 residues) 52: 52: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 2 residues with 8 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 4, now 4 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 0 dihedrals, 0 impropers, 2 angles 52: 0 pairs, 4 bonds and 0 virtual sites 52: 52: Total mass 36.032 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/tip4p.pdb. 52: 52: The Amber99sb-ildn force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (27 ms) 52: [----------] 1 test from AmberTip4p/Pdb2gmxTest (27 ms total) 52: 52: [----------] 12 tests from Charmm/Pdb2gmxTest 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 14 cmap torsion pairs 52: 52: There are 663 dihedrals, 48 impropers, 457 angles 52: 650 pairs, 254 bonds and 0 virtual sites 52: 52: Total mass 1846.115 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (73 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 14 cmap torsion pairs 52: 52: There are 778 dihedrals, 49 impropers, 516 angles 52: 736 pairs, 290 bonds and 0 virtual sites 52: 52: Total mass 2088.361 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (48 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 14 cmap torsion pairs 52: 52: There are 696 dihedrals, 39 impropers, 472 angles 52: 667 pairs, 261 bonds and 0 virtual sites 52: 52: Total mass 1861.130 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (32 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 14 cmap torsion pairs 52: 52: There are 618 dihedrals, 38 impropers, 419 angles 52: 597 pairs, 232 bonds and 0 virtual sites 52: 52: Total mass 1662.885 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (24 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 56 cmap torsion pairs 52: 52: There are 2524 dihedrals, 149 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 0 virtual sites 52: 52: Total mass 6908.566 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (56 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 39 pairs 52: Before cleaning: 39 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/monomer.pdb... 52: Read 'GLU', 9 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 52: 52: chain #res #atoms 52: 52: 1 'X' 1 9 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'X' (9 atoms, 1 residues) 52: 52: Identified residue GLU1 as a starting terminus. 52: 52: Identified residue GLU1 as a ending terminus. 52: Start terminus GLU-1: NH3+ 52: End terminus GLU-1: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 1 residues with 18 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 17, now 17 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 39 dihedrals, 2 impropers, 30 angles 52: 39 pairs, 17 bonds and 0 virtual sites 52: 52: Total mass 146.123 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/monomer.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file (24 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Marked 124 virtual sites 52: Added 16 dummy masses 52: Added 26 new constraints 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 14 cmap torsion pairs 52: 52: There are 663 dihedrals, 48 impropers, 457 angles 52: 650 pairs, 254 bonds and 130 virtual sites 52: 52: Total mass 1846.115 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (58 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Marked 132 virtual sites 52: Added 10 dummy masses 52: Added 19 new constraints 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 14 cmap torsion pairs 52: 52: There are 778 dihedrals, 49 impropers, 516 angles 52: 736 pairs, 290 bonds and 133 virtual sites 52: 52: Total mass 2088.361 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (42 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Marked 123 virtual sites 52: Added 22 dummy masses 52: Added 35 new constraints 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 14 cmap torsion pairs 52: 52: There are 696 dihedrals, 39 impropers, 472 angles 52: 667 pairs, 261 bonds and 132 virtual sites 52: 52: Total mass 1861.130 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (51 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Marked 111 virtual sites 52: Added 18 dummy masses 52: Added 31 new constraints 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 14 cmap torsion pairs 52: 52: There are 618 dihedrals, 38 impropers, 419 angles 52: 597 pairs, 232 bonds and 116 virtual sites 52: 52: Total mass 1662.885 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (39 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Marked 447 virtual sites 52: Added 58 dummy masses 52: Added 101 new constraints 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 56 cmap torsion pairs 52: 52: There are 2524 dihedrals, 149 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 462 virtual sites 52: 52: Total mass 6908.566 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (115 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Marked 8 virtual sites 52: Added 2 dummy masses 52: Added 3 new constraints 52: Before cleaning: 39 pairs 52: Before cleaning: 39 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/monomer.pdb... 52: Read 'GLU', 9 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 52: 52: chain #res #atoms 52: 52: 1 'X' 1 9 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'X' (9 atoms, 1 residues) 52: 52: Identified residue GLU1 as a starting terminus. 52: 52: Identified residue GLU1 as a ending terminus. 52: Start terminus GLU-1: NH3+ 52: End terminus GLU-1: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 1 residues with 18 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 17, now 17 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 39 dihedrals, 2 impropers, 30 angles 52: 39 pairs, 17 bonds and 9 virtual sites 52: 52: Total mass 146.123 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/monomer.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file (27 ms) 52: [----------] 12 tests from Charmm/Pdb2gmxTest (603 ms total) 52: 52: [----------] 8 tests from ChainSep/Pdb2gmxTest 52: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 651 pairs 52: Before cleaning: 661 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on changing chain id only (ignoring TER records). 52: 52: Merged chains into joint molecule definitions at 2 places. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 16 127 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (127 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue GLU5 as a ending terminus. 52: 52: Identified residue PHE6 as a starting terminus. 52: 52: Identified residue MET12 as a ending terminus. 52: 52: Identified residue ASN13 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus GLU-5: COO- 52: Start terminus PHE-6: NH3+ 52: End terminus MET-12: COO- 52: Start terminus ASN-13: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 258 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 258, now 258 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 10 cmap torsion pairs 52: 52: There are 661 dihedrals, 46 impropers, 463 angles 52: 648 pairs, 258 bonds and 0 virtual sites 52: 52: Total mass 1882.146 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file (48 ms) 52: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 123 pairs 52: Before cleaning: 123 dihedrals 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 10 donors and 7 acceptors were found. 52: There are 7 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS8 52: NE223 52: MET12 SD55 0.990 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 317 pairs 52: Before cleaning: 322 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 211 pairs 52: Before cleaning: 216 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on changing chain id only (ignoring TER records). 52: 52: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 4 28 52: 52: 2 'B' 7 58 52: 52: 3 'C' 5 41 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (28 atoms, 4 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue GLU5 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus GLU-5: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 4 residues with 51 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 50, now 50 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2 cmap torsion pairs 52: 52: There are 123 dihedrals, 9 impropers, 88 angles 52: 123 pairs, 50 bonds and 0 virtual sites 52: 52: Total mass 434.421 a.m.u. 52: 52: Total charge -2.000 e 52: 52: Writing topology 52: 52: Processing chain 2 'B' (58 atoms, 7 residues) 52: 52: Identified residue PHE6 as a starting terminus. 52: 52: Identified residue MET12 as a ending terminus. 52: Start terminus PHE-6: NH3+ 52: End terminus MET-12: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 7 residues with 124 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 125, now 125 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 5 cmap torsion pairs 52: 52: There are 322 dihedrals, 19 impropers, 227 angles 52: 314 pairs, 125 bonds and 0 virtual sites 52: 52: Total mass 846.083 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Processing chain 3 'C' (41 atoms, 5 residues) 52: 52: Identified residue ASN13 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ASN-13: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 5 residues with 83 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 83, now 83 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 3 cmap torsion pairs 52: 52: There are 216 dihedrals, 18 impropers, 148 angles 52: 211 pairs, 83 bonds and 0 virtual sites 52: 52: Total mass 601.643 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Including chain 1 in system: 51 atoms 4 residues 52: 52: Including chain 2 in system: 124 atoms 7 residues 52: 52: Including chain 3 in system: 83 atoms 5 residues 52: 52: Now there are 258 atoms and 16 residues 52: 52: Total mass in system 1882.146 a.m.u. 52: 52: Total charge in system 0.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file (39 ms) 52: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 651 pairs 52: Before cleaning: 661 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records only (ignoring chain id). 52: 52: Merged chains into joint molecule definitions at 2 places. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 16 127 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (127 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue ILE9 as a ending terminus. 52: 52: Identified residue LYS10 as a starting terminus. 52: 52: Identified residue MET12 as a ending terminus. 52: 52: Identified residue ASN13 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus ILE-9: COO- 52: Start terminus LYS-10: NH3+ 52: End terminus MET-12: COO- 52: Start terminus ASN-13: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 258 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 258, now 258 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 10 cmap torsion pairs 52: 52: There are 661 dihedrals, 46 impropers, 463 angles 52: 648 pairs, 258 bonds and 0 virtual sites 52: 52: Total mass 1882.146 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file (38 ms) 52: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 10 donors and 12 acceptors were found. 52: There are 13 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 52: SG9 52: HIS8 NE251 1.055 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 288 pairs 52: Before cleaning: 293 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 152 pairs 52: Before cleaning: 152 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 211 pairs 52: Before cleaning: 216 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records only (ignoring chain id). 52: 52: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 8 61 52: 52: 2 'B' 3 25 52: 52: 3 'C' 5 41 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (61 atoms, 8 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue ILE9 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus ILE-9: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 8 residues with 114 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 115, now 115 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 6 cmap torsion pairs 52: 52: There are 293 dihedrals, 23 impropers, 203 angles 52: 285 pairs, 115 bonds and 0 virtual sites 52: 52: Total mass 888.952 a.m.u. 52: 52: Total charge -2.000 e 52: 52: Writing topology 52: 52: Processing chain 2 'B' (25 atoms, 3 residues) 52: 52: Identified residue LYS10 as a starting terminus. 52: 52: Identified residue MET12 as a ending terminus. 52: Start terminus LYS-10: NH3+ 52: End terminus MET-12: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 3 residues with 61 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 60, now 60 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 1 cmap torsion pairs 52: 52: There are 152 dihedrals, 5 impropers, 112 angles 52: 152 pairs, 60 bonds and 0 virtual sites 52: 52: Total mass 391.552 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Processing chain 3 'C' (41 atoms, 5 residues) 52: 52: Identified residue ASN13 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ASN-13: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 5 residues with 83 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 83, now 83 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 3 cmap torsion pairs 52: 52: There are 216 dihedrals, 18 impropers, 148 angles 52: 211 pairs, 83 bonds and 0 virtual sites 52: 52: Total mass 601.643 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Including chain 1 in system: 114 atoms 8 residues 52: 52: Including chain 2 in system: 61 atoms 3 residues 52: 52: Including chain 3 in system: 83 atoms 5 residues 52: 52: Now there are 258 atoms and 16 residues 52: 52: Total mass in system 1882.146 a.m.u. 52: 52: Total charge in system 0.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file (55 ms) 52: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 650 pairs 52: Before cleaning: 660 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: Merged chains into joint molecule definitions at 3 places. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 16 127 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (127 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue GLU5 as a ending terminus. 52: 52: Identified residue PHE6 as a starting terminus. 52: 52: Identified residue ILE9 as a ending terminus. 52: 52: Identified residue LYS10 as a starting terminus. 52: 52: Identified residue MET12 as a ending terminus. 52: 52: Identified residue ASN13 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus GLU-5: COO- 52: Start terminus PHE-6: NH3+ 52: End terminus ILE-9: COO- 52: Start terminus LYS-10: NH3+ 52: End terminus MET-12: COO- 52: Start terminus ASN-13: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 261 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 260, now 260 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 8 cmap torsion pairs 52: 52: There are 660 dihedrals, 45 impropers, 466 angles 52: 647 pairs, 260 bonds and 0 virtual sites 52: 52: Total mass 1900.162 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file (41 ms) 52: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 52: 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 123 pairs 52: Before cleaning: 123 dihedrals 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 6 donors and 4 acceptors were found. 52: There are 3 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 164 pairs 52: Before cleaning: 169 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 152 pairs 52: Before cleaning: 152 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 211 pairs 52: Before cleaning: 216 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 52: 52: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 4 28 52: 52: 2 'B' 4 33 52: 52: 3 'B' 3 25 52: 52: 4 'C' 5 41 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (28 atoms, 4 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue GLU5 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus GLU-5: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 4 residues with 51 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 50, now 50 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2 cmap torsion pairs 52: 52: There are 123 dihedrals, 9 impropers, 88 angles 52: 123 pairs, 50 bonds and 0 virtual sites 52: 52: Total mass 434.421 a.m.u. 52: 52: Total charge -2.000 e 52: 52: Writing topology 52: 52: Processing chain 2 'B' (33 atoms, 4 residues) 52: 52: Identified residue PHE6 as a starting terminus. 52: 52: Identified residue ILE9 as a ending terminus. 52: Start terminus PHE-6: NH3+ 52: End terminus ILE-9: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 4 residues with 66 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 67, now 67 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2 cmap torsion pairs 52: 52: There are 169 dihedrals, 13 impropers, 118 angles 52: 161 pairs, 67 bonds and 0 virtual sites 52: 52: Total mass 472.547 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Processing chain 3 'B' (25 atoms, 3 residues) 52: 52: Identified residue LYS10 as a starting terminus. 52: 52: Identified residue MET12 as a ending terminus. 52: Start terminus LYS-10: NH3+ 52: End terminus MET-12: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 3 residues with 61 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 60, now 60 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 1 cmap torsion pairs 52: 52: There are 152 dihedrals, 5 impropers, 112 angles 52: 152 pairs, 60 bonds and 0 virtual sites 52: 52: Total mass 391.552 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Processing chain 4 'C' (41 atoms, 5 residues) 52: 52: Identified residue ASN13 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ASN-13: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 5 residues with 83 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 83, now 83 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 3 cmap torsion pairs 52: 52: There are 216 dihedrals, 18 impropers, 148 angles 52: 211 pairs, 83 bonds and 0 virtual sites 52: 52: Total mass 601.643 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Including chain 1 in system: 51 atoms 4 residues 52: 52: Including chain 2 in system: 66 atoms 4 residues 52: 52: Including chain 3 in system: 61 atoms 3 residues 52: 52: Including chain 4 in system: 83 atoms 5 residues 52: 52: Now there are 261 atoms and 16 residues 52: 52: Total mass in system 1900.162 a.m.u. 52: 52: Total charge in system 0.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file (44 ms) 52: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 652 pairs 52: Before cleaning: 662 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records and chain id changing. 52: 52: Merged chains into joint molecule definitions at 1 places. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 16 127 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (127 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue MET12 as a ending terminus. 52: 52: Identified residue ASN13 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus MET-12: COO- 52: Start terminus ASN-13: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 256, now 256 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 12 cmap torsion pairs 52: 52: There are 662 dihedrals, 47 impropers, 460 angles 52: 649 pairs, 256 bonds and 0 virtual sites 52: 52: Total mass 1864.131 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file (43 ms) 52: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 14 donors and 15 acceptors were found. 52: There are 20 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 441 pairs 52: Before cleaning: 446 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 211 pairs 52: Before cleaning: 216 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records and chain id changing. 52: 52: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 11 86 52: 52: 2 'C' 5 41 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (86 atoms, 11 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue MET12 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus MET-12: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 11 residues with 172 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 173, now 173 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 9 cmap torsion pairs 52: 52: There are 446 dihedrals, 29 impropers, 312 angles 52: 438 pairs, 173 bonds and 0 virtual sites 52: 52: Total mass 1262.488 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Processing chain 2 'C' (41 atoms, 5 residues) 52: 52: Identified residue ASN13 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ASN-13: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 5 residues with 83 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 83, now 83 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 3 cmap torsion pairs 52: 52: There are 216 dihedrals, 18 impropers, 148 angles 52: 211 pairs, 83 bonds and 0 virtual sites 52: 52: Total mass 601.643 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Including chain 1 in system: 172 atoms 11 residues 52: 52: Including chain 2 in system: 83 atoms 5 residues 52: 52: Now there are 255 atoms and 16 residues 52: 52: Total mass in system 1864.131 a.m.u. 52: 52: Total charge in system 0.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file (38 ms) 52: [----------] 8 tests from ChainSep/Pdb2gmxTest (358 ms total) 52: 52: [----------] 4 tests from ChainChanges/Pdb2gmxTest 52: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 83 pairs 52: Before cleaning: 83 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 145 pairs 52: Before cleaning: 150 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb... 52: Read 'Fragments of peptides and ions', 47 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on changing chain id only (ignoring TER records). 52: 52: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 3 19 52: 52: 2 'B' 3 28 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (19 atoms, 3 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue ASP4 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus ASP-4: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 3 residues with 36 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 35, now 35 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 1 cmap torsion pairs 52: 52: There are 83 dihedrals, 6 impropers, 61 angles 52: 83 pairs, 35 bonds and 0 virtual sites 52: 52: Total mass 306.314 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Processing chain 2 'B' (28 atoms, 3 residues) 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue TRP20 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus TRP-20: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 3 residues with 57 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 58, now 58 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 1 cmap torsion pairs 52: 52: There are 150 dihedrals, 5 impropers, 103 angles 52: 142 pairs, 58 bonds and 0 virtual sites 52: 52: Total mass 404.468 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Including chain 1 in system: 36 atoms 3 residues 52: 52: Including chain 2 in system: 57 atoms 3 residues 52: 52: Now there are 93 atoms and 6 residues 52: 52: Total mass in system 710.782 a.m.u. 52: 52: Total charge in system -1.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file (32 ms) 52: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 83 pairs 52: Before cleaning: 83 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 145 pairs 52: Before cleaning: 150 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb... 52: Read 'Fragments of peptides and ions', 47 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records only (ignoring chain id). 52: 52: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 3 19 52: 52: 2 'B' 3 28 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (19 atoms, 3 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue ASP4 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus ASP-4: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 3 residues with 36 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 35, now 35 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 1 cmap torsion pairs 52: 52: There are 83 dihedrals, 6 impropers, 61 angles 52: 83 pairs, 35 bonds and 0 virtual sites 52: 52: Total mass 306.314 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Processing chain 2 'B' (28 atoms, 3 residues) 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue TRP20 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus TRP-20: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 3 residues with 57 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 58, now 58 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 1 cmap torsion pairs 52: 52: There are 150 dihedrals, 5 impropers, 103 angles 52: 142 pairs, 58 bonds and 0 virtual sites 52: 52: Total mass 404.468 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Including chain 1 in system: 36 atoms 3 residues 52: 52: Including chain 2 in system: 57 atoms 3 residues 52: 52: Now there are 93 atoms and 6 residues 52: 52: Total mass in system 710.782 a.m.u. 52: 52: Total charge in system -1.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file (29 ms) 52: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 83 pairs 52: Before cleaning: 83 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 145 pairs 52: Before cleaning: 150 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb... 52: Read 'Fragments of peptides and ions', 47 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 3 19 52: 52: 2 'B' 3 28 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (19 atoms, 3 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue ASP4 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus ASP-4: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 3 residues with 36 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 35, now 35 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 1 cmap torsion pairs 52: 52: There are 83 dihedrals, 6 impropers, 61 angles 52: 83 pairs, 35 bonds and 0 virtual sites 52: 52: Total mass 306.314 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Processing chain 2 'B' (28 atoms, 3 residues) 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue TRP20 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus TRP-20: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 3 residues with 57 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 58, now 58 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 1 cmap torsion pairs 52: 52: There are 150 dihedrals, 5 impropers, 103 angles 52: 142 pairs, 58 bonds and 0 virtual sites 52: 52: Total mass 404.468 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Including chain 1 in system: 36 atoms 3 residues 52: 52: Including chain 2 in system: 57 atoms 3 residues 52: 52: Now there are 93 atoms and 6 residues 52: 52: Total mass in system 710.782 a.m.u. 52: 52: Total charge in system -1.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file (31 ms) 52: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 83 pairs 52: Before cleaning: 83 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 145 pairs 52: Before cleaning: 150 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb... 52: Read 'Fragments of peptides and ions', 47 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records and chain id changing. 52: 52: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 3 19 52: 52: 2 'B' 3 28 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (19 atoms, 3 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue ASP4 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus ASP-4: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 3 residues with 36 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 35, now 35 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 1 cmap torsion pairs 52: 52: There are 83 dihedrals, 6 impropers, 61 angles 52: 83 pairs, 35 bonds and 0 virtual sites 52: 52: Total mass 306.314 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Processing chain 2 'B' (28 atoms, 3 residues) 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue TRP20 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus TRP-20: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 3 residues with 57 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 58, now 58 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 1 cmap torsion pairs 52: 52: There are 150 dihedrals, 5 impropers, 103 angles 52: 142 pairs, 58 bonds and 0 virtual sites 52: 52: Total mass 404.468 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Including chain 1 in system: 36 atoms 3 residues 52: 52: Including chain 2 in system: 57 atoms 3 residues 52: 52: Now there are 93 atoms and 6 residues 52: 52: Total mass in system 710.782 a.m.u. 52: 52: Total charge in system -1.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file (31 ms) 52: [----------] 4 tests from ChainChanges/Pdb2gmxTest (124 ms total) 52: 52: [----------] 4 tests from Cyclic/Pdb2gmxTest 52: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: WARNING: all CONECT records are ignored 52: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 52: 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 6040 pairs 52: Before cleaning: 6605 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 6040 pairs 52: Before cleaning: 6605 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 52: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 52: 52: Moved all the water blocks to the end 52: 52: There are 3 chains and 2 blocks of water and 175 residues with 3087 atoms 52: 52: chain #res #atoms 52: 52: 1 'P' 71 1527 52: 52: 2 'Q' 71 1527 52: 52: 3 'Q' 7 7 52: 52: 4 ' ' 10 10 (only water) 52: 52: 5 ' ' 16 16 (only water) 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'P' (1527 atoms, 71 residues) 52: 52: Identified residue G1 as a starting terminus. 52: 52: Identified residue U71 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 71 residues with 2297 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 2481, now 2481 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 6605 dihedrals, 183 impropers, 4434 angles 52: 5827 pairs, 2481 bonds and 0 virtual sites 52: 52: Total mass 22984.514 a.m.u. 52: 52: Total charge -71.000 e 52: 52: Writing topology 52: 52: Processing chain 2 'Q' (1527 atoms, 71 residues) 52: 52: Identified residue G1 as a starting terminus. 52: 52: Identified residue U71 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 71 residues with 2297 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 2481, now 2481 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 6605 dihedrals, 183 impropers, 4434 angles 52: 5827 pairs, 2481 bonds and 0 virtual sites 52: 52: Total mass 22984.514 a.m.u. 52: 52: Total charge -71.000 e 52: 52: Writing topology 52: 52: Processing chain 3 'Q' (7 atoms, 7 residues) 52: 52: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 52: 52: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 52: 52: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 52: 52: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 52: 52: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 52: 52: Disabling further notes about ions. 52: 52: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 7 residues with 7 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: No bonds 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 0 dihedrals, 0 impropers, 0 angles 52: 0 pairs, 0 bonds and 0 virtual sites 52: 52: Total mass 170.135 a.m.u. 52: 52: Total charge 14.000 e 52: 52: Writing topology 52: 52: Processing chain 4 (10 atoms, 10 residues) 52: 52: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 10 residues with 30 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 30, now 30 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 0 dihedrals, 0 impropers, 30 angles 52: 0 pairs, 30 bonds and 0 virtual sites 52: 52: Total mass 180.154 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Processing chain 5 (16 atoms, 16 residues) 52: 52: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 48 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 48, now 48 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 0 dihedrals, 0 impropers, 48 angles 52: 0 pairs, 48 bonds and 0 virtual sites 52: 52: Total mass 288.246 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Including chain 1 in system: 2297 atoms 71 residues 52: 52: Including chain 2 in system: 2297 atoms 71 residues 52: 52: Including chain 3 in system: 7 atoms 7 residues 52: 52: Including chain 4 in system: 30 atoms 10 residues 52: 52: Including chain 5 in system: 48 atoms 16 residues 52: 52: Now there are 4679 atoms and 175 residues 52: 52: Total mass in system 46607.562 a.m.u. 52: 52: Total charge in system -128.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file (274 ms) 52: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 2325 pairs 52: Before cleaning: 2325 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 52: Read 'CARNOCYCLIN-A', 413 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 60 413 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (413 atoms, 60 residues) 52: 52: Identified residue LEU1 as a starting terminus. 52: 52: Identified residue LEU60 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 60 residues with 878 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 880, now 880 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 60 cmap torsion pairs 52: 52: There are 2325 dihedrals, 137 impropers, 1614 angles 52: 2319 pairs, 880 bonds and 0 virtual sites 52: 52: Total mass 5866.087 a.m.u. 52: 52: Total charge 4.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file (58 ms) 52: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: WARNING: all CONECT records are ignored 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 12080 pairs 52: Before cleaning: 13210 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 52: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: Moved all the water blocks to the end 52: 52: Merged chains into joint molecule definitions at 2 places. 52: 52: There are 1 chains and 2 blocks of water and 175 residues with 3087 atoms 52: 52: chain #res #atoms 52: 52: 1 'P' 149 3061 52: 52: 2 ' ' 10 10 (only water) 52: 52: 3 ' ' 16 16 (only water) 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'P' (3061 atoms, 149 residues) 52: 52: Identified residue G1 as a starting terminus. 52: 52: Identified residue U71 as a ending terminus. 52: 52: Identified residue G1 as a starting terminus. 52: 52: Identified residue U71 as a ending terminus. 52: 52: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 52: 52: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 52: 52: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 52: 52: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 52: 52: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 52: 52: Disabling further notes about ions. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 149 residues with 4601 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 4962, now 4962 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 13210 dihedrals, 366 impropers, 8868 angles 52: 11654 pairs, 4962 bonds and 0 virtual sites 52: 52: Total mass 46139.162 a.m.u. 52: 52: Total charge -128.000 e 52: 52: Writing topology 52: 52: Processing chain 2 (10 atoms, 10 residues) 52: 52: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 10 residues with 30 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 30, now 30 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 0 dihedrals, 0 impropers, 30 angles 52: 0 pairs, 30 bonds and 0 virtual sites 52: 52: Total mass 180.154 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Processing chain 3 (16 atoms, 16 residues) 52: 52: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 48 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 48, now 48 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 0 dihedrals, 0 impropers, 48 angles 52: 0 pairs, 48 bonds and 0 virtual sites 52: 52: Total mass 288.246 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Including chain 1 in system: 4601 atoms 149 residues 52: 52: Including chain 2 in system: 30 atoms 10 residues 52: 52: Including chain 3 in system: 48 atoms 16 residues 52: 52: Now there are 4679 atoms and 175 residues 52: 52: Total mass in system 46607.562 a.m.u. 52: 52: Total charge in system -128.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file (273 ms) 52: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 2325 pairs 52: Before cleaning: 2325 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 52: Read 'CARNOCYCLIN-A', 413 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 60 413 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (413 atoms, 60 residues) 52: 52: Identified residue LEU1 as a starting terminus. 52: 52: Identified residue LEU60 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 60 residues with 878 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 880, now 880 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 60 cmap torsion pairs 52: 52: There are 2325 dihedrals, 137 impropers, 1614 angles 52: 2319 pairs, 880 bonds and 0 virtual sites 52: 52: Total mass 5866.087 a.m.u. 52: 52: Total charge 4.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file (65 ms) 52: [----------] 4 tests from Cyclic/Pdb2gmxTest (675 ms total) 52: 52: [----------] Global test environment tear-down 52: [==========] 39 tests from 6 test suites ran. (2400 ms total) 52: [ PASSED ] 39 tests. 52/87 Test #52: Pdb2gmx3Test .............................. Passed 2.43 sec test 53 Start 53: CorrelationsTest 53: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/correlations-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/CorrelationsTest.xml" 53: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/correlationfunctions/tests 53: Test timeout computed to be: 30 53: [==========] Running 21 tests from 3 test suites. 53: [----------] Global test environment set-up. 53: [----------] 10 tests from AutocorrTest 53: [ RUN ] AutocorrTest.EacNormal 53: [ OK ] AutocorrTest.EacNormal (59 ms) 53: [ RUN ] AutocorrTest.EacNoNormalize 53: [ OK ] AutocorrTest.EacNoNormalize (52 ms) 53: [ RUN ] AutocorrTest.EacCos 53: [ OK ] AutocorrTest.EacCos (63 ms) 53: [ RUN ] AutocorrTest.EacVector 53: [ OK ] AutocorrTest.EacVector (95 ms) 53: [ RUN ] AutocorrTest.EacRcross 53: [ OK ] AutocorrTest.EacRcross (4 ms) 53: [ RUN ] AutocorrTest.EacP0 53: [ OK ] AutocorrTest.EacP0 (100 ms) 53: [ RUN ] AutocorrTest.EacP1 53: [ OK ] AutocorrTest.EacP1 (96 ms) 53: [ RUN ] AutocorrTest.EacP2 53: [ OK ] AutocorrTest.EacP2 (207 ms) 53: [ RUN ] AutocorrTest.EacP3 53: [ OK ] AutocorrTest.EacP3 (2 ms) 53: [ RUN ] AutocorrTest.EacP4 53: [ OK ] AutocorrTest.EacP4 (92 ms) 53: [----------] 10 tests from AutocorrTest (787 ms total) 53: 53: [----------] 10 tests from ExpfitTest 53: [ RUN ] ExpfitTest.EffnEXP1 53: [ OK ] ExpfitTest.EffnEXP1 (0 ms) 53: [ RUN ] ExpfitTest.EffnEXP2 53: [ OK ] ExpfitTest.EffnEXP2 (1 ms) 53: [ RUN ] ExpfitTest.EffnEXPEXP 53: [ OK ] ExpfitTest.EffnEXPEXP (1 ms) 53: [ RUN ] ExpfitTest.EffnEXP5 53: [ OK ] ExpfitTest.EffnEXP5 (2 ms) 53: [ RUN ] ExpfitTest.EffnEXP7 53: [ OK ] ExpfitTest.EffnEXP7 (2 ms) 53: [ RUN ] ExpfitTest.EffnEXP9 53: [ OK ] ExpfitTest.EffnEXP9 (11 ms) 53: [ RUN ] ExpfitTest.EffnERF 53: [ OK ] ExpfitTest.EffnERF (2 ms) 53: [ RUN ] ExpfitTest.EffnERREST 53: [ OK ] ExpfitTest.EffnERREST (1 ms) 53: [ RUN ] ExpfitTest.EffnVAC 53: [ OK ] ExpfitTest.EffnVAC (3 ms) 53: [ RUN ] ExpfitTest.EffnPRES 53: [ OK ] ExpfitTest.EffnPRES (10 ms) 53: [----------] 10 tests from ExpfitTest (74 ms total) 53: 53: [----------] 1 test from ManyAutocorrelationTest 53: [ RUN ] ManyAutocorrelationTest.Empty 53: [ OK ] ManyAutocorrelationTest.Empty (0 ms) 53: [----------] 1 test from ManyAutocorrelationTest (0 ms total) 53: 53: [----------] Global test environment tear-down 53: [==========] 21 tests from 3 test suites ran. (873 ms total) 53: [ PASSED ] 21 tests. 53/87 Test #53: CorrelationsTest .......................... Passed 0.90 sec test 54 Start 54: AnalysisDataUnitTests 54: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/analysisdata-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/AnalysisDataUnitTests.xml" 54: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/analysisdata/tests 54: Test timeout computed to be: 30 54: [==========] Running 69 tests from 14 test suites. 54: [----------] Global test environment set-up. 54: [----------] 3 tests from AnalysisDataInitializationTest 54: [ RUN ] AnalysisDataInitializationTest.BasicInitialization 54: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms) 54: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules 54: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (2 ms) 54: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules 54: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms) 54: [----------] 3 tests from AnalysisDataInitializationTest (2 ms total) 54: 54: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = (anonymous namespace)::SimpleInputData 54: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly 54: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames 54: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 54: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks 54: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (0 ms) 54: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData 54: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (0 ms) 54: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks 54: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (0 ms) 54: [----------] 8 tests from AnalysisDataCommonTest/0 (2 ms total) 54: 54: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = (anonymous namespace)::DataSetsInputData 54: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly 54: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames 54: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 54: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks 54: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (0 ms) 54: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData 54: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (0 ms) 54: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks 54: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (0 ms) 54: [----------] 8 tests from AnalysisDataCommonTest/1 (0 ms total) 54: 54: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = (anonymous namespace)::MultipointInputData 54: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly 54: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames 54: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 54: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks 54: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (0 ms) 54: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData 54: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (0 ms) 54: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks 54: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (0 ms) 54: [----------] 8 tests from AnalysisDataCommonTest/2 (1 ms total) 54: 54: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = (anonymous namespace)::MultipointDataSetsInputData 54: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly 54: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames 54: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 54: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks 54: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (0 ms) 54: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData 54: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (0 ms) 54: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks 54: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (0 ms) 54: [----------] 8 tests from AnalysisDataCommonTest/3 (1 ms total) 54: 54: [----------] 4 tests from AnalysisArrayDataTest 54: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly 54: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (0 ms) 54: [ RUN ] AnalysisArrayDataTest.StorageWorks 54: [ OK ] AnalysisArrayDataTest.StorageWorks (0 ms) 54: [ RUN ] AnalysisArrayDataTest.CanSetXAxis 54: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms) 54: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount 54: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms) 54: [----------] 4 tests from AnalysisArrayDataTest (0 ms total) 54: 54: [----------] 6 tests from AverageModuleTest 54: [ RUN ] AverageModuleTest.BasicTest 54: [ OK ] AverageModuleTest.BasicTest (1 ms) 54: [ RUN ] AverageModuleTest.HandlesMultipointData 54: [ OK ] AverageModuleTest.HandlesMultipointData (1 ms) 54: [ RUN ] AverageModuleTest.HandlesMultipleDataSets 54: [ OK ] AverageModuleTest.HandlesMultipleDataSets (5 ms) 54: [ RUN ] AverageModuleTest.HandlesDataSetAveraging 54: [ OK ] AverageModuleTest.HandlesDataSetAveraging (0 ms) 54: [ RUN ] AverageModuleTest.CanCustomizeXAxis 54: [ OK ] AverageModuleTest.CanCustomizeXAxis (0 ms) 54: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis 54: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (0 ms) 54: [----------] 6 tests from AverageModuleTest (17 ms total) 54: 54: [----------] 2 tests from FrameAverageModuleTest 54: [ RUN ] FrameAverageModuleTest.BasicTest 54: [ OK ] FrameAverageModuleTest.BasicTest (0 ms) 54: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets 54: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (0 ms) 54: [----------] 2 tests from FrameAverageModuleTest (1 ms total) 54: 54: [----------] 7 tests from AnalysisHistogramSettingsTest 54: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins 54: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms) 54: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins 54: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms) 54: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount 54: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms) 54: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth 54: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms) 54: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins 54: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms) 54: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins 54: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms) 54: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange 54: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms) 54: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total) 54: 54: [----------] 2 tests from SimpleHistogramModuleTest 54: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly 54: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (0 ms) 54: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll 54: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) 54: [----------] 2 tests from SimpleHistogramModuleTest (4 ms total) 54: 54: [----------] 3 tests from WeightedHistogramModuleTest 54: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly 54: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (0 ms) 54: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll 54: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) 54: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets 54: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (0 ms) 54: [----------] 3 tests from WeightedHistogramModuleTest (2 ms total) 54: 54: [----------] 3 tests from BinAverageModuleTest 54: [ RUN ] BinAverageModuleTest.ComputesCorrectly 54: [ OK ] BinAverageModuleTest.ComputesCorrectly (0 ms) 54: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll 54: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (0 ms) 54: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets 54: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (0 ms) 54: [----------] 3 tests from BinAverageModuleTest (2 ms total) 54: 54: [----------] 4 tests from AbstractAverageHistogramTest 54: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly 54: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (0 ms) 54: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram 54: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (1 ms) 54: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth 54: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (0 ms) 54: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins 54: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (0 ms) 54: [----------] 4 tests from AbstractAverageHistogramTest (5 ms total) 54: 54: [----------] 3 tests from LifetimeModuleTest 54: [ RUN ] LifetimeModuleTest.BasicTest 54: [ OK ] LifetimeModuleTest.BasicTest (0 ms) 54: [ RUN ] LifetimeModuleTest.CumulativeTest 54: [ OK ] LifetimeModuleTest.CumulativeTest (4 ms) 54: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets 54: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (0 ms) 54: [----------] 3 tests from LifetimeModuleTest (5 ms total) 54: 54: [----------] Global test environment tear-down 54: [==========] 69 tests from 14 test suites ran. (49 ms total) 54: [ PASSED ] 69 tests. 54/87 Test #54: AnalysisDataUnitTests ..................... Passed 0.08 sec test 55 Start 55: CoordinateIOTests 55: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/coordinateio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/CoordinateIOTests.xml" 55: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/coordinateio/tests 55: Test timeout computed to be: 30 55: [==========] Running 67 tests from 20 test suites. 55: [----------] Global test environment set-up. 55: [----------] 1 test from OutputSelectorDeathTest 55: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (9 ms) 55: [----------] 1 test from OutputSelectorDeathTest (9 ms total) 55: 55: [----------] 5 tests from TrajectoryFrameWriterTest 55: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (0 ms) 55: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (0 ms) 55: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (0 ms) 55: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (5 ms) 55: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks 55: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms) 55: [----------] 5 tests from TrajectoryFrameWriterTest (8 ms total) 55: 55: [----------] 5 tests from OutputAdapterContainer 55: [ RUN ] OutputAdapterContainer.MakeEmpty 55: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms) 55: [ RUN ] OutputAdapterContainer.AddAdapter 55: [ OK ] OutputAdapterContainer.AddAdapter (0 ms) 55: [ RUN ] OutputAdapterContainer.RejectBadAdapter 55: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms) 55: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter 55: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms) 55: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters 55: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms) 55: [----------] 5 tests from OutputAdapterContainer (0 ms total) 55: 55: [----------] 3 tests from RegisterFrameConverterTest 55: [ RUN ] RegisterFrameConverterTest.NoConverterWorks 55: [ OK ] RegisterFrameConverterTest.NoConverterWorks (0 ms) 55: [ RUN ] RegisterFrameConverterTest.RegistrationWorks 55: [ OK ] RegisterFrameConverterTest.RegistrationWorks (0 ms) 55: [ RUN ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees 55: [ OK ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees (0 ms) 55: [----------] 3 tests from RegisterFrameConverterTest (0 ms total) 55: 55: [----------] 5 tests from FlagTest 55: [ RUN ] FlagTest.CanSetSimpleFlag 55: [ OK ] FlagTest.CanSetSimpleFlag (0 ms) 55: [ RUN ] FlagTest.CanAddNewBox 55: [ OK ] FlagTest.CanAddNewBox (0 ms) 55: [ RUN ] FlagTest.SetsImplicitPrecisionChange 55: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms) 55: [ RUN ] FlagTest.SetsImplicitStartTimeChange 55: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms) 55: [ RUN ] FlagTest.SetsImplicitTimeStepChange 55: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms) 55: [----------] 5 tests from FlagTest (0 ms total) 55: 55: [----------] 5 tests from SetAtomsTest 55: [ RUN ] SetAtomsTest.RemovesExistingAtoms 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] SetAtomsTest.RemovesExistingAtoms (0 ms) 55: [ RUN ] SetAtomsTest.AddsNewAtoms 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] SetAtomsTest.AddsNewAtoms (0 ms) 55: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (0 ms) 55: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (0 ms) 55: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (0 ms) 55: [----------] 5 tests from SetAtomsTest (7 ms total) 55: 55: [----------] 2 tests from SetBothTimeTest 55: [ RUN ] SetBothTimeTest.StartTimeZeroWorks 55: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms) 55: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks 55: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms) 55: [----------] 2 tests from SetBothTimeTest (0 ms total) 55: 55: [----------] 2 tests from SetStartTimeTest 55: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart 55: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms) 55: [ RUN ] SetStartTimeTest.WorksWithZeroStart 55: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms) 55: [----------] 2 tests from SetStartTimeTest (0 ms total) 55: 55: [----------] 1 test from SetTimeStepTest 55: [ RUN ] SetTimeStepTest.SetTimeStepWorks 55: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms) 55: [----------] 1 test from SetTimeStepTest (0 ms total) 55: 55: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest 55: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (0 ms) 55: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (8 ms) 55: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (0 ms) 55: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (0 ms) 55: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (0 ms) 55: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (0 ms) 55: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (12 ms total) 55: 55: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles 55: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (0 ms) 55: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (1 ms) 55: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (0 ms) 55: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (3 ms total) 55: 55: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles 55: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 55: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms) 55: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 55: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms) 55: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 55: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms) 55: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (0 ms total) 55: 55: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles 55: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (1 ms) 55: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (1 ms) 55: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (1 ms) 55: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (2 ms) 55: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (14 ms total) 55: 55: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles 55: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (0 ms) 55: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (0 ms) 55: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (0 ms) 55: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (8 ms total) 55: 55: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles 55: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 55: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms) 55: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 55: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms) 55: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 55: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms) 55: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (0 ms total) 55: 55: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles 55: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (0 ms) 55: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (0 ms) 55: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (1 ms total) 55: 55: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles 55: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 55: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms) 55: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 55: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms) 55: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 55: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms) 55: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 55: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms) 55: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (0 ms total) 55: 55: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles 55: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (0 ms) 55: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (0 ms) 55: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (7 ms total) 55: 55: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles 55: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 55: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms) 55: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 55: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms) 55: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 55: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms) 55: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 55: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms) 55: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (0 ms total) 55: 55: [----------] 4 tests from ModuleSupported/NoOptionalOutput 55: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (0 ms) 55: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (0 ms) 55: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (0 ms) 55: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (1 ms) 55: [----------] 4 tests from ModuleSupported/NoOptionalOutput (3 ms total) 55: 55: [----------] Global test environment tear-down 55: [==========] 67 tests from 20 test suites ran. (82 ms total) 55: [ PASSED ] 67 tests. 55/87 Test #55: CoordinateIOTests ......................... Passed 0.11 sec test 56 Start 56: TrajectoryAnalysisUnitTests 56: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/trajectoryanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/TrajectoryAnalysisUnitTests.xml" 56: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests 56: Test timeout computed to be: 1920 56: [==========] Running 385 tests from 24 test suites. 56: [----------] Global test environment set-up. 56: [----------] 11 tests from AngleModuleTest 56: [ RUN ] AngleModuleTest.ComputesSimpleAngles 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.ComputesSimpleAngles (3 ms) 56: [ RUN ] AngleModuleTest.ComputesDihedrals 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.ComputesDihedrals (1 ms) 56: [ RUN ] AngleModuleTest.ComputesVectorPairAngles 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.ComputesVectorPairAngles (1 ms) 56: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (5 ms) 56: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (1 ms) 56: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (1 ms) 56: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles 56: Reading frames from gro file 'Test system for different angles', 33 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (3 ms) 56: [ RUN ] AngleModuleTest.ComputesMultipleAngles 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.ComputesMultipleAngles (2 ms) 56: [ RUN ] AngleModuleTest.HandlesDynamicSelections 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.HandlesDynamicSelections (1 ms) 56: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (6 ms) 56: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (7 ms) 56: [----------] 11 tests from AngleModuleTest (43 ms total) 56: 56: [----------] 5 tests from ClustsizeTest 56: [ RUN ] ClustsizeTest.NoMolDefaultCutoff 56: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 56: There is one group in the index 56: '', 24 atoms 56: Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Total number of atoms in clusters = 24 56: cmid: 2, cmax: 4, max_size: 6 56: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 56: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (5 ms) 56: [ RUN ] ClustsizeTest.NoMolShortCutoff 56: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 56: There is one group in the index 56: '', 24 atoms 56: Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Total number of atoms in clusters = 24 56: cmid: 1, cmax: 6, max_size: 6 56: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 56: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (6 ms) 56: [ RUN ] ClustsizeTest.MolDefaultCutoff 56: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 56: '', 24 atoms 56: Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Total number of atoms in clusters = 8 56: cmid: 2, cmax: 4, max_size: 2 56: 50%100%cmid: 2, cmax: 6, max_size: 2 56: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (6 ms) 56: [ RUN ] ClustsizeTest.MolShortCutoff 56: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 56: '', 24 atoms 56: Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Total number of atoms in clusters = 8 56: cmid: 1, cmax: 6, max_size: 2 56: 50%100%cmid: 2, cmax: 6, max_size: 2 56: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (2 ms) 56: [ RUN ] ClustsizeTest.MolCSize 56: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 56: '', 24 atoms 56: Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Total number of atoms in clusters = 8 56: cmid: 2, cmax: 4, max_size: 2 56: 50%100%cmid: 2, cmax: 6, max_size: 2 56: 50%100%[ OK ] ClustsizeTest.MolCSize (3 ms) 56: [----------] 5 tests from ClustsizeTest (25 ms total) 56: 56: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest 56: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp 56: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (1 ms) 56: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory 56: Reading frames from gro file 'Test system', 8 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (8 ms) 56: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset 56: Reading frames from gro file 'Test system', 8 atoms. 56: Reading frame 0 time 0.000 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (3 ms) 56: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory 56: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (1 ms) 56: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (20 ms total) 56: 56: [----------] 4 tests from ConvertTrjModuleTest 56: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 56: Reading frame 0 time 0.000 Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (13 ms) 56: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 56: Reading frame 0 time 0.000 Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (12 ms) 56: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 56: Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (1 ms) 56: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 56: Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (1 ms) 56: [----------] 4 tests from ConvertTrjModuleTest (29 ms total) 56: 56: [----------] 6 tests from DistanceModuleTest 56: [ RUN ] DistanceModuleTest.ComputesDistances 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: atomname S1 S2: 56: Number of samples: 5 56: Average distance: 1.43246 nm 56: Standard deviation: 0.96700 nm 56: [ OK ] DistanceModuleTest.ComputesDistances (1 ms) 56: [ RUN ] DistanceModuleTest.ComputesMultipleDistances 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: atomname S1 S2: 56: Number of samples: 5 56: Average distance: 1.43246 nm 56: Standard deviation: 0.96700 nm 56: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB: 56: Number of samples: 4 56: Average distance: 1.81066 nm 56: Standard deviation: 0.79289 nm 56: [ OK ] DistanceModuleTest.ComputesMultipleDistances (3 ms) 56: [ RUN ] DistanceModuleTest.HandlesDynamicSelections 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: atomname S1 S2 and res_cog x < 2.8: 56: Number of samples: 3 56: Average distance: 1.72076 nm 56: Standard deviation: 1.24839 nm 56: [ OK ] DistanceModuleTest.HandlesDynamicSelections (4 ms) 56: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroup 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: Contacts: 56: Number of samples: 2 56: Average distance: 1.00000 nm 56: Standard deviation: 0.00000 nm 56: [ OK ] DistanceModuleTest.HandlesSelectionFromGroup (12 ms) 56: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: SuccessiveContacts: 56: Number of samples: 2 56: Average distance: 1.00000 nm 56: Standard deviation: 0.00000 nm 56: [ OK ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices (5 ms) 56: [ RUN ] DistanceModuleTest.HandlesSelectionFromLargeGroup 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: ManyContacts: 56: Number of samples: 10 56: Average distance: 1.82913 nm 56: Standard deviation: 0.78478 nm 56: [ OK ] DistanceModuleTest.HandlesSelectionFromLargeGroup (13 ms) 56: [----------] 6 tests from DistanceModuleTest (42 ms total) 56: 56: [----------] 2 tests from ExtractClusterModuleTest 56: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms 56: trr version: GMX_trn_file (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 56: Analyzed 26 frames, last time 0.050 56: There are 8 clusters containing 26 structures, highest framenr is 25 56: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (6 ms) 56: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset 56: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 56: Analyzed 26 frames, last time 0.050 56: There are 8 clusters containing 26 structures, highest framenr is 25 56: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (8 ms) 56: [----------] 2 tests from ExtractClusterModuleTest (15 ms total) 56: 56: [----------] 2 tests from FreeVolumeModuleTest 56: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 56: from the source below. This means the results may be different 56: compared to previous GROMACS versions. 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. Bondi 56: van der Waals Volumes and Radii 56: J. Phys. Chem. 68 (1964) pp. 441-451 56: -------- -------- --- Thank You --- -------- -------- 56: 56: Could not determine VDW radius for CO2-RM. Set to zero. 56: Could not determine VDW radius for CO2-RM. Set to zero. 56: Could not determine VDW radius for CO2-RM. Set to zero. 56: Could not determine VDW radius for CO2-RM. Set to zero. 56: Could not determine VDW radius for CO2-RM. Set to zero. 56: Could not determine VDW radius for CO2-RM. Set to zero. 56: Could not determine VDW radius for CO2-RM. Set to zero. 56: Could not determine VDW radius for CO2-RM. Set to zero. 56: Could not determine VDW radius for CO2-RM. Set to zero. 56: Could not determine VDW radius for 40 particles. These were set to zero. 56: Reading frame 0 time 0.000 Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: cutoff = 0.18 nm 56: probe_radius = 0 nm 56: seed = 13 56: ninsert = 1000 probes per nm^3 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. Bondi 56: van der Waals Volumes and Radii 56: J. Phys. Chem. 68 (1964) pp. 441-451 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David 56: van der Spoel and Luciano T. Costa 56: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 56: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 56: Environ. Sci. Technol. 47 (2013) pp. 7421-7429 56: -------- -------- --- Thank You --- -------- -------- 56: 56: Free volume 38.02 +/- 0.00 % 56: Total volume 68.92 +/- 0.00 nm^3 56: Number of molecules 340 total mass 63491.38 Dalton 56: Average molar mass: 186.74 Dalton 56: Density rho: 1529.71 +/- 0.00 nm^3 56: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 56: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3 56: Fractional free volume 0.194 +/- 0.000 56: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (76 ms) 56: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 56: from the source below. This means the results may be different 56: compared to previous GROMACS versions. 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. Bondi 56: van der Waals Volumes and Radii 56: J. Phys. Chem. 68 (1964) pp. 441-451 56: -------- -------- --- Thank You --- -------- -------- 56: 56: Reading frame 0 time 0.000 Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: cutoff = 0.18 nm 56: probe_radius = 0 nm 56: seed = 17 56: ninsert = 1000 probes per nm^3 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. Bondi 56: van der Waals Volumes and Radii 56: J. Phys. Chem. 68 (1964) pp. 441-451 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David 56: van der Spoel and Luciano T. Costa 56: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 56: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 56: Environ. Sci. Technol. 47 (2013) pp. 7421-7429 56: -------- -------- --- Thank You --- -------- -------- 56: 56: Free volume 38.48 +/- 0.00 % 56: Total volume 68.92 +/- 0.00 nm^3 56: Number of molecules 340 total mass 63491.38 Dalton 56: Average molar mass: 186.74 Dalton 56: Density rho: 1529.71 +/- 0.00 nm^3 56: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 56: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3 56: Fractional free volume 0.200 +/- 0.000 56: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (75 ms) 56: [----------] 2 tests from FreeVolumeModuleTest (152 ms total) 56: 56: [----------] 11 tests from MsdModuleTest 56: [ RUN ] MsdModuleTest.threeDimensionalDiffusion 56: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 56: Analyzed 10 frames, last time 9.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] MsdModuleTest.threeDimensionalDiffusion (9 ms) 56: [ RUN ] MsdModuleTest.twoDimensionalDiffusion 56: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 56: Analyzed 10 frames, last time 9.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] MsdModuleTest.twoDimensionalDiffusion (2 ms) 56: [ RUN ] MsdModuleTest.oneDimensionalDiffusion 56: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 56: Analyzed 10 frames, last time 9.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] MsdModuleTest.oneDimensionalDiffusion (2 ms) 56: [ RUN ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau 56: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 56: Analyzed 10 frames, last time 9.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau (4 ms) 56: [ RUN ] MsdModuleTest.roundingFail 56: Reading frame 0 time 0.000 Reading frame 1 time 0.001 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] MsdModuleTest.roundingFail (8 ms) 56: [ RUN ] MsdModuleTest.multipleGroupsWork 56: 56: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 56: For a correct single-point energy evaluation with nsteps = 0, use 56: continuation = yes to avoid constraining the input coordinates. 56: 56: Generating 1-4 interactions: fudge = 0.5 56: 56: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 56: For energy conservation with LINCS, lincs_iter should be 2 or larger. 56: 56: 56: Number of degrees of freedom in T-Coupling group rest is 1818.00 56: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 56: 56: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 56: NVE simulation: will use the initial temperature of 288.764 K for 56: determining the Verlet buffer size 56: 56: 56: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 56: There are 9 non-linear virtual site constructions. Their contribution to 56: the energy error is approximated. In most cases this does not affect the 56: error significantly. 56: 56: 56: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 56: You are using a plain Coulomb cut-off, which might produce artifacts. 56: You might want to consider using PME electrostatics. 56: 56: 56: 56: There were 5 NOTEs 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 2.000 56: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 56: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 56: Analyzed 21 frames, last time 40.000 56: Setting the LD random seed to 1610021415 56: 56: Generated 2145 of the 2145 non-bonded parameter combinations 56: 56: Generated 2145 of the 2145 1-4 parameter combinations 56: 56: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 56: 56: Excluding 2 bonded neighbours molecule type 'SOL' 56: 56: Cleaning up constraints and constant bonded interactions with virtual sites 56: 56: Converted 15 Bonds with virtual sites to connections, 7 left 56: 56: Removed 18 Angles with virtual sites, 21 left 56: 56: Removed 10 Proper Dih.s with virtual sites, 44 left 56: 56: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 56: 56: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 56: 56: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 56: 56: Note that mdrun will redetermine rlist based on the actual pair-list setup 56: 56: This run will generate roughly 0 Mb of data 56: [ OK ] MsdModuleTest.multipleGroupsWork (40 ms) 56: [ DISABLED ] MsdModuleTest.DISABLED_trestartLessThanDt 56: [ RUN ] MsdModuleTest.trestartGreaterThanDt 56: 56: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 56: For a correct single-point energy evaluation with nsteps = 0, use 56: continuation = yes to avoid constraining the input coordinates. 56: 56: Generating 1-4 interactions: fudge = 0.5 56: 56: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 56: For energy conservation with LINCS, lincs_iter should be 2 or larger. 56: 56: 56: Number of degrees of freedom in T-Coupling group rest is 1818.00 56: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 56: 56: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 56: NVE simulation: will use the initial temperature of 288.764 K for 56: determining the Verlet buffer size 56: 56: 56: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 56: There are 9 non-linear virtual site constructions. Their contribution to 56: the energy error is approximated. In most cases this does not affect the 56: error significantly. 56: 56: 56: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 56: You are using a plain Coulomb cut-off, which might produce artifacts. 56: You might want to consider using PME electrostatics. 56: 56: 56: 56: There were 5 NOTEs 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 56: Analyzed 21 frames, last time 40.000 56: Setting the LD random seed to -139493377 56: 56: Generated 2145 of the 2145 non-bonded parameter combinations 56: 56: Generated 2145 of the 2145 1-4 parameter combinations 56: 56: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 56: 56: Excluding 2 bonded neighbours molecule type 'SOL' 56: 56: Cleaning up constraints and constant bonded interactions with virtual sites 56: 56: Converted 15 Bonds with virtual sites to connections, 7 left 56: 56: Removed 18 Angles with virtual sites, 21 left 56: 56: Removed 10 Proper Dih.s with virtual sites, 44 left 56: 56: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 56: 56: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 56: 56: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 56: 56: Note that mdrun will redetermine rlist based on the actual pair-list setup 56: 56: This run will generate roughly 0 Mb of data 56: [ OK ] MsdModuleTest.trestartGreaterThanDt (27 ms) 56: [ RUN ] MsdModuleTest.molTest 56: 56: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 56: For a correct single-point energy evaluation with nsteps = 0, use 56: continuation = yes to avoid constraining the input coordinates. 56: 56: Generating 1-4 interactions: fudge = 0.5 56: 56: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 56: For energy conservation with LINCS, lincs_iter should be 2 or larger. 56: 56: 56: Number of degrees of freedom in T-Coupling group rest is 1818.00 56: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 56: 56: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 56: NVE simulation: will use the initial temperature of 288.764 K for 56: determining the Verlet buffer size 56: 56: 56: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 56: There are 9 non-linear virtual site constructions. Their contribution to 56: the energy error is approximated. In most cases this does not affect the 56: error significantly. 56: 56: 56: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 56: You are using a plain Coulomb cut-off, which might produce artifacts. 56: You might want to consider using PME electrostatics. 56: 56: 56: 56: There were 5 NOTEs 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 56: Analyzed 21 frames, last time 40.000 56: Setting the LD random seed to -269750273 56: 56: Generated 2145 of the 2145 non-bonded parameter combinations 56: 56: Generated 2145 of the 2145 1-4 parameter combinations 56: 56: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 56: 56: Excluding 2 bonded neighbours molecule type 'SOL' 56: 56: Cleaning up constraints and constant bonded interactions with virtual sites 56: 56: Converted 15 Bonds with virtual sites to connections, 7 left 56: 56: Removed 18 Angles with virtual sites, 21 left 56: 56: Removed 10 Proper Dih.s with virtual sites, 44 left 56: 56: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 56: 56: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 56: 56: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 56: 56: Note that mdrun will redetermine rlist based on the actual pair-list setup 56: 56: This run will generate roughly 0 Mb of data 56: [ OK ] MsdModuleTest.molTest (29 ms) 56: [ RUN ] MsdModuleTest.beginFit 56: 56: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 56: For a correct single-point energy evaluation with nsteps = 0, use 56: continuation = yes to avoid constraining the input coordinates. 56: 56: Generating 1-4 interactions: fudge = 0.5 56: 56: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 56: For energy conservation with LINCS, lincs_iter should be 2 or larger. 56: 56: 56: Number of degrees of freedom in T-Coupling group rest is 1818.00 56: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 56: 56: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 56: NVE simulation: will use the initial temperature of 288.764 K for 56: determining the Verlet buffer size 56: 56: 56: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 56: There are 9 non-linear virtual site constructions. Their contribution to 56: the energy error is approximated. In most cases this does not affect the 56: error significantly. 56: 56: 56: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 56: You are using a plain Coulomb cut-off, which might produce artifacts. 56: You might want to consider using PME electrostatics. 56: 56: 56: 56: There were 5 NOTEs 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 2.000 56: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 56: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 56: Analyzed 21 frames, last time 40.000 56: Setting the LD random seed to -572563586 56: 56: Generated 2145 of the 2145 non-bonded parameter combinations 56: 56: Generated 2145 of the 2145 1-4 parameter combinations 56: 56: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 56: 56: Excluding 2 bonded neighbours molecule type 'SOL' 56: 56: Cleaning up constraints and constant bonded interactions with virtual sites 56: 56: Converted 15 Bonds with virtual sites to connections, 7 left 56: 56: Removed 18 Angles with virtual sites, 21 left 56: 56: Removed 10 Proper Dih.s with virtual sites, 44 left 56: 56: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 56: 56: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 56: 56: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 56: 56: Note that mdrun will redetermine rlist based on the actual pair-list setup 56: 56: This run will generate roughly 0 Mb of data 56: [ OK ] MsdModuleTest.beginFit (18 ms) 56: [ RUN ] MsdModuleTest.endFit 56: 56: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 56: For a correct single-point energy evaluation with nsteps = 0, use 56: continuation = yes to avoid constraining the input coordinates. 56: 56: Generating 1-4 interactions: fudge = 0.5 56: 56: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 56: For energy conservation with LINCS, lincs_iter should be 2 or larger. 56: 56: 56: Number of degrees of freedom in T-Coupling group rest is 1818.00 56: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 56: 56: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 56: NVE simulation: will use the initial temperature of 288.764 K for 56: determining the Verlet buffer size 56: 56: 56: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 56: There are 9 non-linear virtual site constructions. Their contribution to 56: the energy error is approximated. In most cases this does not affect the 56: error significantly. 56: 56: 56: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 56: You are using a plain Coulomb cut-off, which might produce artifacts. 56: You might want to consider using PME electrostatics. 56: 56: 56: 56: There were 5 NOTEs 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 2.000 56: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 56: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 56: Analyzed 21 frames, last time 40.000 56: Setting the LD random seed to 1929239483 56: 56: Generated 2145 of the 2145 non-bonded parameter combinations 56: 56: Generated 2145 of the 2145 1-4 parameter combinations 56: 56: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 56: 56: Excluding 2 bonded neighbours molecule type 'SOL' 56: 56: Cleaning up constraints and constant bonded interactions with virtual sites 56: 56: Converted 15 Bonds with virtual sites to connections, 7 left 56: 56: Removed 18 Angles with virtual sites, 21 left 56: 56: Removed 10 Proper Dih.s with virtual sites, 44 left 56: 56: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 56: 56: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 56: 56: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 56: 56: Note that mdrun will redetermine rlist based on the actual pair-list setup 56: 56: This run will generate roughly 0 Mb of data 56: [ OK ] MsdModuleTest.endFit (31 ms) 56: [ RUN ] MsdModuleTest.notEnoughPointsForFitErrorEstimate 56: 56: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 56: For a correct single-point energy evaluation with nsteps = 0, use 56: continuation = yes to avoid constraining the input coordinates. 56: 56: Generating 1-4 interactions: fudge = 0.5 56: 56: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 56: For energy conservation with LINCS, lincs_iter should be 2 or larger. 56: 56: 56: Number of degrees of freedom in T-Coupling group rest is 1818.00 56: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 56: 56: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 56: NVE simulation: will use the initial temperature of 288.764 K for 56: determining the Verlet buffer size 56: 56: 56: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 56: There are 9 non-linear virtual site constructions. Their contribution to 56: the energy error is approximated. In most cases this does not affect the 56: error significantly. 56: 56: 56: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 56: You are using a plain Coulomb cut-off, which might produce artifacts. 56: You might want to consider using PME electrostatics. 56: 56: 56: 56: There were 5 NOTEs 56: NOTE: You provided an index file 56: /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/alanine_vsite_solvated.ndx 56: (with -n), but it was not used by any selection. 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 2.000 56: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 56: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 56: Analyzed 21 frames, last time 40.000 56: Setting the LD random seed to 794751998 56: 56: Generated 2145 of the 2145 non-bonded parameter combinations 56: 56: Generated 2145 of the 2145 1-4 parameter combinations 56: 56: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 56: 56: Excluding 2 bonded neighbours molecule type 'SOL' 56: 56: Cleaning up constraints and constant bonded interactions with virtual sites 56: 56: Converted 15 Bonds with virtual sites to connections, 7 left 56: 56: Removed 18 Angles with virtual sites, 21 left 56: 56: Removed 10 Proper Dih.s with virtual sites, 44 left 56: 56: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 56: 56: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 56: 56: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 56: 56: Note that mdrun will redetermine rlist based on the actual pair-list setup 56: 56: This run will generate roughly 0 Mb of data 56: [ OK ] MsdModuleTest.notEnoughPointsForFitErrorEstimate (28 ms) 56: [----------] 11 tests from MsdModuleTest (204 ms total) 56: 56: [----------] 9 tests from PairDistanceModuleTest 56: [ RUN ] PairDistanceModuleTest.ComputesAllDistances 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] PairDistanceModuleTest.ComputesAllDistances (3 ms) 56: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (2 ms) 56: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (2 ms) 56: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (5 ms) 56: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (4 ms) 56: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (1 ms) 56: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (4 ms) 56: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (1 ms) 56: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (1 ms) 56: [----------] 9 tests from PairDistanceModuleTest (44 ms total) 56: 56: [----------] 5 tests from RdfModuleTest 56: [ RUN ] RdfModuleTest.BasicTest 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] RdfModuleTest.BasicTest (20 ms) 56: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork 56: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms. 56: Reading frame 0 time 0.000 Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (24 ms) 56: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (23 ms) 56: [ RUN ] RdfModuleTest.CalculatesSurf 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] RdfModuleTest.CalculatesSurf (11 ms) 56: [ RUN ] RdfModuleTest.CalculatesXY 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] RdfModuleTest.CalculatesXY (23 ms) 56: [----------] 5 tests from RdfModuleTest (106 ms total) 56: 56: [----------] 5 tests from SasaModuleTest 56: [ RUN ] SasaModuleTest.BasicTest 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 56: Michael Scharf 56: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 56: of Surface Area and Volume and to Dot Surface Contouring of Molecular 56: Assemblies 56: J. Comp. Chem. 16 (1995) pp. 273-284 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 56: from the source below. This means the results may be different 56: compared to previous GROMACS versions. 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. Bondi 56: van der Waals Volumes and Radii 56: J. Phys. Chem. 68 (1964) pp. 441-451 56: -------- -------- --- Thank You --- -------- -------- 56: 56: Analyzed topology coordinates 56: [ OK ] SasaModuleTest.BasicTest (14 ms) 56: [ RUN ] SasaModuleTest.HandlesSelectedResidues 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 56: Michael Scharf 56: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 56: of Surface Area and Volume and to Dot Surface Contouring of Molecular 56: Assemblies 56: J. Comp. Chem. 16 (1995) pp. 273-284 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 56: from the source below. This means the results may be different 56: compared to previous GROMACS versions. 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. Bondi 56: van der Waals Volumes and Radii 56: J. Phys. Chem. 68 (1964) pp. 441-451 56: -------- -------- --- Thank You --- -------- -------- 56: 56: Analyzed topology coordinates 56: [ OK ] SasaModuleTest.HandlesSelectedResidues (4 ms) 56: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 56: Michael Scharf 56: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 56: of Surface Area and Volume and to Dot Surface Contouring of Molecular 56: Assemblies 56: J. Comp. Chem. 16 (1995) pp. 273-284 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 56: from the source below. This means the results may be different 56: compared to previous GROMACS versions. 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. Bondi 56: van der Waals Volumes and Radii 56: J. Phys. Chem. 68 (1964) pp. 441-451 56: -------- -------- --- Thank You --- -------- -------- 56: 56: Analyzed topology coordinates 56: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (5 ms) 56: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 56: Michael Scharf 56: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 56: of Surface Area and Volume and to Dot Surface Contouring of Molecular 56: Assemblies 56: J. Comp. Chem. 16 (1995) pp. 273-284 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 56: from the source below. This means the results may be different 56: compared to previous GROMACS versions. 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. Bondi 56: van der Waals Volumes and Radii 56: J. Phys. Chem. 68 (1964) pp. 441-451 56: -------- -------- --- Thank You --- -------- -------- 56: 56: Analyzed topology coordinates 56: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (10 ms) 56: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 56: Michael Scharf 56: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 56: of Surface Area and Volume and to Dot Surface Contouring of Molecular 56: Assemblies 56: J. Comp. Chem. 16 (1995) pp. 273-284 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 56: from the source below. This means the results may be different 56: compared to previous GROMACS versions. 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. Bondi 56: van der Waals Volumes and Radii 56: J. Phys. Chem. 68 (1964) pp. 441-451 56: -------- -------- --- Thank You --- -------- -------- 56: 56: Analyzed topology coordinates 56: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (11 ms) 56: [----------] 5 tests from SasaModuleTest (47 ms total) 56: 56: [----------] 8 tests from SelectModuleTest 56: [ RUN ] SelectModuleTest.BasicTest 56: Reading frames from gro file 'Test system', 15 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] SelectModuleTest.BasicTest (10 ms) 56: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput 56: Reading frames from gro file 'Test system', 15 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (4 ms) 56: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput 56: Reading frames from gro file 'Test system', 15 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (7 ms) 56: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput 56: Reading frames from gro file 'Test system', 15 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (8 ms) 56: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput 56: Reading frames from gro file 'Test system', 15 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (5 ms) 56: [ RUN ] SelectModuleTest.NormalizesSizes 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] SelectModuleTest.NormalizesSizes (6 ms) 56: [ RUN ] SelectModuleTest.WritesResidueNumbers 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] SelectModuleTest.WritesResidueNumbers (2 ms) 56: [ RUN ] SelectModuleTest.WritesResidueIndices 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] SelectModuleTest.WritesResidueIndices (1 ms) 56: [----------] 8 tests from SelectModuleTest (47 ms total) 56: 56: [----------] 10 tests from SurfaceAreaTest 56: [ RUN ] SurfaceAreaTest.ComputesSinglePoint 56: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms) 56: [ RUN ] SurfaceAreaTest.ComputesTwoPoints 56: [ OK ] SurfaceAreaTest.ComputesTwoPoints (0 ms) 56: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius 56: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (0 ms) 56: [ RUN ] SurfaceAreaTest.SurfacePoints12 56: [ OK ] SurfaceAreaTest.SurfacePoints12 (0 ms) 56: [ RUN ] SurfaceAreaTest.SurfacePoints32 56: [ OK ] SurfaceAreaTest.SurfacePoints32 (0 ms) 56: [ RUN ] SurfaceAreaTest.SurfacePoints42 56: [ OK ] SurfaceAreaTest.SurfacePoints42 (0 ms) 56: [ RUN ] SurfaceAreaTest.SurfacePoints122 56: [ OK ] SurfaceAreaTest.SurfacePoints122 (1 ms) 56: [ RUN ] SurfaceAreaTest.Computes100Points 56: [ OK ] SurfaceAreaTest.Computes100Points (1 ms) 56: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC 56: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (7 ms) 56: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC 56: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (2 ms) 56: [----------] 10 tests from SurfaceAreaTest (23 ms total) 56: 56: [----------] 4 tests from TopologyInformation 56: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile 56: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms) 56: [ RUN ] TopologyInformation.WorksWithGroFile 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] TopologyInformation.WorksWithGroFile (1 ms) 56: [ RUN ] TopologyInformation.WorksWithPdbFile 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] TopologyInformation.WorksWithPdbFile (0 ms) 56: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile 56: 56: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 56: For a correct single-point energy evaluation with nsteps = 0, use 56: continuation = yes to avoid constraining the input coordinates. 56: 56: Generating 1-4 interactions: fudge = 0.5 56: 56: NOTE 2 [file lysozyme.top, line 1465]: 56: System has non-zero total charge: 2.000000 56: Total charge should normally be an integer. See 56: https://manual.gromacs.org/current/user-guide/floating-point.html 56: for discussion on how close it should be to an integer. 56: 56: 56: 56: Number of degrees of freedom in T-Coupling group rest is 465.00 56: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 56: 56: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 56: NVE simulation with an initial temperature of zero: will use a Verlet 56: buffer of 10%. Check your energy drift! 56: 56: 56: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 56: You are using a plain Coulomb cut-off, which might produce artifacts. 56: You might want to consider using PME electrostatics. 56: 56: 56: 56: There were 4 NOTEs 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 56: Setting the LD random seed to -50429960 56: 56: Generated 330891 of the 330891 non-bonded parameter combinations 56: 56: Generated 330891 of the 330891 1-4 parameter combinations 56: 56: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 56: Analysing residue names: 56: There are: 10 Protein residues 56: Analysing Protein... 56: 56: This run will generate roughly 0 Mb of data 56: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (377 ms) 56: [----------] 4 tests from TopologyInformation (380 ms total) 56: 56: [----------] 4 tests from TrajectoryModuleTest 56: [ RUN ] TrajectoryModuleTest.BasicTest 56: Reading frames from gro file 'Test system', 15 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] TrajectoryModuleTest.BasicTest (4 ms) 56: [ RUN ] TrajectoryModuleTest.PlotsXOnly 56: Reading frames from gro file 'Test system', 15 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] TrajectoryModuleTest.PlotsXOnly (3 ms) 56: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities 56: Reading frames from gro file 'Test system', 15 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (6 ms) 56: [ RUN ] TrajectoryModuleTest.HandlesNoForces 56: Reading frames from gro file 'Test system', 15 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] TrajectoryModuleTest.HandlesNoForces (5 ms) 56: [----------] 4 tests from TrajectoryModuleTest (21 ms total) 56: 56: [----------] 5 tests from UnionFinderTest 56: [ RUN ] UnionFinderTest.WorksEmpty 56: [ OK ] UnionFinderTest.WorksEmpty (0 ms) 56: [ RUN ] UnionFinderTest.BasicMerges 56: [ OK ] UnionFinderTest.BasicMerges (0 ms) 56: [ RUN ] UnionFinderTest.LargerMerges 56: [ OK ] UnionFinderTest.LargerMerges (0 ms) 56: [ RUN ] UnionFinderTest.LongRightMerge 56: [ OK ] UnionFinderTest.LongRightMerge (0 ms) 56: [ RUN ] UnionFinderTest.LongLeftMerge 56: [ OK ] UnionFinderTest.LongLeftMerge (0 ms) 56: [----------] 5 tests from UnionFinderTest (0 ms total) 56: 56: [----------] 1 test from MappedUnionFinderTest 56: [ RUN ] MappedUnionFinderTest.BasicMerges 56: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms) 56: [----------] 1 test from MappedUnionFinderTest (0 ms total) 56: 56: [----------] 160 tests from MoleculeTests/DsspModuleTestDsspNB 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/0 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/0 (17 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/1 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/1 (14 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/2 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/2 (9 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/3 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/3 (15 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/4 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/4 (15 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/5 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/5 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/6 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/6 (14 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/7 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/7 (17 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/8 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/8 (30 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/9 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/9 (23 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/10 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/10 (24 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/11 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/11 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/12 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/12 (27 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/13 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/13 (24 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/14 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/14 (26 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/15 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/15 (22 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/16 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/16 (37 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/17 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/17 (38 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/18 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/18 (35 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/19 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/19 (40 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/20 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/20 (36 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/21 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/21 (49 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/22 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/22 (37 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/23 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/23 (36 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/24 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/24 (241 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/25 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/25 (44 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/26 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/26 (39 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/27 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/27 (37 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/28 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/28 (41 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/29 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/29 (40 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/30 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/30 (39 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/31 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/31 (45 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/32 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/32 (17 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/33 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/33 (5 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/34 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/34 (18 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/35 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/35 (6 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/36 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/36 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/37 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/37 (5 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/38 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/38 (18 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/39 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/39 (5 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/40 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/40 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/41 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/41 (21 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/42 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/42 (19 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/43 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/43 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/44 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/44 (17 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/45 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/45 (19 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/46 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/46 (23 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/47 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/47 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/48 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/48 (22 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/49 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/49 (15 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/50 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/50 (12 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/51 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/51 (18 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/52 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/52 (11 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/53 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/53 (16 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/54 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/54 (17 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/55 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/55 (7 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/56 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/56 (43 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/57 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/57 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/58 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/58 (25 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/59 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/59 (28 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/60 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/60 (34 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/61 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/61 (38 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/62 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/62 (35 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/63 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/63 (29 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/64 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/64 (39 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/65 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/65 (22 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/66 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/66 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/67 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/67 (33 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/68 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/68 (30 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/69 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/69 (23 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/70 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/70 (34 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/71 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/71 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/72 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/72 (27 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/73 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/73 (18 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/74 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/74 (25 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/75 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/75 (15 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/76 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/76 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/77 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/77 (18 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/78 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/78 (23 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/79 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/79 (15 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/80 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/80 (32 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/81 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/81 (18 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/82 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/82 (16 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/83 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/83 (15 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/84 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/84 (42 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/85 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/85 (36 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/86 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/86 (34 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/87 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/87 (16 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/88 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/88 (23 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/89 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/89 (22 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/90 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/90 (25 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/91 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/91 (14 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/92 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/92 (23 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/93 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/93 (23 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/94 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/94 (19 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/95 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/95 (24 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/96 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/96 (22 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/97 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/97 (21 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/98 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/98 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/99 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/99 (18 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/100 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/100 (17 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/101 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/101 (19 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/102 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/102 (26 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/103 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/103 (21 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/104 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/104 (23 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/105 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/105 (18 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/106 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/106 (25 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/107 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/107 (11 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/108 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/108 (19 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/109 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/109 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/110 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/110 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/111 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/111 (19 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/112 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/112 (16 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/113 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/113 (15 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/114 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/114 (10 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/115 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/115 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/116 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/116 (19 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/117 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/117 (11 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/118 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/118 (12 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/119 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/119 (12 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/120 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/120 (90 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/121 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/121 (50 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/122 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/122 (50 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/123 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/123 (89 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/124 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/124 (78 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/125 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/125 (95 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/126 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/126 (70 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/127 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/127 (58 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/128 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/128 (29 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/129 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/129 (21 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/130 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/130 (22 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/131 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/131 (18 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/132 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/132 (19 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/133 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/133 (29 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/134 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/134 (24 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/135 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/135 (18 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/136 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/136 (25 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/137 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/137 (57 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/138 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/138 (19 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/139 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/139 (21 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/140 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/140 (70 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/141 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/141 (18 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/142 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/142 (19 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/143 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/143 (22 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/144 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/144 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/145 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/145 (21 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/146 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/146 (17 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/147 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/147 (17 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/148 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/148 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/149 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/149 (15 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/150 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/150 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/151 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/151 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/152 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/152 (42 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/153 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/153 (34 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/154 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/154 (164 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/155 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/155 (34 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/156 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/156 (39 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/157 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/157 (38 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/158 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/158 (31 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/159 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/159 (34 ms) 56: [----------] 160 tests from MoleculeTests/DsspModuleTestDsspNB (4622 ms total) 56: 56: [----------] 24 tests from MoleculeTests/DsspModuleTestGromacsNB 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/0 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/0 (62 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/1 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/1 (53 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/2 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/2 (49 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/3 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/3 (55 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/4 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/4 (64 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/5 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/5 (72 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/6 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/6 (64 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/7 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/7 (59 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/8 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/8 (22 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/9 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/9 (21 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/10 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/10 (24 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/11 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/11 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/12 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/12 (22 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/13 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/13 (25 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/14 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/14 (14 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/15 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/15 (22 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/16 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/16 (16 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/17 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/17 (19 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/18 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/18 (11 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/19 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/19 (14 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/20 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/20 (16 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/21 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/21 (17 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/22 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/22 (16 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/23 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/23 (20 ms) 56: [----------] 24 tests from MoleculeTests/DsspModuleTestGromacsNB (786 ms total) 56: 56: [----------] 80 tests from MoleculeTests/DsspModuleTestDsspNoNB 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/0 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/0 (11 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/1 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/1 (11 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/2 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/2 (12 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/3 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/3 (11 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/4 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/4 (23 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/5 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/5 (29 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/6 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/6 (26 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/7 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/7 (22 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/8 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/8 (32 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/9 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/9 (22 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/10 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/10 (28 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/11 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/11 (31 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/12 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/12 (34 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/13 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/13 (40 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/14 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/14 (40 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/15 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/15 (34 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/16 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/16 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/17 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/17 (10 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/18 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/18 (12 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/19 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/19 (11 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/20 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/20 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/21 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/21 (15 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/22 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/22 (12 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/23 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/23 (19 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/24 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/24 (9 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/25 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/25 (14 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/26 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/26 (16 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/27 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/27 (18 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/28 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/28 (33 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/29 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/29 (25 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/30 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/30 (32 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/31 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/31 (27 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/32 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/32 (22 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/33 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/33 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/34 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/34 (22 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/35 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/35 (30 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/36 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/36 (15 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/37 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/37 (12 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/38 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/38 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/39 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/39 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/40 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/40 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/41 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/41 (23 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/42 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/42 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/43 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/43 (29 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/44 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/44 (19 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/45 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/45 (15 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/46 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/46 (14 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/47 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/47 (25 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/48 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/48 (24 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/49 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/49 (28 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/50 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/50 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/51 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/51 (17 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/52 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/52 (18 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/53 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/53 (15 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/54 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/54 (16 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/55 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/55 (14 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/56 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/56 (10 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/57 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/57 (19 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/58 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/58 (19 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/59 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/59 (16 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/60 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/60 (63 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/61 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/61 (58 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/62 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/62 (83 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/63 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/63 (53 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/64 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/64 (17 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/65 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/65 (16 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/66 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/66 (12 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/67 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/67 (21 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/68 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/68 (16 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/69 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/69 (19 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/70 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/70 (21 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/71 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/71 (19 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/72 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/72 (17 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/73 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/73 (14 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/74 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/74 (15 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/75 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/75 (19 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/76 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/76 (15 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/77 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/77 (22 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/78 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/78 (17 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/79 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/79 (22 ms) 56: [----------] 80 tests from MoleculeTests/DsspModuleTestDsspNoNB (1801 ms total) 56: 56: [----------] 12 tests from MoleculeTests/DsspModuleTestGromacsNoNB 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/0 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/0 (40 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/1 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/1 (38 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/2 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/2 (41 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/3 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/3 (45 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/4 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/4 (15 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/5 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/5 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/6 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/6 (14 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/7 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/7 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/8 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/8 (12 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/9 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/9 (11 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/10 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/10 (11 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/11 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/11 (11 ms) 56: [----------] 12 tests from MoleculeTests/DsspModuleTestGromacsNoNB (271 ms total) 56: 56: [----------] 3 tests from GyrateTests/GyrateModuleTest 56: [ RUN ] GyrateTests/GyrateModuleTest.Works/0 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 56: Analyzed 2 frames, last time 10.000 56: [ OK ] GyrateTests/GyrateModuleTest.Works/0 (9 ms) 56: [ RUN ] GyrateTests/GyrateModuleTest.Works/1 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 56: Analyzed 2 frames, last time 10.000 56: [ OK ] GyrateTests/GyrateModuleTest.Works/1 (8 ms) 56: [ RUN ] GyrateTests/GyrateModuleTest.Works/2 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 56: Analyzed 2 frames, last time 10.000 56: [ OK ] GyrateTests/GyrateModuleTest.Works/2 (5 ms) 56: [----------] 3 tests from GyrateTests/GyrateModuleTest (24 ms total) 56: 56: [----------] 6 tests from HBondTests/HbondModuleTest 56: [ RUN ] HBondTests/HbondModuleTest.Works/0 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 56: Analyzed 2 frames, last time 10.000 56: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 56: [ OK ] HBondTests/HbondModuleTest.Works/0 (14 ms) 56: [ RUN ] HBondTests/HbondModuleTest.Works/1 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 56: Analyzed 2 frames, last time 10.000 56: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 56: [ OK ] HBondTests/HbondModuleTest.Works/1 (13 ms) 56: [ RUN ] HBondTests/HbondModuleTest.Works/2 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 56: Analyzed 2 frames, last time 10.000 56: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 56: [ OK ] HBondTests/HbondModuleTest.Works/2 (45 ms) 56: [ RUN ] HBondTests/HbondModuleTest.Works/3 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 56: Analyzed 2 frames, last time 10.000 56: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 56: Merging hbonds with Acceptor and Donor swapped 56: [ OK ] HBondTests/HbondModuleTest.Works/3 (51 ms) 56: [ RUN ] HBondTests/HbondModuleTest.Works/4 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 56: Analyzed 2 frames, last time 10.000 56: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 56: [ OK ] HBondTests/HbondModuleTest.Works/4 (48 ms) 56: [ RUN ] HBondTests/HbondModuleTest.Works/5 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 56: Analyzed 2 frames, last time 10.000 56: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 56: [ OK ] HBondTests/HbondModuleTest.Works/5 (76 ms) 56: [----------] 6 tests from HBondTests/HbondModuleTest (274 ms total) 56: 56: [----------] 4 tests from MoleculeTests/ScatteringModule 56: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/0 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev & V. V. Isaev-Ivanov 56: Method for calculating small-angle neutron scattering spectra using all-atom 56: molecular dynamics trajectories 56: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques 7 (2013) pp. 1124–1127 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/ScatteringModule.DirectMode/0 (18 ms) 56: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/1 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev & V. V. Isaev-Ivanov 56: Method for calculating small-angle neutron scattering spectra using all-atom 56: molecular dynamics trajectories 56: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques 7 (2013) pp. 1124–1127 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: D. T. Cromer & J. B. Mann 56: X-ray scattering factors computed from numerical Hartree-Fock wave functions 56: Acta Cryst. A 24 (1968) pp. 321 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/ScatteringModule.DirectMode/1 (132 ms) 56: [ RUN ] MoleculeTests/ScatteringModule.MCMode/0 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev & V. V. Isaev-Ivanov 56: Method for calculating small-angle neutron scattering spectra using all-atom 56: molecular dynamics trajectories 56: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques 7 (2013) pp. 1124–1127 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/ScatteringModule.MCMode/0 (11 ms) 56: [ RUN ] MoleculeTests/ScatteringModule.MCMode/1 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev & V. V. Isaev-Ivanov 56: Method for calculating small-angle neutron scattering spectra using all-atom 56: molecular dynamics trajectories 56: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques 7 (2013) pp. 1124–1127 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: D. T. Cromer & J. B. Mann 56: X-ray scattering factors computed from numerical Hartree-Fock wave functions 56: Acta Cryst. A 24 (1968) pp. 321 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/ScatteringModule.MCMode/1 (52 ms) 56: [----------] 4 tests from MoleculeTests/ScatteringModule (216 ms total) 56: 56: [----------] Global test environment tear-down 56: [==========] 385 tests from 24 test suites ran. (9207 ms total) 56: [ PASSED ] 385 tests. 56: 56: YOU HAVE 1 DISABLED TEST 56: 56/87 Test #56: TrajectoryAnalysisUnitTests ............... Passed 9.26 sec test 57 Start 57: EnergyAnalysisUnitTests 57: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/energyanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/EnergyAnalysisUnitTests.xml" 57: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/energyanalysis/tests 57: Test timeout computed to be: 30 57: [==========] Running 11 tests from 5 test suites. 57: [----------] Global test environment set-up. 57: [----------] 2 tests from EnergyTermTest 57: [ RUN ] EnergyTermTest.ConstructWorks 57: [ OK ] EnergyTermTest.ConstructWorks (0 ms) 57: [ RUN ] EnergyTermTest.AddFrameWorks 57: [ OK ] EnergyTermTest.AddFrameWorks (0 ms) 57: [----------] 2 tests from EnergyTermTest (0 ms total) 57: 57: [----------] 1 test from DhdlTest 57: [ RUN ] DhdlTest.ExtractDhdl 57: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file 57: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision) 57: Note: file tpx version 110, software tpx version 134 57: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Reading energy frame 6 time 0.060 Reading energy frame 7 time 0.070 Reading energy frame 8 time 0.080 Reading energy frame 9 time 0.090 Reading energy frame 10 time 0.100 Reading energy frame 11 time 0.110 Reading energy frame 12 time 0.120 Reading energy frame 13 time 0.130 Reading energy frame 14 time 0.140 Reading energy frame 15 time 0.150 Reading energy frame 16 time 0.160 Reading energy frame 17 time 0.170 Reading energy frame 18 time 0.180 Reading energy frame 19 time 0.190 Reading energy frame 20 time 0.200 Reading energy frame 30 time 0.300 Reading energy frame 40 time 0.400 Reading energy frame 50 time 0.500 Reading energy frame 60 time 0.600 Reading energy frame 70 time 0.700 Reading energy frame 80 time 0.800 Reading energy frame 90 time 0.900 Reading energy frame 100 time 1.000 Last energy frame read 100 time 1.000 57: 57: 57: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg 57: [ OK ] DhdlTest.ExtractDhdl (12 ms) 57: [----------] 1 test from DhdlTest (12 ms total) 57: 57: [----------] 1 test from OriresTest 57: [ RUN ] OriresTest.ExtractOrires 57: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file 57: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision) 57: Note: file tpx version 111, software tpx version 134 57: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all) 57: End your selection with 0 57: Selecting all 7 orientation restraints 57: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Reading energy frame 3 time 0.006 Reading energy frame 4 time 0.008 Reading energy frame 5 time 0.010 Reading energy frame 6 time 0.012 Reading energy frame 7 time 0.014 Reading energy frame 8 time 0.016 Reading energy frame 9 time 0.018 Reading energy frame 10 time 0.020 Last energy frame read 10 time 0.020 57: [ OK ] OriresTest.ExtractOrires (14 ms) 57: [----------] 1 test from OriresTest (14 ms total) 57: 57: [----------] 5 tests from EnergyTest 57: [ RUN ] EnergyTest.ExtractEnergy 57: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 57: 57: Select the terms you want from the following list by 57: selecting either (part of) the name or the number or a combination. 57: End your selection with an empty line or a zero. 57: ------------------------------------------------------------------- 57: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 57: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 57: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 57: 13 Box-Z 14 Volume 15 Density 16 pV 57: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 57: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 57: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 57: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 57: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 57: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 57: 57: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 57: 57: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 57: All statistics are over 5001 points 57: 57: Energy Average Err.Est. RMSD Tot-Drift 57: ------------------------------------------------------------------------------- 57: Potential -34142.2 39 228.993 -62.8906 (kJ/mol) 57: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 57: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 57: [ OK ] EnergyTest.ExtractEnergy (8 ms) 57: [ RUN ] EnergyTest.ExtractEnergyByNumber 57: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 57: 57: Select the terms you want from the following list by 57: selecting either (part of) the name or the number or a combination. 57: End your selection with an empty line or a zero. 57: ------------------------------------------------------------------- 57: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 57: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 57: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 57: 13 Box-Z 14 Volume 15 Density 16 pV 57: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 57: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 57: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 57: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 57: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 57: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 57: 57: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 57: 57: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 57: All statistics are over 5001 points 57: 57: Energy Average Err.Est. RMSD Tot-Drift 57: ------------------------------------------------------------------------------- 57: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol) 57: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 57: Pres. DC -268.49 3 8.52175 13.2804 (bar) 57: [ OK ] EnergyTest.ExtractEnergyByNumber (1 ms) 57: [ RUN ] EnergyTest.ExtractEnergyMixed 57: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 57: 57: Select the terms you want from the following list by 57: selecting either (part of) the name or the number or a combination. 57: End your selection with an empty line or a zero. 57: ------------------------------------------------------------------- 57: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 57: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 57: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 57: 13 Box-Z 14 Volume 15 Density 16 pV 57: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 57: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 57: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 57: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 57: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 57: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 57: 57: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 57: 57: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets 57: All statistics are over 5001 points 57: 57: Energy Average Err.Est. RMSD Tot-Drift 57: ------------------------------------------------------------------------------- 57: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 57: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 57: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm) 57: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 57: [ OK ] EnergyTest.ExtractEnergyMixed (7 ms) 57: [ RUN ] EnergyTest.ExtractEnergyWithNumberInName 57: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 57: 57: Select the terms you want from the following list by 57: selecting either (part of) the name or the number or a combination. 57: End your selection with an empty line or a zero. 57: ------------------------------------------------------------------- 57: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 57: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 57: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 57: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 57: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 57: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 57: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 57: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 57: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 57: 37 1/Viscosity 38 T-System 39 Lamb-System 57: 57: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 57: 57: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 1 data sets 57: All statistics are over 3 points (frames) 57: 57: Energy Average Err.Est. RMSD Tot-Drift 57: ------------------------------------------------------------------------------- 57: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 57: [ OK ] EnergyTest.ExtractEnergyWithNumberInName (3 ms) 57: [ RUN ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber 57: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 57: 57: Select the terms you want from the following list by 57: selecting either (part of) the name or the number or a combination. 57: End your selection with an empty line or a zero. 57: ------------------------------------------------------------------- 57: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 57: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 57: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 57: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 57: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 57: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 57: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 57: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 57: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 57: 37 1/Viscosity 38 T-System 39 Lamb-System 57: 57: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 57: 57: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 2 data sets 57: All statistics are over 3 points (frames) 57: 57: Energy Average Err.Est. RMSD Tot-Drift 57: ------------------------------------------------------------------------------- 57: LJ (SR) -14.1095 -- 0.384124 0.932214 (kJ/mol) 57: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 57: [ OK ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber (2 ms) 57: [----------] 5 tests from EnergyTest (27 ms total) 57: 57: [----------] 2 tests from ViscosityTest 57: [ RUN ] ViscosityTest.EinsteinViscosity 57: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 57: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 57: 57: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 57: All statistics are over 5001 points 57: 57: Energy Average Err.Est. RMSD Tot-Drift 57: ------------------------------------------------------------------------------- 57: Pres-XX 20.2092 65 717.193 185.978 (bar) 57: Pres-XY -47.7351 39 372.522 207.456 (bar) 57: Pres-XZ 11.477 31 379.79 6.80818 (bar) 57: Pres-YX -47.7106 39 372.525 207.5 (bar) 57: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 57: Pres-YZ -41.3534 45 401.216 114.663 (bar) 57: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 57: Pres-ZY -41.3119 45 401.196 114.743 (bar) 57: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 57: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 57: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 57: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 57: 57: Computing shear viscosity using the Einstein relation with 14 start points separated by 0.2 ps 57: [ OK ] ViscosityTest.EinsteinViscosity (76 ms) 57: [ RUN ] ViscosityTest.EinsteinViscosityIntegral 57: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 57: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 57: 57: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 57: All statistics are over 5001 points 57: 57: Energy Average Err.Est. RMSD Tot-Drift 57: ------------------------------------------------------------------------------- 57: Pres-XX 20.2092 65 717.193 185.978 (bar) 57: Pres-XY -47.7351 39 372.522 207.456 (bar) 57: Pres-XZ 11.477 31 379.79 6.80818 (bar) 57: Pres-YX -47.7106 39 372.525 207.5 (bar) 57: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 57: Pres-YZ -41.3534 45 401.216 114.663 (bar) 57: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 57: Pres-ZY -41.3119 45 401.196 114.743 (bar) 57: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 57: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 57: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 57: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 57: 57: Computing shear viscosity using the Einstein relation with 14 start points separated by 0.2 ps 57: [ OK ] ViscosityTest.EinsteinViscosityIntegral (101 ms) 57: [----------] 2 tests from ViscosityTest (179 ms total) 57: 57: [----------] Global test environment tear-down 57: [==========] 11 tests from 5 test suites ran. (233 ms total) 57: [ PASSED ] 11 tests. 57/87 Test #57: EnergyAnalysisUnitTests ................... Passed 0.26 sec test 58 Start 58: ToolUnitTests 58: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/tool-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/ToolUnitTests.xml" 58: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests 58: Test timeout computed to be: 1920 58: [==========] Running 62 tests from 7 test suites. 58: [----------] Global test environment set-up. 58: [----------] 2 tests from DumpTest 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file lysozyme.top, line 1465]: 58: System has non-zero total charge: 2.000000 58: Total charge should normally be an integer. See 58: https://manual.gromacs.org/current/user-guide/floating-point.html 58: for discussion on how close it should be to an integer. 58: 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 465.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 58: NVE simulation with an initial temperature of zero: will use a Verlet 58: buffer of 10%. Check your energy drift! 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 4 NOTEs 58: Setting the LD random seed to -16909369 58: 58: Generated 330891 of the 330891 non-bonded parameter combinations 58: 58: Generated 330891 of the 330891 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 58: Analysing residue names: 58: There are: 10 Protein residues 58: Analysing Protein... 58: 58: This run will generate roughly 0 Mb of data 58: [ RUN ] DumpTest.WorksWithTpr 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr: 58: inputrec: 58: integrator = md 58: tinit = 0 58: dt = 0.001 58: nsteps = 0 58: init-step = 0 58: simulation-part = 1 58: mts = false 58: mass-repartition-factor = 1 58: comm-mode = Linear 58: nstcomm = 100 58: bd-fric = 0 58: ld-seed = -16909369 58: emtol = 10 58: emstep = 0.01 58: niter = 20 58: fcstep = 0 58: nstcgsteep = 1000 58: nbfgscorr = 10 58: rtpi = 0.05 58: nstxout = 0 58: nstvout = 0 58: nstfout = 0 58: nstlog = 1000 58: nstcalcenergy = 100 58: nstenergy = 1000 58: nstxout-compressed = 0 58: compressed-x-precision = 1000 58: cutoff-scheme = Verlet 58: nstlist = 10 58: pbc = xyz 58: periodic-molecules = false 58: verlet-buffer-tolerance = -1 58: verlet-buffer-pressure-tolerance = 0.5 58: rlist = 1.1 58: coulombtype = Cut-off 58: coulomb-modifier = Potential-shift 58: rcoulomb-switch = 0 58: rcoulomb = 1 58: epsilon-r = 1 58: epsilon-rf = inf 58: vdw-type = Cut-off 58: vdw-modifier = Potential-shift 58: rvdw-switch = 0 58: rvdw = 1 58: DispCorr = No 58: table-extension = 1 58: fourierspacing = 0.12 58: fourier-nx = 0 58: fourier-ny = 0 58: fourier-nz = 0 58: pme-order = 4 58: ewald-rtol = 1e-05 58: ewald-rtol-lj = 0.001 58: lj-pme-comb-rule = Geometric 58: ewald-geometry = 3d 58: epsilon-surface = 0 58: ensemble-temperature-setting = not available 58: tcoupl = No 58: nsttcouple = -1 58: nh-chain-length = 0 58: print-nose-hoover-chain-variables = false 58: pcoupl = No 58: refcoord-scaling = No 58: posres-com (3): 58: posres-com[0]= 0.00000e+00 58: posres-com[1]= 0.00000e+00 58: posres-com[2]= 0.00000e+00 58: posres-comB (3): 58: posres-comB[0]= 0.00000e+00 58: posres-comB[1]= 0.00000e+00 58: posres-comB[2]= 0.00000e+00 58: QMMM = false 58: qm-opts: 58: ngQM = 0 58: constraint-algorithm = Lincs 58: continuation = false 58: Shake-SOR = false 58: shake-tol = 0.0001 58: lincs-order = 4 58: lincs-iter = 1 58: lincs-warnangle = 30 58: nwall = 0 58: wall-type = 9-3 58: wall-r-linpot = -1 58: wall-atomtype[0] = -1 58: wall-atomtype[1] = -1 58: wall-density[0] = 0 58: wall-density[1] = 0 58: wall-ewald-zfac = 3 58: pull = false 58: awh = false 58: rotation = false 58: interactiveMD = false 58: disre = No 58: disre-weighting = Conservative 58: disre-mixed = false 58: dr-fc = 1000 58: dr-tau = 0 58: nstdisreout = 100 58: orire-fc = 0 58: orire-tau = 0 58: nstorireout = 100 58: free-energy = no 58: cos-acceleration = 0 58: deform (3x3): 58: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: simulated-tempering = false 58: swapcoords = no 58: userint1 = 0 58: userint2 = 0 58: userint3 = 0 58: userint4 = 0 58: userreal1 = 0 58: userreal2 = 0 58: userreal3 = 0 58: userreal4 = 0 58: applied-forces: 58: electric-field: 58: x: 58: E0 = 0 58: omega = 0 58: t0 = 0 58: sigma = 0 58: y: 58: E0 = 0 58: omega = 0 58: t0 = 0 58: sigma = 0 58: z: 58: E0 = 0 58: omega = 0 58: t0 = 0 58: sigma = 0 58: density-guided-simulation: 58: active = false 58: group = protein 58: similarity-measure = inner-product 58: atom-spreading-weight = unity 58: force-constant = 1e+09 58: gaussian-transform-spreading-width = 0.2 58: gaussian-transform-spreading-range-in-multiples-of-width = 4 58: reference-density-filename = reference.mrc 58: nst = 1 58: normalize-densities = true 58: adaptive-force-scaling = false 58: adaptive-force-scaling-time-constant = 4 58: shift-vector = 58: transformation-matrix = 58: qmmm-cp2k: 58: active = false 58: qmgroup = System 58: qmmethod = PBE 58: qmfilenames = 58: qmcharge = 0 58: qmmultiplicity = 1 58: colvars: 58: active = false 58: configfile = 58: seed = -1 58: grpopts: 58: nrdf: 465 58: ref-t: 0 58: tau-t: 0 58: annealing: No 58: annealing-npoints: 0 58: acc: 0 0 0 58: nfreeze: N N N 58: energygrp-flags[ 0]: 0 58: header: 58: bIr = present 58: bBox = present 58: bTop = present 58: bX = present 58: bV = present 58: bF = not present 58: natoms = 156 58: lambda = 0.000000e+00 58: buffer size = 46180 58: topology: 58: name="First 10 residues from 1AKI" 58: #atoms = 156 58: #molblock = 1 58: molblock (0): 58: moltype = 0 "Protein_chain_B" 58: #molecules = 1 58: #posres_xA = 0 58: #posres_xB = 0 58: bIntermolecularInteractions = false 58: ffparams: 58: atnr=10 58: ntypes=212 58: functype[0]=LJ_SR, c6= 3.35274590e-03, c12= 3.95094276e-06 58: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 58: functype[2]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06 58: functype[3]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07 58: functype[4]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06 58: functype[5]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06 58: functype[6]=LJ_SR, c6= 2.80388421e-03, c12= 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functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02 58: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02 58: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02 58: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02 58: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02 58: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02 58: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02 58: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02 58: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02 58: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39319992e+01, phiB= 1.80000000e+02, cpB= 4.39319992e+01, mult=2 58: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400002e+00, phiB= 1.80000000e+02, cpB= 4.18400002e+00, mult=2 58: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60239983e+00, phiB= 1.80000000e+02, cpB= 4.60239983e+00, mult=2 58: functype[143]=RBDIHS, rbcA[0]= 5.46010017e-01, rbcA[1]= 1.63803005e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405008e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 5.46010017e-01, rbcB[1]= 1.63803005e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405008e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[144]=RBDIHS, rbcA[0]= 7.25920022e-01, rbcA[1]= 2.17776990e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 7.25920022e-01, rbcB[1]= 2.17776990e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[145]=RBDIHS, rbcA[0]= 1.27611995e+00, rbcA[1]= 1.16734004e+00, rbcA[2]= 8.95380020e-01, rbcA[3]=-3.33884001e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 1.27611995e+00, rbcB[1]= 1.16734004e+00, rbcB[2]= 8.95380020e-01, rbcB[3]=-3.33884001e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[146]=RBDIHS, rbcA[0]=-6.91824007e+00, rbcA[1]= 4.67562008e+00, rbcA[2]= 2.24261999e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-6.91824007e+00, rbcB[1]= 4.67562008e+00, rbcB[2]= 2.24261999e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[147]=RBDIHS, rbcA[0]= 9.70690012e-01, rbcA[1]= 2.91206002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275003e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 9.70690012e-01, rbcB[1]= 2.91206002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275003e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[148]=RBDIHS, rbcA[0]= 6.27600014e-01, rbcA[1]= 1.88279998e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040006e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 6.27600014e-01, rbcB[1]= 1.88279998e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040006e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[149]=RBDIHS, rbcA[0]=-1.58989996e-01, rbcA[1]=-4.76980001e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35959983e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-1.58989996e-01, rbcB[1]=-4.76980001e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35959983e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654020e+00, rbcA[2]=-1.04934702e+01, rbcA[3]= 6.73623991e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654020e+00, rbcB[2]=-1.04934702e+01, rbcB[3]= 6.73623991e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[151]=RBDIHS, rbcA[0]= 5.00825024e+00, rbcA[1]=-1.69869995e+00, rbcA[2]=-3.72379988e-01, rbcA[3]=-2.93716002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 5.00825024e+00, rbcB[1]=-1.69869995e+00, rbcB[2]=-3.72379988e-01, rbcB[3]=-2.93716002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[152]=RBDIHS, rbcA[0]= 2.92880011e+00, rbcA[1]=-1.46440005e+00, rbcA[2]= 2.09199995e-01, rbcA[3]=-1.67359996e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 2.92880011e+00, rbcB[1]=-1.46440005e+00, rbcB[2]= 2.09199995e-01, rbcB[3]=-1.67359996e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[153]=RBDIHS, rbcA[0]= 5.77183008e+00, rbcA[1]=-2.67147994e+00, rbcA[2]= 9.58140016e-01, rbcA[3]=-4.05847979e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 5.77183008e+00, rbcB[1]=-2.67147994e+00, rbcB[2]= 9.58140016e-01, rbcB[3]=-4.05847979e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[154]=RBDIHS, rbcA[0]= 8.03330004e-01, rbcA[1]= 2.40999007e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 8.03330004e-01, rbcB[1]= 2.40999007e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[155]=RBDIHS, rbcA[0]= 2.05016003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 2.05016003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[156]=RBDIHS, rbcA[0]= 3.02879791e+01, rbcA[1]=-4.81160021e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 3.02879791e+01, rbcB[1]=-4.81160021e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[157]=RBDIHS, rbcA[0]= 2.54763794e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 2.54763794e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[158]=RBDIHS, rbcA[0]= 1.57025499e+01, rbcA[1]= 3.17565594e+01, rbcA[2]=-3.66935992e+00, rbcA[3]=-4.37897491e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 1.57025499e+01, rbcB[1]= 3.17565594e+01, rbcB[2]=-3.66935992e+00, rbcB[3]=-4.37897491e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[159]=RBDIHS, rbcA[0]=-1.03574896e+01, rbcA[1]=-2.95871601e+01, rbcA[2]=-1.16734004e+00, rbcA[3]= 4.11119919e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-1.03574896e+01, rbcB[1]=-2.95871601e+01, rbcB[2]=-1.16734004e+00, rbcB[3]= 4.11119919e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[160]=RBDIHS, rbcA[0]= 4.50198984e+00, rbcA[1]= 7.82410026e-01, rbcA[2]=-1.60247004e+00, rbcA[3]=-3.68192005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 4.50198984e+00, rbcB[1]= 7.82410026e-01, rbcB[2]=-1.60247004e+00, rbcB[3]=-3.68192005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[161]=RBDIHS, rbcA[0]= 4.22589988e-01, rbcA[1]= 2.70705009e+00, rbcA[2]=-3.12964010e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 4.22589988e-01, rbcB[1]= 2.70705009e+00, rbcB[2]=-3.12964010e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[162]=RBDIHS, rbcA[0]=-7.65670002e-01, rbcA[1]= 2.70705009e+00, rbcA[2]= 4.02501011e+00, rbcA[3]=-5.96639013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-7.65670002e-01, rbcB[1]= 2.70705009e+00, rbcB[2]= 4.02501011e+00, rbcB[3]=-5.96639013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[163]=RBDIHS, rbcA[0]= 9.66499984e-01, rbcA[1]= 2.89950991e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86600995e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 9.66499984e-01, rbcB[1]= 2.89950991e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86600995e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[164]=RBDIHS, rbcA[0]=-4.23421001e+00, rbcA[1]= 7.22159004e+00, rbcA[2]= 1.90789998e+00, rbcA[3]=-4.89527988e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-4.23421001e+00, rbcB[1]= 7.22159004e+00, rbcB[2]= 1.90789998e+00, rbcB[3]=-4.89527988e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[165]=RBDIHS, rbcA[0]= 3.03339996e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03339996e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 3.03339996e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03339996e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[166]=RBDIHS, rbcA[0]= 1.02319698e+01, rbcA[1]= 3.52082992e+00, rbcA[2]=-3.97899008e+00, rbcA[3]=-9.77381992e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 1.02319698e+01, rbcB[1]= 3.52082992e+00, rbcB[2]=-3.97899008e+00, rbcB[3]=-9.77381992e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[167]=RBDIHS, rbcA[0]= 5.49777985e+00, rbcA[1]= 1.41838002e+00, rbcA[2]=-6.91615009e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 5.49777985e+00, rbcB[1]= 1.41838002e+00, rbcB[2]=-6.91615009e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[168]=RBDIHS, rbcA[0]=-1.21755004e+00, rbcA[1]=-3.65264010e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-1.21755004e+00, rbcB[1]=-3.65264010e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[169]=RBDIHS, rbcA[0]=-1.26775002e+00, rbcA[1]= 3.02084994e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49781990e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-1.26775002e+00, rbcB[1]= 3.02084994e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49781990e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[170]=RBDIHS, rbcA[0]= 3.80117011e+00, rbcA[1]=-6.95172024e+00, rbcA[2]=-1.01671004e+00, rbcA[3]= 4.16726017e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 3.80117011e+00, rbcB[1]=-6.95172024e+00, rbcB[2]=-1.01671004e+00, rbcB[3]= 4.16726017e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[171]=RBDIHS, rbcA[0]= 3.70279998e-01, rbcA[1]= 1.11085999e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 3.70279998e-01, rbcB[1]= 1.11085999e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[172]=RBDIHS, rbcA[0]= 3.32042198e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042198e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 3.32042198e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042198e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[173]=RBDIHS, rbcA[0]= 1.63176003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 1.63176003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[174]=RBDIHS, rbcA[0]= 3.40787005e+00, rbcA[1]=-2.80537009e+00, rbcA[2]=-3.59820008e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 3.40787005e+00, rbcB[1]=-2.80537009e+00, rbcB[2]=-3.59820008e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[175]=RBDIHS, rbcA[0]=-1.62590199e+01, rbcA[1]= 9.08765030e+00, rbcA[2]= 7.17138004e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-1.62590199e+01, rbcB[1]= 9.08765030e+00, rbcB[2]= 7.17138004e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[176]=RBDIHS, rbcA[0]= 9.45590019e-01, rbcA[1]= 2.83675003e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 9.45590019e-01, rbcB[1]= 2.83675003e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[177]=RBDIHS, rbcA[0]=-1.50624001e+00, rbcA[1]= 5.37225008e+00, rbcA[2]= 1.17989004e+00, rbcA[3]=-5.04589987e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-1.50624001e+00, rbcB[1]= 5.37225008e+00, rbcB[2]= 1.17989004e+00, rbcB[3]=-5.04589987e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[178]=RBDIHS, rbcA[0]= 1.00416005e+00, rbcA[1]= 3.01248002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664019e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 1.00416005e+00, rbcB[1]= 3.01248002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664019e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[179]=RBDIHS, rbcA[0]= 8.79267979e+00, rbcA[1]=-1.18344402e+01, rbcA[2]= 1.07528996e+00, rbcA[3]= 1.96648002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 8.79267979e+00, rbcB[1]=-1.18344402e+01, rbcB[2]= 1.07528996e+00, rbcB[3]= 1.96648002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[180]=RBDIHS, rbcA[0]=-5.77392006e+00, rbcA[1]= 3.38485003e+00, rbcA[2]= 2.38906002e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-5.77392006e+00, rbcB[1]= 3.38485003e+00, rbcB[2]= 2.38906002e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[181]=RBDIHS, rbcA[0]=-9.08345985e+00, rbcA[1]= 9.75708961e+00, rbcA[2]= 3.45180011e+00, rbcA[3]=-4.12542009e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-9.08345985e+00, rbcB[1]= 9.75708961e+00, rbcB[2]= 3.45180011e+00, rbcB[3]=-4.12542009e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[182]=RBDIHS, rbcA[0]=-4.70699996e-01, rbcA[1]=-1.41209996e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88279998e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-4.70699996e-01, rbcB[1]=-1.41209996e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88279998e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[183]=RBDIHS, rbcA[0]= 3.43088007e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088007e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 3.43088007e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088007e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[184]=RBDIHS, rbcA[0]= 2.57315993e+00, rbcA[1]= 3.49781990e+00, rbcA[2]=-1.10038996e+00, rbcA[3]=-4.97059011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 2.57315993e+00, rbcB[1]= 3.49781990e+00, rbcB[2]=-1.10038996e+00, rbcB[3]=-4.97059011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[185]=RBDIHS, rbcA[0]=-8.22160006e-01, rbcA[1]= 1.12758994e+00, rbcA[2]=-3.05440009e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-8.22160006e-01, rbcB[1]= 1.12758994e+00, rbcB[2]=-3.05440009e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[186]=LJ14, c6A= 3.20536114e-04, c12A= 1.71928207e-07, c6B= 3.20536114e-04, c12B= 1.71928207e-07 58: functype[187]=LJ14, c6A= 1.30458479e-03, c12A= 1.92011203e-06, c6B= 1.30458479e-03, c12B= 1.92011203e-06 58: functype[188]=LJ14, c6A= 1.40760513e-03, c12A= 1.25315830e-06, c6B= 1.40760513e-03, c12B= 1.25315830e-06 58: functype[189]=LJ14, c6A= 1.67637295e-03, c12A= 1.97547138e-06, c6B= 1.67637295e-03, c12B= 1.97547138e-06 58: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00 58: functype[191]=LJ14, c6A= 2.49447097e-04, c12A= 1.67110088e-07, c6B= 2.49447097e-04, c12B= 1.67110088e-07 58: functype[192]=LJ14, c6A= 1.01525197e-03, c12A= 1.86630257e-06, c6B= 1.01525197e-03, c12B= 1.86630257e-06 58: functype[193]=LJ14, c6A= 6.12890653e-05, c12A= 1.49631507e-08, c6B= 6.12890653e-05, c12B= 1.49631507e-08 58: functype[194]=LJ14, c6A= 2.69145414e-04, c12A= 1.09064160e-07, c6B= 2.69145414e-04, c12B= 1.09064160e-07 58: functype[195]=LJ14, c6A= 1.09542510e-03, c12A= 1.21804135e-06, c6B= 1.09542510e-03, c12B= 1.21804135e-06 58: functype[196]=LJ14, c6A= 3.86982108e-04, c12A= 3.18863499e-07, c6B= 3.86982108e-04, c12B= 3.18863499e-07 58: functype[197]=LJ14, c6A= 1.57502061e-03, c12A= 3.56110013e-06, c6B= 1.57502061e-03, c12B= 3.56110013e-06 58: functype[198]=LJ14, c6A= 2.44342256e-03, c12A= 6.79494860e-06, c6B= 2.44342256e-03, c12B= 6.79494860e-06 58: functype[199]=LJ14, c6A= 1.40194211e-03, c12A= 2.15310411e-06, c6B= 1.40194211e-03, c12B= 2.15310411e-06 58: functype[200]=LJ14, c6A= 1.09101785e-03, c12A= 2.09276800e-06, c6B= 1.09101785e-03, c12B= 2.09276800e-06 58: functype[201]=LJ14, c6A= 2.68062693e-04, c12A= 1.87387855e-07, c6B= 2.68062693e-04, c12B= 1.87387855e-07 58: functype[202]=LJ14, c6A= 2.26258271e-04, c12A= 1.37484790e-07, c6B= 2.26258271e-04, c12B= 1.37484790e-07 58: functype[203]=LJ14, c6A= 2.43143426e-04, c12A= 1.54167822e-07, c6B= 2.43143426e-04, c12B= 1.54167822e-07 58: functype[204]=LJ14, c6A= 1.17243768e-03, c12A= 2.34671188e-06, c6B= 1.17243768e-03, c12B= 2.34671188e-06 58: functype[205]=LJ14, c6A= 1.69256027e-03, c12A= 3.99321743e-06, c6B= 1.69256027e-03, c12B= 3.99321743e-06 58: functype[206]=LJ14, c6A= 5.04237469e-05, c12A= 1.01280841e-08, c6B= 5.04237469e-05, c12B= 1.01280841e-08 58: functype[207]=LJ14, c6A= 2.34763342e-04, c12A= 1.14652082e-07, c6B= 2.34763342e-04, c12B= 1.14652082e-07 58: functype[208]=LJ14, c6A= 5.76812672e-05, c12A= 1.02660236e-08, c6B= 5.76812672e-05, c12B= 1.02660236e-08 58: functype[209]=LJ14, c6A= 3.60245234e-03, c12A= 5.76973571e-06, c6B= 3.60245234e-03, c12B= 5.76973571e-06 58: functype[210]=LJ14, c6A= 6.88817876e-04, c12A= 5.02148339e-07, c6B= 6.88817876e-04, c12B= 5.02148339e-07 58: functype[211]=LJ14, c6A= 4.34922846e-03, c12A= 1.07007354e-05, c6B= 4.34922846e-03, c12B= 1.07007354e-05 58: reppow = 12 58: fudgeQQ = 0.5 58: cmap 58: moltype (0): 58: name="Protein_chain_B" 58: atoms: 58: atom (156): 58: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 58: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 58: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 58: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 58: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6} 58: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 58: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 58: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 58: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 58: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 58: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 58: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 58: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 58: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 58: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 58: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6} 58: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 58: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 58: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 58: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 58: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 58: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 58: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6} 58: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8} 58: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7} 58: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1} 58: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6} 58: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 58: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6} 58: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 58: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 58: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 58: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 58: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 58: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 58: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 58: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 58: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 58: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6} 58: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8} 58: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7} 58: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1} 58: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6} 58: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 58: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6} 58: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 58: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 58: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 58: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 58: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 58: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 58: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 58: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 58: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 58: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 58: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 58: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 58: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 58: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6} 58: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8} 58: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7} 58: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1} 58: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6} 58: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 58: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 58: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6} 58: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8} 58: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7} 58: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1} 58: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6} 58: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 58: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6} 58: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 58: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 58: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6} 58: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 58: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 58: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6} 58: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 58: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 58: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7} 58: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1} 58: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6} 58: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 58: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 58: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 58: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 58: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 58: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 58: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6} 58: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8} 58: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7} 58: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1} 58: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6} 58: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 58: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6} 58: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 58: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 58: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16} 58: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1} 58: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6} 58: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8} 58: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7} 58: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1} 58: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6} 58: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 58: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6} 58: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 58: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 58: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6} 58: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 58: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 58: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6} 58: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 58: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 58: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6} 58: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8} 58: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7} 58: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1} 58: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6} 58: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 58: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6} 58: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 58: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 58: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6} 58: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 58: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 58: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 58: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 58: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 58: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 58: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 58: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 58: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 58: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6} 58: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8} 58: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7} 58: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1} 58: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6} 58: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 58: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6} 58: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 58: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 58: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 58: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6} 58: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8} 58: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7} 58: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1} 58: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6} 58: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 58: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6} 58: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 58: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 58: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 58: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6} 58: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8} 58: atom (156): 58: atom[0]={name="N"} 58: atom[1]={name="H1"} 58: atom[2]={name="H2"} 58: atom[3]={name="H3"} 58: atom[4]={name="CA"} 58: atom[5]={name="HA"} 58: atom[6]={name="CB"} 58: atom[7]={name="HB1"} 58: atom[8]={name="HB2"} 58: atom[9]={name="CG"} 58: atom[10]={name="HG1"} 58: atom[11]={name="HG2"} 58: atom[12]={name="CD"} 58: atom[13]={name="HD1"} 58: atom[14]={name="HD2"} 58: atom[15]={name="CE"} 58: atom[16]={name="HE1"} 58: atom[17]={name="HE2"} 58: atom[18]={name="NZ"} 58: atom[19]={name="HZ1"} 58: atom[20]={name="HZ2"} 58: atom[21]={name="HZ3"} 58: atom[22]={name="C"} 58: atom[23]={name="O"} 58: atom[24]={name="N"} 58: atom[25]={name="H"} 58: atom[26]={name="CA"} 58: atom[27]={name="HA"} 58: atom[28]={name="CB"} 58: atom[29]={name="HB"} 58: atom[30]={name="CG1"} 58: atom[31]={name="HG11"} 58: atom[32]={name="HG12"} 58: atom[33]={name="HG13"} 58: atom[34]={name="CG2"} 58: atom[35]={name="HG21"} 58: atom[36]={name="HG22"} 58: atom[37]={name="HG23"} 58: atom[38]={name="C"} 58: atom[39]={name="O"} 58: atom[40]={name="N"} 58: atom[41]={name="H"} 58: atom[42]={name="CA"} 58: atom[43]={name="HA"} 58: atom[44]={name="CB"} 58: atom[45]={name="HB1"} 58: atom[46]={name="HB2"} 58: atom[47]={name="CG"} 58: atom[48]={name="CD1"} 58: atom[49]={name="HD1"} 58: atom[50]={name="CD2"} 58: atom[51]={name="HD2"} 58: atom[52]={name="CE1"} 58: atom[53]={name="HE1"} 58: atom[54]={name="CE2"} 58: atom[55]={name="HE2"} 58: atom[56]={name="CZ"} 58: atom[57]={name="HZ"} 58: atom[58]={name="C"} 58: atom[59]={name="O"} 58: atom[60]={name="N"} 58: atom[61]={name="H"} 58: atom[62]={name="CA"} 58: atom[63]={name="HA1"} 58: atom[64]={name="HA2"} 58: atom[65]={name="C"} 58: atom[66]={name="O"} 58: atom[67]={name="N"} 58: atom[68]={name="H"} 58: atom[69]={name="CA"} 58: atom[70]={name="HA"} 58: atom[71]={name="CB"} 58: atom[72]={name="HB1"} 58: atom[73]={name="HB2"} 58: atom[74]={name="CG"} 58: atom[75]={name="HG1"} 58: atom[76]={name="HG2"} 58: atom[77]={name="CD"} 58: atom[78]={name="HD1"} 58: atom[79]={name="HD2"} 58: atom[80]={name="NE"} 58: atom[81]={name="HE"} 58: atom[82]={name="CZ"} 58: atom[83]={name="NH1"} 58: atom[84]={name="HH11"} 58: atom[85]={name="HH12"} 58: atom[86]={name="NH2"} 58: atom[87]={name="HH21"} 58: atom[88]={name="HH22"} 58: atom[89]={name="C"} 58: atom[90]={name="O"} 58: atom[91]={name="N"} 58: atom[92]={name="H"} 58: atom[93]={name="CA"} 58: atom[94]={name="HA"} 58: atom[95]={name="CB"} 58: atom[96]={name="HB1"} 58: atom[97]={name="HB2"} 58: atom[98]={name="SG"} 58: atom[99]={name="HG"} 58: atom[100]={name="C"} 58: atom[101]={name="O"} 58: atom[102]={name="N"} 58: atom[103]={name="H"} 58: atom[104]={name="CA"} 58: atom[105]={name="HA"} 58: atom[106]={name="CB"} 58: atom[107]={name="HB1"} 58: atom[108]={name="HB2"} 58: atom[109]={name="CG"} 58: atom[110]={name="HG1"} 58: atom[111]={name="HG2"} 58: atom[112]={name="CD"} 58: atom[113]={name="OE1"} 58: atom[114]={name="OE2"} 58: atom[115]={name="C"} 58: atom[116]={name="O"} 58: atom[117]={name="N"} 58: atom[118]={name="H"} 58: atom[119]={name="CA"} 58: atom[120]={name="HA"} 58: atom[121]={name="CB"} 58: atom[122]={name="HB1"} 58: atom[123]={name="HB2"} 58: atom[124]={name="CG"} 58: atom[125]={name="HG"} 58: atom[126]={name="CD1"} 58: atom[127]={name="HD11"} 58: atom[128]={name="HD12"} 58: atom[129]={name="HD13"} 58: atom[130]={name="CD2"} 58: atom[131]={name="HD21"} 58: atom[132]={name="HD22"} 58: atom[133]={name="HD23"} 58: atom[134]={name="C"} 58: atom[135]={name="O"} 58: atom[136]={name="N"} 58: atom[137]={name="H"} 58: atom[138]={name="CA"} 58: atom[139]={name="HA"} 58: atom[140]={name="CB"} 58: atom[141]={name="HB1"} 58: atom[142]={name="HB2"} 58: atom[143]={name="HB3"} 58: atom[144]={name="C"} 58: atom[145]={name="O"} 58: atom[146]={name="N"} 58: atom[147]={name="H"} 58: atom[148]={name="CA"} 58: atom[149]={name="HA"} 58: atom[150]={name="CB"} 58: atom[151]={name="HB1"} 58: atom[152]={name="HB2"} 58: atom[153]={name="HB3"} 58: atom[154]={name="C"} 58: atom[155]={name="O"} 58: type (156): 58: type[0]={name="opls_287",nameB="opls_287"} 58: type[1]={name="opls_290",nameB="opls_290"} 58: type[2]={name="opls_290",nameB="opls_290"} 58: type[3]={name="opls_290",nameB="opls_290"} 58: type[4]={name="opls_293B",nameB="opls_293B"} 58: type[5]={name="opls_140",nameB="opls_140"} 58: type[6]={name="opls_136",nameB="opls_136"} 58: type[7]={name="opls_140",nameB="opls_140"} 58: type[8]={name="opls_140",nameB="opls_140"} 58: type[9]={name="opls_136",nameB="opls_136"} 58: type[10]={name="opls_140",nameB="opls_140"} 58: type[11]={name="opls_140",nameB="opls_140"} 58: type[12]={name="opls_136",nameB="opls_136"} 58: type[13]={name="opls_140",nameB="opls_140"} 58: type[14]={name="opls_140",nameB="opls_140"} 58: type[15]={name="opls_292",nameB="opls_292"} 58: type[16]={name="opls_140",nameB="opls_140"} 58: type[17]={name="opls_140",nameB="opls_140"} 58: type[18]={name="opls_287",nameB="opls_287"} 58: type[19]={name="opls_290",nameB="opls_290"} 58: type[20]={name="opls_290",nameB="opls_290"} 58: type[21]={name="opls_290",nameB="opls_290"} 58: type[22]={name="opls_235",nameB="opls_235"} 58: type[23]={name="opls_236",nameB="opls_236"} 58: type[24]={name="opls_238",nameB="opls_238"} 58: type[25]={name="opls_241",nameB="opls_241"} 58: type[26]={name="opls_224B",nameB="opls_224B"} 58: type[27]={name="opls_140",nameB="opls_140"} 58: type[28]={name="opls_137",nameB="opls_137"} 58: type[29]={name="opls_140",nameB="opls_140"} 58: type[30]={name="opls_135",nameB="opls_135"} 58: type[31]={name="opls_140",nameB="opls_140"} 58: type[32]={name="opls_140",nameB="opls_140"} 58: type[33]={name="opls_140",nameB="opls_140"} 58: type[34]={name="opls_135",nameB="opls_135"} 58: type[35]={name="opls_140",nameB="opls_140"} 58: type[36]={name="opls_140",nameB="opls_140"} 58: type[37]={name="opls_140",nameB="opls_140"} 58: type[38]={name="opls_235",nameB="opls_235"} 58: type[39]={name="opls_236",nameB="opls_236"} 58: type[40]={name="opls_238",nameB="opls_238"} 58: type[41]={name="opls_241",nameB="opls_241"} 58: type[42]={name="opls_224B",nameB="opls_224B"} 58: type[43]={name="opls_140",nameB="opls_140"} 58: type[44]={name="opls_149",nameB="opls_149"} 58: type[45]={name="opls_140",nameB="opls_140"} 58: type[46]={name="opls_140",nameB="opls_140"} 58: type[47]={name="opls_145",nameB="opls_145"} 58: type[48]={name="opls_145",nameB="opls_145"} 58: type[49]={name="opls_146",nameB="opls_146"} 58: type[50]={name="opls_145",nameB="opls_145"} 58: type[51]={name="opls_146",nameB="opls_146"} 58: type[52]={name="opls_145",nameB="opls_145"} 58: type[53]={name="opls_146",nameB="opls_146"} 58: type[54]={name="opls_145",nameB="opls_145"} 58: type[55]={name="opls_146",nameB="opls_146"} 58: type[56]={name="opls_145",nameB="opls_145"} 58: type[57]={name="opls_146",nameB="opls_146"} 58: type[58]={name="opls_235",nameB="opls_235"} 58: type[59]={name="opls_236",nameB="opls_236"} 58: type[60]={name="opls_238",nameB="opls_238"} 58: type[61]={name="opls_241",nameB="opls_241"} 58: type[62]={name="opls_223B",nameB="opls_223B"} 58: type[63]={name="opls_140",nameB="opls_140"} 58: type[64]={name="opls_140",nameB="opls_140"} 58: type[65]={name="opls_235",nameB="opls_235"} 58: type[66]={name="opls_236",nameB="opls_236"} 58: type[67]={name="opls_238",nameB="opls_238"} 58: type[68]={name="opls_241",nameB="opls_241"} 58: type[69]={name="opls_224B",nameB="opls_224B"} 58: type[70]={name="opls_140",nameB="opls_140"} 58: type[71]={name="opls_136",nameB="opls_136"} 58: type[72]={name="opls_140",nameB="opls_140"} 58: type[73]={name="opls_140",nameB="opls_140"} 58: type[74]={name="opls_308",nameB="opls_308"} 58: type[75]={name="opls_140",nameB="opls_140"} 58: type[76]={name="opls_140",nameB="opls_140"} 58: type[77]={name="opls_307",nameB="opls_307"} 58: type[78]={name="opls_140",nameB="opls_140"} 58: type[79]={name="opls_140",nameB="opls_140"} 58: type[80]={name="opls_303",nameB="opls_303"} 58: type[81]={name="opls_304",nameB="opls_304"} 58: type[82]={name="opls_302",nameB="opls_302"} 58: type[83]={name="opls_300",nameB="opls_300"} 58: type[84]={name="opls_301",nameB="opls_301"} 58: type[85]={name="opls_301",nameB="opls_301"} 58: type[86]={name="opls_300",nameB="opls_300"} 58: type[87]={name="opls_301",nameB="opls_301"} 58: type[88]={name="opls_301",nameB="opls_301"} 58: type[89]={name="opls_235",nameB="opls_235"} 58: type[90]={name="opls_236",nameB="opls_236"} 58: type[91]={name="opls_238",nameB="opls_238"} 58: type[92]={name="opls_241",nameB="opls_241"} 58: type[93]={name="opls_224B",nameB="opls_224B"} 58: type[94]={name="opls_140",nameB="opls_140"} 58: type[95]={name="opls_206",nameB="opls_206"} 58: type[96]={name="opls_140",nameB="opls_140"} 58: type[97]={name="opls_140",nameB="opls_140"} 58: type[98]={name="opls_200",nameB="opls_200"} 58: type[99]={name="opls_204",nameB="opls_204"} 58: type[100]={name="opls_235",nameB="opls_235"} 58: type[101]={name="opls_236",nameB="opls_236"} 58: type[102]={name="opls_238",nameB="opls_238"} 58: type[103]={name="opls_241",nameB="opls_241"} 58: type[104]={name="opls_224B",nameB="opls_224B"} 58: type[105]={name="opls_140",nameB="opls_140"} 58: type[106]={name="opls_136",nameB="opls_136"} 58: type[107]={name="opls_140",nameB="opls_140"} 58: type[108]={name="opls_140",nameB="opls_140"} 58: type[109]={name="opls_274",nameB="opls_274"} 58: type[110]={name="opls_140",nameB="opls_140"} 58: type[111]={name="opls_140",nameB="opls_140"} 58: type[112]={name="opls_271",nameB="opls_271"} 58: type[113]={name="opls_272",nameB="opls_272"} 58: type[114]={name="opls_272",nameB="opls_272"} 58: type[115]={name="opls_235",nameB="opls_235"} 58: type[116]={name="opls_236",nameB="opls_236"} 58: type[117]={name="opls_238",nameB="opls_238"} 58: type[118]={name="opls_241",nameB="opls_241"} 58: type[119]={name="opls_224B",nameB="opls_224B"} 58: type[120]={name="opls_140",nameB="opls_140"} 58: type[121]={name="opls_136",nameB="opls_136"} 58: type[122]={name="opls_140",nameB="opls_140"} 58: type[123]={name="opls_140",nameB="opls_140"} 58: type[124]={name="opls_137",nameB="opls_137"} 58: type[125]={name="opls_140",nameB="opls_140"} 58: type[126]={name="opls_135",nameB="opls_135"} 58: type[127]={name="opls_140",nameB="opls_140"} 58: type[128]={name="opls_140",nameB="opls_140"} 58: type[129]={name="opls_140",nameB="opls_140"} 58: type[130]={name="opls_135",nameB="opls_135"} 58: type[131]={name="opls_140",nameB="opls_140"} 58: type[132]={name="opls_140",nameB="opls_140"} 58: type[133]={name="opls_140",nameB="opls_140"} 58: type[134]={name="opls_235",nameB="opls_235"} 58: type[135]={name="opls_236",nameB="opls_236"} 58: type[136]={name="opls_238",nameB="opls_238"} 58: type[137]={name="opls_241",nameB="opls_241"} 58: type[138]={name="opls_224B",nameB="opls_224B"} 58: type[139]={name="opls_140",nameB="opls_140"} 58: type[140]={name="opls_135",nameB="opls_135"} 58: type[141]={name="opls_140",nameB="opls_140"} 58: type[142]={name="opls_140",nameB="opls_140"} 58: type[143]={name="opls_140",nameB="opls_140"} 58: type[144]={name="opls_235",nameB="opls_235"} 58: type[145]={name="opls_236",nameB="opls_236"} 58: type[146]={name="opls_238",nameB="opls_238"} 58: type[147]={name="opls_241",nameB="opls_241"} 58: type[148]={name="opls_224B",nameB="opls_224B"} 58: type[149]={name="opls_140",nameB="opls_140"} 58: type[150]={name="opls_135",nameB="opls_135"} 58: type[151]={name="opls_140",nameB="opls_140"} 58: type[152]={name="opls_140",nameB="opls_140"} 58: type[153]={name="opls_140",nameB="opls_140"} 58: type[154]={name="opls_235",nameB="opls_235"} 58: type[155]={name="opls_236",nameB="opls_236"} 58: residue (10): 58: residue[0]={name="LYS", nr=1, ic=' '} 58: residue[1]={name="VAL", nr=2, ic=' '} 58: residue[2]={name="PHE", nr=3, ic=' '} 58: residue[3]={name="GLY", nr=4, ic=' '} 58: residue[4]={name="ARG", nr=5, ic=' '} 58: residue[5]={name="CYS", nr=6, ic=' '} 58: residue[6]={name="GLU", nr=7, ic=' '} 58: residue[7]={name="LEU", nr=8, ic=' '} 58: residue[8]={name="ALA", nr=9, ic=' '} 58: residue[9]={name="ALA", nr=10, ic=' '} 58: excls: 58: numLists=156 58: numElements=1828 58: excls[0][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 58: excls[1][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 58: excls[2][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 58: excls[3][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 58: excls[4][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 58: 23, 24, 25, 26} 58: excls[5][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 58: excls[6][num=19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 58: 14, 15, 22, 23, 24} 58: excls[7][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 58: excls[8][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 58: excls[9][num=17]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 58: 16, 17, 18, 22} 58: excls[10][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 58: excls[11][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 58: excls[12][num=17]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 58: 17, 18, 19, 20, 21} 58: excls[13][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 58: excls[14][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 58: excls[15][num=14]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 58: 20, 21} 58: excls[16][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 58: excls[17][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 58: excls[18][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 58: excls[19][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 58: excls[20][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 58: excls[21][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 58: excls[22][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 58: 26, 27, 28, 38} 58: excls[23][num=9]={0, 4, 5, 6, 22, 23, 24, 25, 26} 58: excls[24][num=17]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 58: 30, 34, 38, 39, 40} 58: excls[25][num=9]={4, 22, 23, 24, 25, 26, 27, 28, 38} 58: excls[26][num=22]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 58: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42} 58: excls[27][num=12]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 58: 40} 58: excls[28][num=18]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 58: 34, 35, 36, 37, 38, 39, 40} 58: excls[29][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 58: 36, 37, 38} 58: excls[30][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 58: 36, 37, 38} 58: excls[31][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 58: excls[32][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 58: excls[33][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 58: excls[34][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 58: 36, 37, 38} 58: excls[35][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 58: excls[36][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 58: excls[37][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 58: excls[38][num=17]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 58: 40, 41, 42, 43, 44, 58} 58: excls[39][num=9]={24, 26, 27, 28, 38, 39, 40, 41, 42} 58: excls[40][num=17]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 58: 45, 46, 47, 58, 59, 60} 58: excls[41][num=9]={26, 38, 39, 40, 41, 42, 43, 44, 58} 58: excls[42][num=18]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 58: 48, 50, 58, 59, 60, 61, 62} 58: excls[43][num=12]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 58: 60} 58: excls[44][num=18]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 58: 50, 51, 52, 54, 58, 59, 60} 58: excls[45][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 58: excls[46][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 58: excls[47][num=17]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 58: 52, 53, 54, 55, 56, 58} 58: excls[48][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 58: 54, 56, 57} 58: excls[49][num=8]={44, 47, 48, 49, 50, 52, 53, 56} 58: excls[50][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 58: 55, 56, 57} 58: excls[51][num=8]={44, 47, 48, 50, 51, 54, 55, 56} 58: excls[52][num=11]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57} 58: excls[53][num=8]={47, 48, 49, 52, 53, 54, 56, 57} 58: excls[54][num=11]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57} 58: excls[55][num=8]={47, 50, 51, 52, 54, 55, 56, 57} 58: excls[56][num=11]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57} 58: excls[57][num=8]={48, 50, 52, 53, 54, 55, 56, 57} 58: excls[58][num=17]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 58: 60, 61, 62, 63, 64, 65} 58: excls[59][num=9]={40, 42, 43, 44, 58, 59, 60, 61, 62} 58: excls[60][num=14]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64, 58: 65, 66, 67} 58: excls[61][num=9]={42, 58, 59, 60, 61, 62, 63, 64, 65} 58: excls[62][num=13]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 58: 68, 69} 58: excls[63][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 58: excls[64][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 58: excls[65][num=14]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 58: 70, 71, 89} 58: excls[66][num=9]={60, 62, 63, 64, 65, 66, 67, 68, 69} 58: excls[67][num=17]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 58: 72, 73, 74, 89, 90, 91} 58: excls[68][num=9]={62, 65, 66, 67, 68, 69, 70, 71, 89} 58: excls[69][num=19]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 58: 75, 76, 77, 89, 90, 91, 92, 93} 58: excls[70][num=12]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 58: 91} 58: excls[71][num=18]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 58: 77, 78, 79, 80, 89, 90, 91} 58: excls[72][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 58: excls[73][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 58: excls[74][num=16]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 58: 79, 80, 81, 82, 89} 58: excls[75][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 58: excls[76][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 58: excls[77][num=15]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 58: 81, 82, 83, 86} 58: excls[78][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 58: excls[79][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 58: excls[80][num=16]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 58: 84, 85, 86, 87, 88} 58: excls[81][num=9]={74, 77, 78, 79, 80, 81, 82, 83, 86} 58: excls[82][num=13]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 58: 87, 88} 58: excls[83][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 58: excls[84][num=6]={80, 82, 83, 84, 85, 86} 58: excls[85][num=6]={80, 82, 83, 84, 85, 86} 58: excls[86][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 58: excls[87][num=6]={80, 82, 83, 86, 87, 88} 58: excls[88][num=6]={80, 82, 83, 86, 87, 88} 58: excls[89][num=17]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 58: 91, 92, 93, 94, 95, 100} 58: excls[90][num=9]={67, 69, 70, 71, 89, 90, 91, 92, 93} 58: excls[91][num=17]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94, 95, 58: 96, 97, 98, 100, 101, 102} 58: excls[92][num=9]={69, 89, 90, 91, 92, 93, 94, 95, 100} 58: excls[93][num=17]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 58: 99, 100, 101, 102, 103, 104} 58: excls[94][num=12]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 58: 102} 58: excls[95][num=13]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 58: 101, 102} 58: excls[96][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 58: excls[97][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 58: excls[98][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 58: excls[99][num=6]={93, 95, 96, 97, 98, 99} 58: excls[100][num=17]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 58: 102, 103, 104, 105, 106, 115} 58: excls[101][num=9]={91, 93, 94, 95, 100, 101, 102, 103, 104} 58: excls[102][num=17]={91, 93, 94, 95, 100, 101, 102, 103, 104, 105, 58: 106, 107, 108, 109, 115, 116, 117} 58: excls[103][num=9]={93, 100, 101, 102, 103, 104, 105, 106, 115} 58: excls[104][num=19]={93, 100, 101, 102, 103, 104, 105, 106, 107, 58: 108, 109, 110, 111, 112, 115, 116, 117, 118, 119} 58: excls[105][num=12]={100, 102, 103, 104, 105, 106, 107, 108, 109, 58: 115, 116, 117} 58: excls[106][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 58: 110, 111, 112, 113, 114, 115, 116, 117} 58: excls[107][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 58: 112, 115} 58: excls[108][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 58: 112, 115} 58: excls[109][num=13]={102, 104, 105, 106, 107, 108, 109, 110, 111, 58: 112, 113, 114, 115} 58: excls[110][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 58: 114} 58: excls[111][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 58: 114} 58: excls[112][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 58: 114} 58: excls[113][num=7]={106, 109, 110, 111, 112, 113, 114} 58: excls[114][num=7]={106, 109, 110, 111, 112, 113, 114} 58: excls[115][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 58: 115, 116, 117, 118, 119, 120, 121, 134} 58: excls[116][num=9]={102, 104, 105, 106, 115, 116, 117, 118, 119} 58: excls[117][num=17]={102, 104, 105, 106, 115, 116, 117, 118, 119, 58: 120, 121, 122, 123, 124, 134, 135, 136} 58: excls[118][num=9]={104, 115, 116, 117, 118, 119, 120, 121, 134} 58: excls[119][num=19]={104, 115, 116, 117, 118, 119, 120, 121, 122, 58: 123, 124, 125, 126, 130, 134, 135, 136, 137, 138} 58: excls[120][num=12]={115, 117, 118, 119, 120, 121, 122, 123, 124, 58: 134, 135, 136} 58: excls[121][num=21]={115, 117, 118, 119, 120, 121, 122, 123, 124, 58: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136} 58: excls[122][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 58: 130, 134} 58: excls[123][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 58: 130, 134} 58: excls[124][num=17]={117, 119, 120, 121, 122, 123, 124, 125, 126, 58: 127, 128, 129, 130, 131, 132, 133, 134} 58: excls[125][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 58: 129, 130, 131, 132, 133} 58: excls[126][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 58: 129, 130, 131, 132, 133} 58: excls[127][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 58: excls[128][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 58: excls[129][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 58: excls[130][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 58: 129, 130, 131, 132, 133} 58: excls[131][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 58: excls[132][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 58: excls[133][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 58: excls[134][num=17]={115, 117, 118, 119, 120, 121, 122, 123, 124, 58: 134, 135, 136, 137, 138, 139, 140, 144} 58: excls[135][num=9]={117, 119, 120, 121, 134, 135, 136, 137, 138} 58: excls[136][num=17]={117, 119, 120, 121, 134, 135, 136, 137, 138, 58: 139, 140, 141, 142, 143, 144, 145, 146} 58: excls[137][num=9]={119, 134, 135, 136, 137, 138, 139, 140, 144} 58: excls[138][num=16]={119, 134, 135, 136, 137, 138, 139, 140, 141, 58: 142, 143, 144, 145, 146, 147, 148} 58: excls[139][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 58: 144, 145, 146} 58: excls[140][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 58: 144, 145, 146} 58: excls[141][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 58: excls[142][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 58: excls[143][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 58: excls[144][num=17]={134, 136, 137, 138, 139, 140, 141, 142, 143, 58: 144, 145, 146, 147, 148, 149, 150, 154} 58: excls[145][num=9]={136, 138, 139, 140, 144, 145, 146, 147, 148} 58: excls[146][num=16]={136, 138, 139, 140, 144, 145, 146, 147, 148, 58: 149, 150, 151, 152, 153, 154, 155} 58: excls[147][num=9]={138, 144, 145, 146, 147, 148, 149, 150, 154} 58: excls[148][num=13]={138, 144, 145, 146, 147, 148, 149, 150, 151, 58: 152, 153, 154, 155} 58: excls[149][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 58: 154, 155} 58: excls[150][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 58: 154, 155} 58: excls[151][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 58: excls[152][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 58: excls[153][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 58: excls[154][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 58: 154, 155} 58: excls[155][num=6]={146, 148, 149, 150, 154, 155} 58: Bond: 58: nr: 468 58: iatoms: 58: 0 type=100 (BONDS) 0 1 58: 1 type=100 (BONDS) 0 2 58: 2 type=100 (BONDS) 0 3 58: 3 type=101 (BONDS) 0 4 58: 4 type=102 (BONDS) 4 5 58: 5 type=103 (BONDS) 4 6 58: 6 type=104 (BONDS) 4 22 58: 7 type=102 (BONDS) 6 7 58: 8 type=102 (BONDS) 6 8 58: 9 type=103 (BONDS) 6 9 58: 10 type=102 (BONDS) 9 10 58: 11 type=102 (BONDS) 9 11 58: 12 type=103 (BONDS) 9 12 58: 13 type=102 (BONDS) 12 13 58: 14 type=102 (BONDS) 12 14 58: 15 type=103 (BONDS) 12 15 58: 16 type=102 (BONDS) 15 16 58: 17 type=102 (BONDS) 15 17 58: 18 type=101 (BONDS) 15 18 58: 19 type=100 (BONDS) 18 19 58: 20 type=100 (BONDS) 18 20 58: 21 type=100 (BONDS) 18 21 58: 22 type=105 (BONDS) 22 23 58: 23 type=106 (BONDS) 22 24 58: 24 type=100 (BONDS) 24 25 58: 25 type=107 (BONDS) 24 26 58: 26 type=102 (BONDS) 26 27 58: 27 type=103 (BONDS) 26 28 58: 28 type=104 (BONDS) 26 38 58: 29 type=102 (BONDS) 28 29 58: 30 type=103 (BONDS) 28 30 58: 31 type=103 (BONDS) 28 34 58: 32 type=102 (BONDS) 30 31 58: 33 type=102 (BONDS) 30 32 58: 34 type=102 (BONDS) 30 33 58: 35 type=102 (BONDS) 34 35 58: 36 type=102 (BONDS) 34 36 58: 37 type=102 (BONDS) 34 37 58: 38 type=105 (BONDS) 38 39 58: 39 type=106 (BONDS) 38 40 58: 40 type=100 (BONDS) 40 41 58: 41 type=107 (BONDS) 40 42 58: 42 type=102 (BONDS) 42 43 58: 43 type=103 (BONDS) 42 44 58: 44 type=104 (BONDS) 42 58 58: 45 type=102 (BONDS) 44 45 58: 46 type=102 (BONDS) 44 46 58: 47 type=108 (BONDS) 44 47 58: 48 type=109 (BONDS) 47 48 58: 49 type=109 (BONDS) 47 50 58: 50 type=110 (BONDS) 48 49 58: 51 type=109 (BONDS) 48 52 58: 52 type=110 (BONDS) 50 51 58: 53 type=109 (BONDS) 50 54 58: 54 type=110 (BONDS) 52 53 58: 55 type=109 (BONDS) 52 56 58: 56 type=110 (BONDS) 54 55 58: 57 type=109 (BONDS) 54 56 58: 58 type=110 (BONDS) 56 57 58: 59 type=105 (BONDS) 58 59 58: 60 type=106 (BONDS) 58 60 58: 61 type=100 (BONDS) 60 61 58: 62 type=107 (BONDS) 60 62 58: 63 type=102 (BONDS) 62 63 58: 64 type=102 (BONDS) 62 64 58: 65 type=104 (BONDS) 62 65 58: 66 type=105 (BONDS) 65 66 58: 67 type=106 (BONDS) 65 67 58: 68 type=100 (BONDS) 67 68 58: 69 type=107 (BONDS) 67 69 58: 70 type=102 (BONDS) 69 70 58: 71 type=103 (BONDS) 69 71 58: 72 type=104 (BONDS) 69 89 58: 73 type=102 (BONDS) 71 72 58: 74 type=102 (BONDS) 71 73 58: 75 type=103 (BONDS) 71 74 58: 76 type=102 (BONDS) 74 75 58: 77 type=102 (BONDS) 74 76 58: 78 type=103 (BONDS) 74 77 58: 79 type=102 (BONDS) 77 78 58: 80 type=102 (BONDS) 77 79 58: 81 type=111 (BONDS) 77 80 58: 82 type=100 (BONDS) 80 81 58: 83 type=112 (BONDS) 80 82 58: 84 type=112 (BONDS) 82 83 58: 85 type=112 (BONDS) 82 86 58: 86 type=100 (BONDS) 83 84 58: 87 type=100 (BONDS) 83 85 58: 88 type=100 (BONDS) 86 87 58: 89 type=100 (BONDS) 86 88 58: 90 type=105 (BONDS) 89 90 58: 91 type=106 (BONDS) 89 91 58: 92 type=100 (BONDS) 91 92 58: 93 type=107 (BONDS) 91 93 58: 94 type=102 (BONDS) 93 94 58: 95 type=103 (BONDS) 93 95 58: 96 type=104 (BONDS) 93 100 58: 97 type=102 (BONDS) 95 96 58: 98 type=102 (BONDS) 95 97 58: 99 type=113 (BONDS) 95 98 58: 100 type=114 (BONDS) 98 99 58: 101 type=105 (BONDS) 100 101 58: 102 type=106 (BONDS) 100 102 58: 103 type=100 (BONDS) 102 103 58: 104 type=107 (BONDS) 102 104 58: 105 type=102 (BONDS) 104 105 58: 106 type=103 (BONDS) 104 106 58: 107 type=104 (BONDS) 104 115 58: 108 type=102 (BONDS) 106 107 58: 109 type=102 (BONDS) 106 108 58: 110 type=103 (BONDS) 106 109 58: 111 type=102 (BONDS) 109 110 58: 112 type=102 (BONDS) 109 111 58: 113 type=104 (BONDS) 109 112 58: 114 type=115 (BONDS) 112 113 58: 115 type=115 (BONDS) 112 114 58: 116 type=105 (BONDS) 115 116 58: 117 type=106 (BONDS) 115 117 58: 118 type=100 (BONDS) 117 118 58: 119 type=107 (BONDS) 117 119 58: 120 type=102 (BONDS) 119 120 58: 121 type=103 (BONDS) 119 121 58: 122 type=104 (BONDS) 119 134 58: 123 type=102 (BONDS) 121 122 58: 124 type=102 (BONDS) 121 123 58: 125 type=103 (BONDS) 121 124 58: 126 type=102 (BONDS) 124 125 58: 127 type=103 (BONDS) 124 126 58: 128 type=103 (BONDS) 124 130 58: 129 type=102 (BONDS) 126 127 58: 130 type=102 (BONDS) 126 128 58: 131 type=102 (BONDS) 126 129 58: 132 type=102 (BONDS) 130 131 58: 133 type=102 (BONDS) 130 132 58: 134 type=102 (BONDS) 130 133 58: 135 type=105 (BONDS) 134 135 58: 136 type=106 (BONDS) 134 136 58: 137 type=100 (BONDS) 136 137 58: 138 type=107 (BONDS) 136 138 58: 139 type=102 (BONDS) 138 139 58: 140 type=103 (BONDS) 138 140 58: 141 type=104 (BONDS) 138 144 58: 142 type=102 (BONDS) 140 141 58: 143 type=102 (BONDS) 140 142 58: 144 type=102 (BONDS) 140 143 58: 145 type=105 (BONDS) 144 145 58: 146 type=106 (BONDS) 144 146 58: 147 type=100 (BONDS) 146 147 58: 148 type=107 (BONDS) 146 148 58: 149 type=102 (BONDS) 148 149 58: 150 type=103 (BONDS) 148 150 58: 151 type=104 (BONDS) 148 154 58: 152 type=102 (BONDS) 150 151 58: 153 type=102 (BONDS) 150 152 58: 154 type=102 (BONDS) 150 153 58: 155 type=105 (BONDS) 154 155 58: G96Bond: 58: nr: 0 58: Morse: 58: nr: 0 58: Cubic Bonds: 58: nr: 0 58: Connect Bonds: 58: nr: 0 58: Harmonic Pot.: 58: nr: 0 58: FENE Bonds: 58: nr: 0 58: Tab. Bonds: 58: nr: 0 58: Tab. Bonds NC: 58: nr: 0 58: Restraint Pot.: 58: nr: 0 58: Angle: 58: nr: 1124 58: iatoms: 58: 0 type=116 (ANGLES) 1 0 2 58: 1 type=116 (ANGLES) 1 0 3 58: 2 type=116 (ANGLES) 1 0 4 58: 3 type=116 (ANGLES) 2 0 3 58: 4 type=116 (ANGLES) 2 0 4 58: 5 type=116 (ANGLES) 3 0 4 58: 6 type=116 (ANGLES) 0 4 5 58: 7 type=117 (ANGLES) 0 4 6 58: 8 type=117 (ANGLES) 0 4 22 58: 9 type=118 (ANGLES) 5 4 6 58: 10 type=116 (ANGLES) 5 4 22 58: 11 type=119 (ANGLES) 6 4 22 58: 12 type=118 (ANGLES) 4 6 7 58: 13 type=118 (ANGLES) 4 6 8 58: 14 type=120 (ANGLES) 4 6 9 58: 15 type=121 (ANGLES) 7 6 8 58: 16 type=118 (ANGLES) 7 6 9 58: 17 type=118 (ANGLES) 8 6 9 58: 18 type=118 (ANGLES) 6 9 10 58: 19 type=118 (ANGLES) 6 9 11 58: 20 type=120 (ANGLES) 6 9 12 58: 21 type=121 (ANGLES) 10 9 11 58: 22 type=118 (ANGLES) 10 9 12 58: 23 type=118 (ANGLES) 11 9 12 58: 24 type=118 (ANGLES) 9 12 13 58: 25 type=118 (ANGLES) 9 12 14 58: 26 type=120 (ANGLES) 9 12 15 58: 27 type=121 (ANGLES) 13 12 14 58: 28 type=118 (ANGLES) 13 12 15 58: 29 type=118 (ANGLES) 14 12 15 58: 30 type=118 (ANGLES) 12 15 16 58: 31 type=118 (ANGLES) 12 15 17 58: 32 type=117 (ANGLES) 12 15 18 58: 33 type=121 (ANGLES) 16 15 17 58: 34 type=116 (ANGLES) 16 15 18 58: 35 type=116 (ANGLES) 17 15 18 58: 36 type=116 (ANGLES) 15 18 19 58: 37 type=116 (ANGLES) 15 18 20 58: 38 type=116 (ANGLES) 15 18 21 58: 39 type=116 (ANGLES) 19 18 20 58: 40 type=116 (ANGLES) 19 18 21 58: 41 type=116 (ANGLES) 20 18 21 58: 42 type=122 (ANGLES) 4 22 23 58: 43 type=123 (ANGLES) 4 22 24 58: 44 type=124 (ANGLES) 23 22 24 58: 45 type=125 (ANGLES) 22 24 25 58: 46 type=126 (ANGLES) 22 24 26 58: 47 type=127 (ANGLES) 25 24 26 58: 48 type=116 (ANGLES) 24 26 27 58: 49 type=128 (ANGLES) 24 26 28 58: 50 type=129 (ANGLES) 24 26 38 58: 51 type=118 (ANGLES) 27 26 28 58: 52 type=116 (ANGLES) 27 26 38 58: 53 type=119 (ANGLES) 28 26 38 58: 54 type=118 (ANGLES) 26 28 29 58: 55 type=120 (ANGLES) 26 28 30 58: 56 type=120 (ANGLES) 26 28 34 58: 57 type=118 (ANGLES) 29 28 30 58: 58 type=118 (ANGLES) 29 28 34 58: 59 type=120 (ANGLES) 30 28 34 58: 60 type=118 (ANGLES) 28 30 31 58: 61 type=118 (ANGLES) 28 30 32 58: 62 type=118 (ANGLES) 28 30 33 58: 63 type=121 (ANGLES) 31 30 32 58: 64 type=121 (ANGLES) 31 30 33 58: 65 type=121 (ANGLES) 32 30 33 58: 66 type=118 (ANGLES) 28 34 35 58: 67 type=118 (ANGLES) 28 34 36 58: 68 type=118 (ANGLES) 28 34 37 58: 69 type=121 (ANGLES) 35 34 36 58: 70 type=121 (ANGLES) 35 34 37 58: 71 type=121 (ANGLES) 36 34 37 58: 72 type=122 (ANGLES) 26 38 39 58: 73 type=123 (ANGLES) 26 38 40 58: 74 type=124 (ANGLES) 39 38 40 58: 75 type=125 (ANGLES) 38 40 41 58: 76 type=126 (ANGLES) 38 40 42 58: 77 type=127 (ANGLES) 41 40 42 58: 78 type=116 (ANGLES) 40 42 43 58: 79 type=128 (ANGLES) 40 42 44 58: 80 type=129 (ANGLES) 40 42 58 58: 81 type=118 (ANGLES) 43 42 44 58: 82 type=116 (ANGLES) 43 42 58 58: 83 type=119 (ANGLES) 44 42 58 58: 84 type=118 (ANGLES) 42 44 45 58: 85 type=118 (ANGLES) 42 44 46 58: 86 type=130 (ANGLES) 42 44 47 58: 87 type=121 (ANGLES) 45 44 46 58: 88 type=116 (ANGLES) 45 44 47 58: 89 type=116 (ANGLES) 46 44 47 58: 90 type=131 (ANGLES) 44 47 48 58: 91 type=131 (ANGLES) 44 47 50 58: 92 type=132 (ANGLES) 48 47 50 58: 93 type=133 (ANGLES) 47 48 49 58: 94 type=132 (ANGLES) 47 48 52 58: 95 type=133 (ANGLES) 49 48 52 58: 96 type=133 (ANGLES) 47 50 51 58: 97 type=132 (ANGLES) 47 50 54 58: 98 type=133 (ANGLES) 51 50 54 58: 99 type=133 (ANGLES) 48 52 53 58: 100 type=132 (ANGLES) 48 52 56 58: 101 type=133 (ANGLES) 53 52 56 58: 102 type=133 (ANGLES) 50 54 55 58: 103 type=132 (ANGLES) 50 54 56 58: 104 type=133 (ANGLES) 55 54 56 58: 105 type=132 (ANGLES) 52 56 54 58: 106 type=133 (ANGLES) 52 56 57 58: 107 type=133 (ANGLES) 54 56 57 58: 108 type=122 (ANGLES) 42 58 59 58: 109 type=123 (ANGLES) 42 58 60 58: 110 type=124 (ANGLES) 59 58 60 58: 111 type=125 (ANGLES) 58 60 61 58: 112 type=126 (ANGLES) 58 60 62 58: 113 type=127 (ANGLES) 61 60 62 58: 114 type=116 (ANGLES) 60 62 63 58: 115 type=116 (ANGLES) 60 62 64 58: 116 type=129 (ANGLES) 60 62 65 58: 117 type=121 (ANGLES) 63 62 64 58: 118 type=116 (ANGLES) 63 62 65 58: 119 type=116 (ANGLES) 64 62 65 58: 120 type=122 (ANGLES) 62 65 66 58: 121 type=123 (ANGLES) 62 65 67 58: 122 type=124 (ANGLES) 66 65 67 58: 123 type=125 (ANGLES) 65 67 68 58: 124 type=126 (ANGLES) 65 67 69 58: 125 type=127 (ANGLES) 68 67 69 58: 126 type=116 (ANGLES) 67 69 70 58: 127 type=128 (ANGLES) 67 69 71 58: 128 type=129 (ANGLES) 67 69 89 58: 129 type=118 (ANGLES) 70 69 71 58: 130 type=116 (ANGLES) 70 69 89 58: 131 type=119 (ANGLES) 71 69 89 58: 132 type=118 (ANGLES) 69 71 72 58: 133 type=118 (ANGLES) 69 71 73 58: 134 type=120 (ANGLES) 69 71 74 58: 135 type=121 (ANGLES) 72 71 73 58: 136 type=118 (ANGLES) 72 71 74 58: 137 type=118 (ANGLES) 73 71 74 58: 138 type=118 (ANGLES) 71 74 75 58: 139 type=118 (ANGLES) 71 74 76 58: 140 type=120 (ANGLES) 71 74 77 58: 141 type=121 (ANGLES) 75 74 76 58: 142 type=118 (ANGLES) 75 74 77 58: 143 type=118 (ANGLES) 76 74 77 58: 144 type=118 (ANGLES) 74 77 78 58: 145 type=118 (ANGLES) 74 77 79 58: 146 type=117 (ANGLES) 74 77 80 58: 147 type=121 (ANGLES) 78 77 79 58: 148 type=116 (ANGLES) 78 77 80 58: 149 type=116 (ANGLES) 79 77 80 58: 150 type=134 (ANGLES) 77 80 81 58: 151 type=135 (ANGLES) 77 80 82 58: 152 type=133 (ANGLES) 81 80 82 58: 153 type=131 (ANGLES) 80 82 83 58: 154 type=131 (ANGLES) 80 82 86 58: 155 type=131 (ANGLES) 83 82 86 58: 156 type=133 (ANGLES) 82 83 84 58: 157 type=133 (ANGLES) 82 83 85 58: 158 type=133 (ANGLES) 84 83 85 58: 159 type=133 (ANGLES) 82 86 87 58: 160 type=133 (ANGLES) 82 86 88 58: 161 type=133 (ANGLES) 87 86 88 58: 162 type=122 (ANGLES) 69 89 90 58: 163 type=123 (ANGLES) 69 89 91 58: 164 type=124 (ANGLES) 90 89 91 58: 165 type=125 (ANGLES) 89 91 92 58: 166 type=126 (ANGLES) 89 91 93 58: 167 type=127 (ANGLES) 92 91 93 58: 168 type=116 (ANGLES) 91 93 94 58: 169 type=128 (ANGLES) 91 93 95 58: 170 type=129 (ANGLES) 91 93 100 58: 171 type=118 (ANGLES) 94 93 95 58: 172 type=116 (ANGLES) 94 93 100 58: 173 type=119 (ANGLES) 95 93 100 58: 174 type=118 (ANGLES) 93 95 96 58: 175 type=118 (ANGLES) 93 95 97 58: 176 type=136 (ANGLES) 93 95 98 58: 177 type=121 (ANGLES) 96 95 97 58: 178 type=116 (ANGLES) 96 95 98 58: 179 type=116 (ANGLES) 97 95 98 58: 180 type=137 (ANGLES) 95 98 99 58: 181 type=122 (ANGLES) 93 100 101 58: 182 type=123 (ANGLES) 93 100 102 58: 183 type=124 (ANGLES) 101 100 102 58: 184 type=125 (ANGLES) 100 102 103 58: 185 type=126 (ANGLES) 100 102 104 58: 186 type=127 (ANGLES) 103 102 104 58: 187 type=116 (ANGLES) 102 104 105 58: 188 type=128 (ANGLES) 102 104 106 58: 189 type=129 (ANGLES) 102 104 115 58: 190 type=118 (ANGLES) 105 104 106 58: 191 type=116 (ANGLES) 105 104 115 58: 192 type=119 (ANGLES) 106 104 115 58: 193 type=118 (ANGLES) 104 106 107 58: 194 type=118 (ANGLES) 104 106 108 58: 195 type=120 (ANGLES) 104 106 109 58: 196 type=121 (ANGLES) 107 106 108 58: 197 type=118 (ANGLES) 107 106 109 58: 198 type=118 (ANGLES) 108 106 109 58: 199 type=118 (ANGLES) 106 109 110 58: 200 type=118 (ANGLES) 106 109 111 58: 201 type=119 (ANGLES) 106 109 112 58: 202 type=121 (ANGLES) 110 109 111 58: 203 type=116 (ANGLES) 110 109 112 58: 204 type=116 (ANGLES) 111 109 112 58: 205 type=138 (ANGLES) 109 112 113 58: 206 type=138 (ANGLES) 109 112 114 58: 207 type=139 (ANGLES) 113 112 114 58: 208 type=122 (ANGLES) 104 115 116 58: 209 type=123 (ANGLES) 104 115 117 58: 210 type=124 (ANGLES) 116 115 117 58: 211 type=125 (ANGLES) 115 117 118 58: 212 type=126 (ANGLES) 115 117 119 58: 213 type=127 (ANGLES) 118 117 119 58: 214 type=116 (ANGLES) 117 119 120 58: 215 type=128 (ANGLES) 117 119 121 58: 216 type=129 (ANGLES) 117 119 134 58: 217 type=118 (ANGLES) 120 119 121 58: 218 type=116 (ANGLES) 120 119 134 58: 219 type=119 (ANGLES) 121 119 134 58: 220 type=118 (ANGLES) 119 121 122 58: 221 type=118 (ANGLES) 119 121 123 58: 222 type=120 (ANGLES) 119 121 124 58: 223 type=121 (ANGLES) 122 121 123 58: 224 type=118 (ANGLES) 122 121 124 58: 225 type=118 (ANGLES) 123 121 124 58: 226 type=118 (ANGLES) 121 124 125 58: 227 type=120 (ANGLES) 121 124 126 58: 228 type=120 (ANGLES) 121 124 130 58: 229 type=118 (ANGLES) 125 124 126 58: 230 type=118 (ANGLES) 125 124 130 58: 231 type=120 (ANGLES) 126 124 130 58: 232 type=118 (ANGLES) 124 126 127 58: 233 type=118 (ANGLES) 124 126 128 58: 234 type=118 (ANGLES) 124 126 129 58: 235 type=121 (ANGLES) 127 126 128 58: 236 type=121 (ANGLES) 127 126 129 58: 237 type=121 (ANGLES) 128 126 129 58: 238 type=118 (ANGLES) 124 130 131 58: 239 type=118 (ANGLES) 124 130 132 58: 240 type=118 (ANGLES) 124 130 133 58: 241 type=121 (ANGLES) 131 130 132 58: 242 type=121 (ANGLES) 131 130 133 58: 243 type=121 (ANGLES) 132 130 133 58: 244 type=122 (ANGLES) 119 134 135 58: 245 type=123 (ANGLES) 119 134 136 58: 246 type=124 (ANGLES) 135 134 136 58: 247 type=125 (ANGLES) 134 136 137 58: 248 type=126 (ANGLES) 134 136 138 58: 249 type=127 (ANGLES) 137 136 138 58: 250 type=116 (ANGLES) 136 138 139 58: 251 type=128 (ANGLES) 136 138 140 58: 252 type=129 (ANGLES) 136 138 144 58: 253 type=118 (ANGLES) 139 138 140 58: 254 type=116 (ANGLES) 139 138 144 58: 255 type=119 (ANGLES) 140 138 144 58: 256 type=118 (ANGLES) 138 140 141 58: 257 type=118 (ANGLES) 138 140 142 58: 258 type=118 (ANGLES) 138 140 143 58: 259 type=121 (ANGLES) 141 140 142 58: 260 type=121 (ANGLES) 141 140 143 58: 261 type=121 (ANGLES) 142 140 143 58: 262 type=122 (ANGLES) 138 144 145 58: 263 type=123 (ANGLES) 138 144 146 58: 264 type=124 (ANGLES) 145 144 146 58: 265 type=125 (ANGLES) 144 146 147 58: 266 type=126 (ANGLES) 144 146 148 58: 267 type=127 (ANGLES) 147 146 148 58: 268 type=116 (ANGLES) 146 148 149 58: 269 type=128 (ANGLES) 146 148 150 58: 270 type=129 (ANGLES) 146 148 154 58: 271 type=118 (ANGLES) 149 148 150 58: 272 type=116 (ANGLES) 149 148 154 58: 273 type=119 (ANGLES) 150 148 154 58: 274 type=118 (ANGLES) 148 150 151 58: 275 type=118 (ANGLES) 148 150 152 58: 276 type=118 (ANGLES) 148 150 153 58: 277 type=121 (ANGLES) 151 150 152 58: 278 type=121 (ANGLES) 151 150 153 58: 279 type=121 (ANGLES) 152 150 153 58: 280 type=122 (ANGLES) 148 154 155 58: G96Angle: 58: nr: 0 58: Restr. Angles: 58: nr: 0 58: Lin. Angle: 58: nr: 0 58: Bond-Cross: 58: nr: 0 58: BA-Cross: 58: nr: 0 58: U-B: 58: nr: 0 58: Quartic Angles: 58: nr: 0 58: Tab. Angles: 58: nr: 0 58: Proper Dih.: 58: nr: 145 58: iatoms: 58: 0 type=140 (PDIHS) 4 24 22 23 58: 1 type=141 (PDIHS) 22 26 24 25 58: 2 type=140 (PDIHS) 26 40 38 39 58: 3 type=141 (PDIHS) 38 42 40 41 58: 4 type=140 (PDIHS) 42 60 58 59 58: 5 type=142 (PDIHS) 44 47 50 48 58: 6 type=142 (PDIHS) 47 52 48 49 58: 7 type=142 (PDIHS) 47 54 50 51 58: 8 type=142 (PDIHS) 48 56 52 53 58: 9 type=142 (PDIHS) 50 56 54 55 58: 10 type=142 (PDIHS) 52 54 56 57 58: 11 type=141 (PDIHS) 58 62 60 61 58: 12 type=140 (PDIHS) 62 67 65 66 58: 13 type=141 (PDIHS) 65 69 67 68 58: 14 type=140 (PDIHS) 69 91 89 90 58: 15 type=141 (PDIHS) 77 82 80 81 58: 16 type=140 (PDIHS) 80 83 82 86 58: 17 type=141 (PDIHS) 82 84 83 85 58: 18 type=141 (PDIHS) 82 87 86 88 58: 19 type=141 (PDIHS) 89 93 91 92 58: 20 type=140 (PDIHS) 93 102 100 101 58: 21 type=141 (PDIHS) 100 104 102 103 58: 22 type=140 (PDIHS) 104 117 115 116 58: 23 type=140 (PDIHS) 109 113 112 114 58: 24 type=141 (PDIHS) 115 119 117 118 58: 25 type=140 (PDIHS) 119 136 134 135 58: 26 type=141 (PDIHS) 134 138 136 137 58: 27 type=140 (PDIHS) 138 146 144 145 58: 28 type=141 (PDIHS) 144 148 146 147 58: Ryckaert-Bell.: 58: nr: 1565 58: iatoms: 58: 0 type=143 (RBDIHS) 1 0 4 5 58: 1 type=144 (RBDIHS) 1 0 4 6 58: 2 type=144 (RBDIHS) 1 0 4 22 58: 3 type=143 (RBDIHS) 2 0 4 5 58: 4 type=144 (RBDIHS) 2 0 4 6 58: 5 type=144 (RBDIHS) 2 0 4 22 58: 6 type=143 (RBDIHS) 3 0 4 5 58: 7 type=144 (RBDIHS) 3 0 4 6 58: 8 type=144 (RBDIHS) 3 0 4 22 58: 9 type=145 (RBDIHS) 0 4 6 9 58: 10 type=146 (RBDIHS) 22 4 6 9 58: 11 type=147 (RBDIHS) 0 4 6 7 58: 12 type=147 (RBDIHS) 0 4 6 8 58: 13 type=148 (RBDIHS) 5 4 6 7 58: 14 type=148 (RBDIHS) 5 4 6 8 58: 15 type=148 (RBDIHS) 5 4 6 9 58: 16 type=149 (RBDIHS) 22 4 6 7 58: 17 type=149 (RBDIHS) 22 4 6 8 58: 18 type=150 (RBDIHS) 0 4 22 24 58: 19 type=151 (RBDIHS) 6 4 22 24 58: 20 type=148 (RBDIHS) 4 6 9 10 58: 21 type=148 (RBDIHS) 4 6 9 11 58: 22 type=152 (RBDIHS) 4 6 9 12 58: 23 type=148 (RBDIHS) 7 6 9 10 58: 24 type=148 (RBDIHS) 7 6 9 11 58: 25 type=148 (RBDIHS) 7 6 9 12 58: 26 type=148 (RBDIHS) 8 6 9 10 58: 27 type=148 (RBDIHS) 8 6 9 11 58: 28 type=148 (RBDIHS) 8 6 9 12 58: 29 type=148 (RBDIHS) 6 9 12 13 58: 30 type=148 (RBDIHS) 6 9 12 14 58: 31 type=152 (RBDIHS) 6 9 12 15 58: 32 type=148 (RBDIHS) 10 9 12 13 58: 33 type=148 (RBDIHS) 10 9 12 14 58: 34 type=148 (RBDIHS) 10 9 12 15 58: 35 type=148 (RBDIHS) 11 9 12 13 58: 36 type=148 (RBDIHS) 11 9 12 14 58: 37 type=148 (RBDIHS) 11 9 12 15 58: 38 type=148 (RBDIHS) 9 12 15 16 58: 39 type=148 (RBDIHS) 9 12 15 17 58: 40 type=153 (RBDIHS) 9 12 15 18 58: 41 type=148 (RBDIHS) 13 12 15 16 58: 42 type=148 (RBDIHS) 13 12 15 17 58: 43 type=154 (RBDIHS) 13 12 15 18 58: 44 type=148 (RBDIHS) 14 12 15 16 58: 45 type=148 (RBDIHS) 14 12 15 17 58: 46 type=154 (RBDIHS) 14 12 15 18 58: 47 type=144 (RBDIHS) 12 15 18 19 58: 48 type=144 (RBDIHS) 12 15 18 20 58: 49 type=144 (RBDIHS) 12 15 18 21 58: 50 type=143 (RBDIHS) 16 15 18 19 58: 51 type=143 (RBDIHS) 16 15 18 20 58: 52 type=143 (RBDIHS) 16 15 18 21 58: 53 type=143 (RBDIHS) 17 15 18 19 58: 54 type=143 (RBDIHS) 17 15 18 20 58: 55 type=143 (RBDIHS) 17 15 18 21 58: 56 type=155 (RBDIHS) 4 22 24 25 58: 57 type=156 (RBDIHS) 4 22 24 26 58: 58 type=155 (RBDIHS) 23 22 24 25 58: 59 type=157 (RBDIHS) 23 22 24 26 58: 60 type=158 (RBDIHS) 22 24 26 28 58: 61 type=159 (RBDIHS) 22 24 26 38 58: 62 type=160 (RBDIHS) 24 26 28 30 58: 63 type=160 (RBDIHS) 24 26 28 34 58: 64 type=161 (RBDIHS) 38 26 28 30 58: 65 type=161 (RBDIHS) 38 26 28 34 58: 66 type=147 (RBDIHS) 24 26 28 29 58: 67 type=148 (RBDIHS) 27 26 28 29 58: 68 type=148 (RBDIHS) 27 26 28 30 58: 69 type=148 (RBDIHS) 27 26 28 34 58: 70 type=149 (RBDIHS) 38 26 28 29 58: 71 type=150 (RBDIHS) 24 26 38 40 58: 72 type=151 (RBDIHS) 28 26 38 40 58: 73 type=148 (RBDIHS) 26 28 30 31 58: 74 type=148 (RBDIHS) 26 28 30 32 58: 75 type=148 (RBDIHS) 26 28 30 33 58: 76 type=148 (RBDIHS) 29 28 30 31 58: 77 type=148 (RBDIHS) 29 28 30 32 58: 78 type=148 (RBDIHS) 29 28 30 33 58: 79 type=148 (RBDIHS) 34 28 30 31 58: 80 type=148 (RBDIHS) 34 28 30 32 58: 81 type=148 (RBDIHS) 34 28 30 33 58: 82 type=148 (RBDIHS) 26 28 34 35 58: 83 type=148 (RBDIHS) 26 28 34 36 58: 84 type=148 (RBDIHS) 26 28 34 37 58: 85 type=148 (RBDIHS) 29 28 34 35 58: 86 type=148 (RBDIHS) 29 28 34 36 58: 87 type=148 (RBDIHS) 29 28 34 37 58: 88 type=148 (RBDIHS) 30 28 34 35 58: 89 type=148 (RBDIHS) 30 28 34 36 58: 90 type=148 (RBDIHS) 30 28 34 37 58: 91 type=155 (RBDIHS) 26 38 40 41 58: 92 type=156 (RBDIHS) 26 38 40 42 58: 93 type=155 (RBDIHS) 39 38 40 41 58: 94 type=157 (RBDIHS) 39 38 40 42 58: 95 type=158 (RBDIHS) 38 40 42 44 58: 96 type=159 (RBDIHS) 38 40 42 58 58: 97 type=147 (RBDIHS) 40 42 44 45 58: 98 type=147 (RBDIHS) 40 42 44 46 58: 99 type=162 (RBDIHS) 40 42 44 47 58: 100 type=148 (RBDIHS) 43 42 44 45 58: 101 type=148 (RBDIHS) 43 42 44 46 58: 102 type=163 (RBDIHS) 43 42 44 47 58: 103 type=149 (RBDIHS) 58 42 44 45 58: 104 type=149 (RBDIHS) 58 42 44 46 58: 105 type=164 (RBDIHS) 58 42 44 47 58: 106 type=150 (RBDIHS) 40 42 58 60 58: 107 type=151 (RBDIHS) 44 42 58 60 58: 108 type=165 (RBDIHS) 44 47 48 49 58: 109 type=165 (RBDIHS) 44 47 48 52 58: 110 type=165 (RBDIHS) 50 47 48 49 58: 111 type=165 (RBDIHS) 50 47 48 52 58: 112 type=165 (RBDIHS) 44 47 50 51 58: 113 type=165 (RBDIHS) 44 47 50 54 58: 114 type=165 (RBDIHS) 48 47 50 51 58: 115 type=165 (RBDIHS) 48 47 50 54 58: 116 type=165 (RBDIHS) 47 48 52 53 58: 117 type=165 (RBDIHS) 47 48 52 56 58: 118 type=165 (RBDIHS) 49 48 52 53 58: 119 type=165 (RBDIHS) 49 48 52 56 58: 120 type=165 (RBDIHS) 47 50 54 55 58: 121 type=165 (RBDIHS) 47 50 54 56 58: 122 type=165 (RBDIHS) 51 50 54 55 58: 123 type=165 (RBDIHS) 51 50 54 56 58: 124 type=165 (RBDIHS) 48 52 56 54 58: 125 type=165 (RBDIHS) 48 52 56 57 58: 126 type=165 (RBDIHS) 53 52 56 54 58: 127 type=165 (RBDIHS) 53 52 56 57 58: 128 type=165 (RBDIHS) 50 54 56 52 58: 129 type=165 (RBDIHS) 50 54 56 57 58: 130 type=165 (RBDIHS) 55 54 56 52 58: 131 type=165 (RBDIHS) 55 54 56 57 58: 132 type=155 (RBDIHS) 42 58 60 61 58: 133 type=156 (RBDIHS) 42 58 60 62 58: 134 type=155 (RBDIHS) 59 58 60 61 58: 135 type=157 (RBDIHS) 59 58 60 62 58: 136 type=159 (RBDIHS) 58 60 62 65 58: 137 type=150 (RBDIHS) 60 62 65 67 58: 138 type=155 (RBDIHS) 62 65 67 68 58: 139 type=156 (RBDIHS) 62 65 67 69 58: 140 type=155 (RBDIHS) 66 65 67 68 58: 141 type=157 (RBDIHS) 66 65 67 69 58: 142 type=158 (RBDIHS) 65 67 69 71 58: 143 type=159 (RBDIHS) 65 67 69 89 58: 144 type=166 (RBDIHS) 67 69 71 74 58: 145 type=167 (RBDIHS) 89 69 71 74 58: 146 type=147 (RBDIHS) 67 69 71 72 58: 147 type=147 (RBDIHS) 67 69 71 73 58: 148 type=148 (RBDIHS) 70 69 71 72 58: 149 type=148 (RBDIHS) 70 69 71 73 58: 150 type=148 (RBDIHS) 70 69 71 74 58: 151 type=149 (RBDIHS) 89 69 71 72 58: 152 type=149 (RBDIHS) 89 69 71 73 58: 153 type=150 (RBDIHS) 67 69 89 91 58: 154 type=151 (RBDIHS) 71 69 89 91 58: 155 type=148 (RBDIHS) 69 71 74 75 58: 156 type=148 (RBDIHS) 69 71 74 76 58: 157 type=152 (RBDIHS) 69 71 74 77 58: 158 type=148 (RBDIHS) 72 71 74 75 58: 159 type=148 (RBDIHS) 72 71 74 76 58: 160 type=148 (RBDIHS) 72 71 74 77 58: 161 type=148 (RBDIHS) 73 71 74 75 58: 162 type=148 (RBDIHS) 73 71 74 76 58: 163 type=148 (RBDIHS) 73 71 74 77 58: 164 type=148 (RBDIHS) 71 74 77 78 58: 165 type=148 (RBDIHS) 71 74 77 79 58: 166 type=153 (RBDIHS) 71 74 77 80 58: 167 type=148 (RBDIHS) 75 74 77 78 58: 168 type=148 (RBDIHS) 75 74 77 79 58: 169 type=168 (RBDIHS) 75 74 77 80 58: 170 type=148 (RBDIHS) 76 74 77 78 58: 171 type=148 (RBDIHS) 76 74 77 79 58: 172 type=168 (RBDIHS) 76 74 77 80 58: 173 type=169 (RBDIHS) 74 77 80 81 58: 174 type=170 (RBDIHS) 74 77 80 82 58: 175 type=171 (RBDIHS) 78 77 80 82 58: 176 type=171 (RBDIHS) 79 77 80 82 58: 177 type=172 (RBDIHS) 77 80 82 83 58: 178 type=172 (RBDIHS) 77 80 82 86 58: 179 type=173 (RBDIHS) 81 80 82 83 58: 180 type=173 (RBDIHS) 81 80 82 86 58: 181 type=173 (RBDIHS) 80 82 83 84 58: 182 type=173 (RBDIHS) 80 82 83 85 58: 183 type=173 (RBDIHS) 86 82 83 84 58: 184 type=173 (RBDIHS) 86 82 83 85 58: 185 type=173 (RBDIHS) 80 82 86 87 58: 186 type=173 (RBDIHS) 80 82 86 88 58: 187 type=173 (RBDIHS) 83 82 86 87 58: 188 type=173 (RBDIHS) 83 82 86 88 58: 189 type=155 (RBDIHS) 69 89 91 92 58: 190 type=156 (RBDIHS) 69 89 91 93 58: 191 type=155 (RBDIHS) 90 89 91 92 58: 192 type=157 (RBDIHS) 90 89 91 93 58: 193 type=158 (RBDIHS) 89 91 93 95 58: 194 type=159 (RBDIHS) 89 91 93 100 58: 195 type=174 (RBDIHS) 91 93 95 98 58: 196 type=175 (RBDIHS) 100 93 95 98 58: 197 type=147 (RBDIHS) 91 93 95 96 58: 198 type=147 (RBDIHS) 91 93 95 97 58: 199 type=148 (RBDIHS) 94 93 95 96 58: 200 type=148 (RBDIHS) 94 93 95 97 58: 201 type=176 (RBDIHS) 94 93 95 98 58: 202 type=149 (RBDIHS) 100 93 95 96 58: 203 type=149 (RBDIHS) 100 93 95 97 58: 204 type=150 (RBDIHS) 91 93 100 102 58: 205 type=151 (RBDIHS) 95 93 100 102 58: 206 type=177 (RBDIHS) 93 95 98 99 58: 207 type=178 (RBDIHS) 96 95 98 99 58: 208 type=178 (RBDIHS) 97 95 98 99 58: 209 type=155 (RBDIHS) 93 100 102 103 58: 210 type=156 (RBDIHS) 93 100 102 104 58: 211 type=155 (RBDIHS) 101 100 102 103 58: 212 type=157 (RBDIHS) 101 100 102 104 58: 213 type=158 (RBDIHS) 100 102 104 106 58: 214 type=159 (RBDIHS) 100 102 104 115 58: 215 type=179 (RBDIHS) 102 104 106 109 58: 216 type=180 (RBDIHS) 115 104 106 109 58: 217 type=147 (RBDIHS) 102 104 106 107 58: 218 type=147 (RBDIHS) 102 104 106 108 58: 219 type=148 (RBDIHS) 105 104 106 107 58: 220 type=148 (RBDIHS) 105 104 106 108 58: 221 type=148 (RBDIHS) 105 104 106 109 58: 222 type=149 (RBDIHS) 115 104 106 107 58: 223 type=149 (RBDIHS) 115 104 106 108 58: 224 type=150 (RBDIHS) 102 104 115 117 58: 225 type=151 (RBDIHS) 106 104 115 117 58: 226 type=148 (RBDIHS) 104 106 109 110 58: 227 type=148 (RBDIHS) 104 106 109 111 58: 228 type=181 (RBDIHS) 104 106 109 112 58: 229 type=148 (RBDIHS) 107 106 109 110 58: 230 type=148 (RBDIHS) 107 106 109 111 58: 231 type=182 (RBDIHS) 107 106 109 112 58: 232 type=148 (RBDIHS) 108 106 109 110 58: 233 type=148 (RBDIHS) 108 106 109 111 58: 234 type=182 (RBDIHS) 108 106 109 112 58: 235 type=183 (RBDIHS) 106 109 112 113 58: 236 type=183 (RBDIHS) 106 109 112 114 58: 237 type=155 (RBDIHS) 104 115 117 118 58: 238 type=156 (RBDIHS) 104 115 117 119 58: 239 type=155 (RBDIHS) 116 115 117 118 58: 240 type=157 (RBDIHS) 116 115 117 119 58: 241 type=158 (RBDIHS) 115 117 119 121 58: 242 type=159 (RBDIHS) 115 117 119 134 58: 243 type=184 (RBDIHS) 117 119 121 124 58: 244 type=185 (RBDIHS) 134 119 121 124 58: 245 type=147 (RBDIHS) 117 119 121 122 58: 246 type=147 (RBDIHS) 117 119 121 123 58: 247 type=148 (RBDIHS) 120 119 121 122 58: 248 type=148 (RBDIHS) 120 119 121 123 58: 249 type=148 (RBDIHS) 120 119 121 124 58: 250 type=149 (RBDIHS) 134 119 121 122 58: 251 type=149 (RBDIHS) 134 119 121 123 58: 252 type=150 (RBDIHS) 117 119 134 136 58: 253 type=151 (RBDIHS) 121 119 134 136 58: 254 type=148 (RBDIHS) 119 121 124 125 58: 255 type=152 (RBDIHS) 119 121 124 126 58: 256 type=152 (RBDIHS) 119 121 124 130 58: 257 type=148 (RBDIHS) 122 121 124 125 58: 258 type=148 (RBDIHS) 122 121 124 126 58: 259 type=148 (RBDIHS) 122 121 124 130 58: 260 type=148 (RBDIHS) 123 121 124 125 58: 261 type=148 (RBDIHS) 123 121 124 126 58: 262 type=148 (RBDIHS) 123 121 124 130 58: 263 type=148 (RBDIHS) 121 124 126 127 58: 264 type=148 (RBDIHS) 121 124 126 128 58: 265 type=148 (RBDIHS) 121 124 126 129 58: 266 type=148 (RBDIHS) 125 124 126 127 58: 267 type=148 (RBDIHS) 125 124 126 128 58: 268 type=148 (RBDIHS) 125 124 126 129 58: 269 type=148 (RBDIHS) 130 124 126 127 58: 270 type=148 (RBDIHS) 130 124 126 128 58: 271 type=148 (RBDIHS) 130 124 126 129 58: 272 type=148 (RBDIHS) 121 124 130 131 58: 273 type=148 (RBDIHS) 121 124 130 132 58: 274 type=148 (RBDIHS) 121 124 130 133 58: 275 type=148 (RBDIHS) 125 124 130 131 58: 276 type=148 (RBDIHS) 125 124 130 132 58: 277 type=148 (RBDIHS) 125 124 130 133 58: 278 type=148 (RBDIHS) 126 124 130 131 58: 279 type=148 (RBDIHS) 126 124 130 132 58: 280 type=148 (RBDIHS) 126 124 130 133 58: 281 type=155 (RBDIHS) 119 134 136 137 58: 282 type=156 (RBDIHS) 119 134 136 138 58: 283 type=155 (RBDIHS) 135 134 136 137 58: 284 type=157 (RBDIHS) 135 134 136 138 58: 285 type=158 (RBDIHS) 134 136 138 140 58: 286 type=159 (RBDIHS) 134 136 138 144 58: 287 type=147 (RBDIHS) 136 138 140 141 58: 288 type=147 (RBDIHS) 136 138 140 142 58: 289 type=147 (RBDIHS) 136 138 140 143 58: 290 type=148 (RBDIHS) 139 138 140 141 58: 291 type=148 (RBDIHS) 139 138 140 142 58: 292 type=148 (RBDIHS) 139 138 140 143 58: 293 type=149 (RBDIHS) 144 138 140 141 58: 294 type=149 (RBDIHS) 144 138 140 142 58: 295 type=149 (RBDIHS) 144 138 140 143 58: 296 type=150 (RBDIHS) 136 138 144 146 58: 297 type=151 (RBDIHS) 140 138 144 146 58: 298 type=155 (RBDIHS) 138 144 146 147 58: 299 type=156 (RBDIHS) 138 144 146 148 58: 300 type=155 (RBDIHS) 145 144 146 147 58: 301 type=157 (RBDIHS) 145 144 146 148 58: 302 type=158 (RBDIHS) 144 146 148 150 58: 303 type=159 (RBDIHS) 144 146 148 154 58: 304 type=147 (RBDIHS) 146 148 150 151 58: 305 type=147 (RBDIHS) 146 148 150 152 58: 306 type=147 (RBDIHS) 146 148 150 153 58: 307 type=148 (RBDIHS) 149 148 150 151 58: 308 type=148 (RBDIHS) 149 148 150 152 58: 309 type=148 (RBDIHS) 149 148 150 153 58: 310 type=149 (RBDIHS) 154 148 150 151 58: 311 type=149 (RBDIHS) 154 148 150 152 58: 312 type=149 (RBDIHS) 154 148 150 153 58: Restr. Dih.: 58: nr: 0 58: CBT Dih.: 58: nr: 0 58: Fourier Dih.: 58: nr: 0 58: Improper Dih.: 58: nr: 0 58: Per. Imp. Dih.: 58: nr: 0 58: Tab. Dih.: 58: nr: 0 58: CMAP Dih.: 58: nr: 0 58: GB 1-2 Pol.: 58: nr: 0 58: GB 1-3 Pol.: 58: nr: 0 58: GB 1-4 Pol.: 58: nr: 0 58: GB Polariz.: 58: nr: 0 58: Nonpolar Sol.: 58: nr: 0 58: LJ-14: 58: nr: 1197 58: iatoms: 58: 0 type=186 (LJ14) 0 7 58: 1 type=186 (LJ14) 0 8 58: 2 type=187 (LJ14) 0 9 58: 3 type=188 (LJ14) 0 23 58: 4 type=189 (LJ14) 0 24 58: 5 type=190 (LJ14) 1 5 58: 6 type=190 (LJ14) 1 6 58: 7 type=190 (LJ14) 1 22 58: 8 type=190 (LJ14) 2 5 58: 9 type=190 (LJ14) 2 6 58: 10 type=190 (LJ14) 2 22 58: 11 type=190 (LJ14) 3 5 58: 12 type=190 (LJ14) 3 6 58: 13 type=190 (LJ14) 3 22 58: 14 type=191 (LJ14) 4 10 58: 15 type=191 (LJ14) 4 11 58: 16 type=192 (LJ14) 4 12 58: 17 type=190 (LJ14) 4 25 58: 18 type=192 (LJ14) 4 26 58: 19 type=193 (LJ14) 5 7 58: 20 type=193 (LJ14) 5 8 58: 21 type=191 (LJ14) 5 9 58: 22 type=194 (LJ14) 5 23 58: 23 type=186 (LJ14) 5 24 58: 24 type=191 (LJ14) 6 13 58: 25 type=191 (LJ14) 6 14 58: 26 type=192 (LJ14) 6 15 58: 27 type=195 (LJ14) 6 23 58: 28 type=187 (LJ14) 6 24 58: 29 type=193 (LJ14) 7 10 58: 30 type=193 (LJ14) 7 11 58: 31 type=191 (LJ14) 7 12 58: 32 type=196 (LJ14) 7 22 58: 33 type=193 (LJ14) 8 10 58: 34 type=193 (LJ14) 8 11 58: 35 type=191 (LJ14) 8 12 58: 36 type=196 (LJ14) 8 22 58: 37 type=191 (LJ14) 9 16 58: 38 type=191 (LJ14) 9 17 58: 39 type=187 (LJ14) 9 18 58: 40 type=197 (LJ14) 9 22 58: 41 type=193 (LJ14) 10 13 58: 42 type=193 (LJ14) 10 14 58: 43 type=191 (LJ14) 10 15 58: 44 type=193 (LJ14) 11 13 58: 45 type=193 (LJ14) 11 14 58: 46 type=191 (LJ14) 11 15 58: 47 type=190 (LJ14) 12 19 58: 48 type=190 (LJ14) 12 20 58: 49 type=190 (LJ14) 12 21 58: 50 type=193 (LJ14) 13 16 58: 51 type=193 (LJ14) 13 17 58: 52 type=186 (LJ14) 13 18 58: 53 type=193 (LJ14) 14 16 58: 54 type=193 (LJ14) 14 17 58: 55 type=186 (LJ14) 14 18 58: 56 type=190 (LJ14) 16 19 58: 57 type=190 (LJ14) 16 20 58: 58 type=190 (LJ14) 16 21 58: 59 type=190 (LJ14) 17 19 58: 60 type=190 (LJ14) 17 20 58: 61 type=190 (LJ14) 17 21 58: 62 type=196 (LJ14) 22 27 58: 63 type=197 (LJ14) 22 28 58: 64 type=198 (LJ14) 22 38 58: 65 type=190 (LJ14) 23 25 58: 66 type=195 (LJ14) 23 26 58: 67 type=186 (LJ14) 24 29 58: 68 type=187 (LJ14) 24 30 58: 69 type=187 (LJ14) 24 34 58: 70 type=188 (LJ14) 24 39 58: 71 type=189 (LJ14) 24 40 58: 72 type=190 (LJ14) 25 27 58: 73 type=190 (LJ14) 25 28 58: 74 type=190 (LJ14) 25 38 58: 75 type=191 (LJ14) 26 31 58: 76 type=191 (LJ14) 26 32 58: 77 type=191 (LJ14) 26 33 58: 78 type=191 (LJ14) 26 35 58: 79 type=191 (LJ14) 26 36 58: 80 type=191 (LJ14) 26 37 58: 81 type=190 (LJ14) 26 41 58: 82 type=192 (LJ14) 26 42 58: 83 type=193 (LJ14) 27 29 58: 84 type=191 (LJ14) 27 30 58: 85 type=191 (LJ14) 27 34 58: 86 type=194 (LJ14) 27 39 58: 87 type=186 (LJ14) 27 40 58: 88 type=195 (LJ14) 28 39 58: 89 type=187 (LJ14) 28 40 58: 90 type=193 (LJ14) 29 31 58: 91 type=193 (LJ14) 29 32 58: 92 type=193 (LJ14) 29 33 58: 93 type=193 (LJ14) 29 35 58: 94 type=193 (LJ14) 29 36 58: 95 type=193 (LJ14) 29 37 58: 96 type=196 (LJ14) 29 38 58: 97 type=191 (LJ14) 30 35 58: 98 type=191 (LJ14) 30 36 58: 99 type=191 (LJ14) 30 37 58: 100 type=197 (LJ14) 30 38 58: 101 type=191 (LJ14) 31 34 58: 102 type=191 (LJ14) 32 34 58: 103 type=191 (LJ14) 33 34 58: 104 type=197 (LJ14) 34 38 58: 105 type=196 (LJ14) 38 43 58: 106 type=197 (LJ14) 38 44 58: 107 type=198 (LJ14) 38 58 58: 108 type=190 (LJ14) 39 41 58: 109 type=195 (LJ14) 39 42 58: 110 type=186 (LJ14) 40 45 58: 111 type=186 (LJ14) 40 46 58: 112 type=199 (LJ14) 40 47 58: 113 type=188 (LJ14) 40 59 58: 114 type=189 (LJ14) 40 60 58: 115 type=190 (LJ14) 41 43 58: 116 type=190 (LJ14) 41 44 58: 117 type=190 (LJ14) 41 58 58: 118 type=200 (LJ14) 42 48 58: 119 type=200 (LJ14) 42 50 58: 120 type=190 (LJ14) 42 61 58: 121 type=192 (LJ14) 42 62 58: 122 type=193 (LJ14) 43 45 58: 123 type=193 (LJ14) 43 46 58: 124 type=201 (LJ14) 43 47 58: 125 type=194 (LJ14) 43 59 58: 126 type=186 (LJ14) 43 60 58: 127 type=202 (LJ14) 44 49 58: 128 type=202 (LJ14) 44 51 58: 129 type=200 (LJ14) 44 52 58: 130 type=200 (LJ14) 44 54 58: 131 type=195 (LJ14) 44 59 58: 132 type=187 (LJ14) 44 60 58: 133 type=201 (LJ14) 45 48 58: 134 type=201 (LJ14) 45 50 58: 135 type=196 (LJ14) 45 58 58: 136 type=201 (LJ14) 46 48 58: 137 type=201 (LJ14) 46 50 58: 138 type=196 (LJ14) 46 58 58: 139 type=203 (LJ14) 47 53 58: 140 type=203 (LJ14) 47 55 58: 141 type=204 (LJ14) 47 56 58: 142 type=205 (LJ14) 47 58 58: 143 type=203 (LJ14) 48 51 58: 144 type=204 (LJ14) 48 54 58: 145 type=203 (LJ14) 48 57 58: 146 type=203 (LJ14) 49 50 58: 147 type=206 (LJ14) 49 53 58: 148 type=203 (LJ14) 49 56 58: 149 type=204 (LJ14) 50 52 58: 150 type=203 (LJ14) 50 57 58: 151 type=206 (LJ14) 51 55 58: 152 type=203 (LJ14) 51 56 58: 153 type=203 (LJ14) 52 55 58: 154 type=203 (LJ14) 53 54 58: 155 type=206 (LJ14) 53 57 58: 156 type=206 (LJ14) 55 57 58: 157 type=196 (LJ14) 58 63 58: 158 type=196 (LJ14) 58 64 58: 159 type=198 (LJ14) 58 65 58: 160 type=190 (LJ14) 59 61 58: 161 type=195 (LJ14) 59 62 58: 162 type=188 (LJ14) 60 66 58: 163 type=189 (LJ14) 60 67 58: 164 type=190 (LJ14) 61 63 58: 165 type=190 (LJ14) 61 64 58: 166 type=190 (LJ14) 61 65 58: 167 type=190 (LJ14) 62 68 58: 168 type=192 (LJ14) 62 69 58: 169 type=194 (LJ14) 63 66 58: 170 type=186 (LJ14) 63 67 58: 171 type=194 (LJ14) 64 66 58: 172 type=186 (LJ14) 64 67 58: 173 type=196 (LJ14) 65 70 58: 174 type=197 (LJ14) 65 71 58: 175 type=198 (LJ14) 65 89 58: 176 type=190 (LJ14) 66 68 58: 177 type=195 (LJ14) 66 69 58: 178 type=186 (LJ14) 67 72 58: 179 type=186 (LJ14) 67 73 58: 180 type=187 (LJ14) 67 74 58: 181 type=188 (LJ14) 67 90 58: 182 type=189 (LJ14) 67 91 58: 183 type=190 (LJ14) 68 70 58: 184 type=190 (LJ14) 68 71 58: 185 type=190 (LJ14) 68 89 58: 186 type=191 (LJ14) 69 75 58: 187 type=191 (LJ14) 69 76 58: 188 type=192 (LJ14) 69 77 58: 189 type=190 (LJ14) 69 92 58: 190 type=192 (LJ14) 69 93 58: 191 type=193 (LJ14) 70 72 58: 192 type=193 (LJ14) 70 73 58: 193 type=191 (LJ14) 70 74 58: 194 type=194 (LJ14) 70 90 58: 195 type=186 (LJ14) 70 91 58: 196 type=191 (LJ14) 71 78 58: 197 type=191 (LJ14) 71 79 58: 198 type=187 (LJ14) 71 80 58: 199 type=195 (LJ14) 71 90 58: 200 type=187 (LJ14) 71 91 58: 201 type=193 (LJ14) 72 75 58: 202 type=193 (LJ14) 72 76 58: 203 type=191 (LJ14) 72 77 58: 204 type=196 (LJ14) 72 89 58: 205 type=193 (LJ14) 73 75 58: 206 type=193 (LJ14) 73 76 58: 207 type=191 (LJ14) 73 77 58: 208 type=196 (LJ14) 73 89 58: 209 type=190 (LJ14) 74 81 58: 210 type=207 (LJ14) 74 82 58: 211 type=197 (LJ14) 74 89 58: 212 type=193 (LJ14) 75 78 58: 213 type=193 (LJ14) 75 79 58: 214 type=186 (LJ14) 75 80 58: 215 type=193 (LJ14) 76 78 58: 216 type=193 (LJ14) 76 79 58: 217 type=186 (LJ14) 76 80 58: 218 type=187 (LJ14) 77 83 58: 219 type=187 (LJ14) 77 86 58: 220 type=190 (LJ14) 78 81 58: 221 type=208 (LJ14) 78 82 58: 222 type=190 (LJ14) 79 81 58: 223 type=208 (LJ14) 79 82 58: 224 type=190 (LJ14) 80 84 58: 225 type=190 (LJ14) 80 85 58: 226 type=190 (LJ14) 80 87 58: 227 type=190 (LJ14) 80 88 58: 228 type=190 (LJ14) 81 83 58: 229 type=190 (LJ14) 81 86 58: 230 type=190 (LJ14) 83 87 58: 231 type=190 (LJ14) 83 88 58: 232 type=190 (LJ14) 84 86 58: 233 type=190 (LJ14) 85 86 58: 234 type=196 (LJ14) 89 94 58: 235 type=197 (LJ14) 89 95 58: 236 type=198 (LJ14) 89 100 58: 237 type=190 (LJ14) 90 92 58: 238 type=195 (LJ14) 90 93 58: 239 type=186 (LJ14) 91 96 58: 240 type=186 (LJ14) 91 97 58: 241 type=209 (LJ14) 91 98 58: 242 type=188 (LJ14) 91 101 58: 243 type=189 (LJ14) 91 102 58: 244 type=190 (LJ14) 92 94 58: 245 type=190 (LJ14) 92 95 58: 246 type=190 (LJ14) 92 100 58: 247 type=190 (LJ14) 93 99 58: 248 type=190 (LJ14) 93 103 58: 249 type=192 (LJ14) 93 104 58: 250 type=193 (LJ14) 94 96 58: 251 type=193 (LJ14) 94 97 58: 252 type=210 (LJ14) 94 98 58: 253 type=194 (LJ14) 94 101 58: 254 type=186 (LJ14) 94 102 58: 255 type=195 (LJ14) 95 101 58: 256 type=187 (LJ14) 95 102 58: 257 type=190 (LJ14) 96 99 58: 258 type=196 (LJ14) 96 100 58: 259 type=190 (LJ14) 97 99 58: 260 type=196 (LJ14) 97 100 58: 261 type=211 (LJ14) 98 100 58: 262 type=196 (LJ14) 100 105 58: 263 type=197 (LJ14) 100 106 58: 264 type=198 (LJ14) 100 115 58: 265 type=190 (LJ14) 101 103 58: 266 type=195 (LJ14) 101 104 58: 267 type=186 (LJ14) 102 107 58: 268 type=186 (LJ14) 102 108 58: 269 type=187 (LJ14) 102 109 58: 270 type=188 (LJ14) 102 116 58: 271 type=189 (LJ14) 102 117 58: 272 type=190 (LJ14) 103 105 58: 273 type=190 (LJ14) 103 106 58: 274 type=190 (LJ14) 103 115 58: 275 type=191 (LJ14) 104 110 58: 276 type=191 (LJ14) 104 111 58: 277 type=197 (LJ14) 104 112 58: 278 type=190 (LJ14) 104 118 58: 279 type=192 (LJ14) 104 119 58: 280 type=193 (LJ14) 105 107 58: 281 type=193 (LJ14) 105 108 58: 282 type=191 (LJ14) 105 109 58: 283 type=194 (LJ14) 105 116 58: 284 type=186 (LJ14) 105 117 58: 285 type=195 (LJ14) 106 113 58: 286 type=195 (LJ14) 106 114 58: 287 type=195 (LJ14) 106 116 58: 288 type=187 (LJ14) 106 117 58: 289 type=193 (LJ14) 107 110 58: 290 type=193 (LJ14) 107 111 58: 291 type=196 (LJ14) 107 112 58: 292 type=196 (LJ14) 107 115 58: 293 type=193 (LJ14) 108 110 58: 294 type=193 (LJ14) 108 111 58: 295 type=196 (LJ14) 108 112 58: 296 type=196 (LJ14) 108 115 58: 297 type=197 (LJ14) 109 115 58: 298 type=194 (LJ14) 110 113 58: 299 type=194 (LJ14) 110 114 58: 300 type=194 (LJ14) 111 113 58: 301 type=194 (LJ14) 111 114 58: 302 type=196 (LJ14) 115 120 58: 303 type=197 (LJ14) 115 121 58: 304 type=198 (LJ14) 115 134 58: 305 type=190 (LJ14) 116 118 58: 306 type=195 (LJ14) 116 119 58: 307 type=186 (LJ14) 117 122 58: 308 type=186 (LJ14) 117 123 58: 309 type=187 (LJ14) 117 124 58: 310 type=188 (LJ14) 117 135 58: 311 type=189 (LJ14) 117 136 58: 312 type=190 (LJ14) 118 120 58: 313 type=190 (LJ14) 118 121 58: 314 type=190 (LJ14) 118 134 58: 315 type=191 (LJ14) 119 125 58: 316 type=192 (LJ14) 119 126 58: 317 type=192 (LJ14) 119 130 58: 318 type=190 (LJ14) 119 137 58: 319 type=192 (LJ14) 119 138 58: 320 type=193 (LJ14) 120 122 58: 321 type=193 (LJ14) 120 123 58: 322 type=191 (LJ14) 120 124 58: 323 type=194 (LJ14) 120 135 58: 324 type=186 (LJ14) 120 136 58: 325 type=191 (LJ14) 121 127 58: 326 type=191 (LJ14) 121 128 58: 327 type=191 (LJ14) 121 129 58: 328 type=191 (LJ14) 121 131 58: 329 type=191 (LJ14) 121 132 58: 330 type=191 (LJ14) 121 133 58: 331 type=195 (LJ14) 121 135 58: 332 type=187 (LJ14) 121 136 58: 333 type=193 (LJ14) 122 125 58: 334 type=191 (LJ14) 122 126 58: 335 type=191 (LJ14) 122 130 58: 336 type=196 (LJ14) 122 134 58: 337 type=193 (LJ14) 123 125 58: 338 type=191 (LJ14) 123 126 58: 339 type=191 (LJ14) 123 130 58: 340 type=196 (LJ14) 123 134 58: 341 type=197 (LJ14) 124 134 58: 342 type=193 (LJ14) 125 127 58: 343 type=193 (LJ14) 125 128 58: 344 type=193 (LJ14) 125 129 58: 345 type=193 (LJ14) 125 131 58: 346 type=193 (LJ14) 125 132 58: 347 type=193 (LJ14) 125 133 58: 348 type=191 (LJ14) 126 131 58: 349 type=191 (LJ14) 126 132 58: 350 type=191 (LJ14) 126 133 58: 351 type=191 (LJ14) 127 130 58: 352 type=191 (LJ14) 128 130 58: 353 type=191 (LJ14) 129 130 58: 354 type=196 (LJ14) 134 139 58: 355 type=197 (LJ14) 134 140 58: 356 type=198 (LJ14) 134 144 58: 357 type=190 (LJ14) 135 137 58: 358 type=195 (LJ14) 135 138 58: 359 type=186 (LJ14) 136 141 58: 360 type=186 (LJ14) 136 142 58: 361 type=186 (LJ14) 136 143 58: 362 type=188 (LJ14) 136 145 58: 363 type=189 (LJ14) 136 146 58: 364 type=190 (LJ14) 137 139 58: 365 type=190 (LJ14) 137 140 58: 366 type=190 (LJ14) 137 144 58: 367 type=190 (LJ14) 138 147 58: 368 type=192 (LJ14) 138 148 58: 369 type=193 (LJ14) 139 141 58: 370 type=193 (LJ14) 139 142 58: 371 type=193 (LJ14) 139 143 58: 372 type=194 (LJ14) 139 145 58: 373 type=186 (LJ14) 139 146 58: 374 type=195 (LJ14) 140 145 58: 375 type=187 (LJ14) 140 146 58: 376 type=196 (LJ14) 141 144 58: 377 type=196 (LJ14) 142 144 58: 378 type=196 (LJ14) 143 144 58: 379 type=196 (LJ14) 144 149 58: 380 type=197 (LJ14) 144 150 58: 381 type=198 (LJ14) 144 154 58: 382 type=190 (LJ14) 145 147 58: 383 type=195 (LJ14) 145 148 58: 384 type=186 (LJ14) 146 151 58: 385 type=186 (LJ14) 146 152 58: 386 type=186 (LJ14) 146 153 58: 387 type=188 (LJ14) 146 155 58: 388 type=190 (LJ14) 147 149 58: 389 type=190 (LJ14) 147 150 58: 390 type=190 (LJ14) 147 154 58: 391 type=193 (LJ14) 149 151 58: 392 type=193 (LJ14) 149 152 58: 393 type=193 (LJ14) 149 153 58: 394 type=194 (LJ14) 149 155 58: 395 type=195 (LJ14) 150 155 58: 396 type=196 (LJ14) 151 154 58: 397 type=196 (LJ14) 152 154 58: 398 type=196 (LJ14) 153 154 58: Coulomb-14: 58: nr: 0 58: LJC-14 q: 58: nr: 0 58: LJC Pairs NB: 58: nr: 0 58: LJ (SR): 58: nr: 0 58: Buck.ham (SR): 58: nr: 0 58: LJ: 58: nr: 0 58: B.ham: 58: nr: 0 58: Disper. corr.: 58: nr: 0 58: Coulomb (SR): 58: nr: 0 58: Coul: 58: nr: 0 58: RF excl.: 58: nr: 0 58: Coul. recip.: 58: nr: 0 58: LJ recip.: 58: nr: 0 58: DPD: 58: nr: 0 58: Polarization: 58: nr: 0 58: Water Pol.: 58: nr: 0 58: Thole Pol.: 58: nr: 0 58: Anharm. Pol.: 58: nr: 0 58: Position Rest.: 58: nr: 0 58: Flat-b. P-R.: 58: nr: 0 58: Dis. Rest.: 58: nr: 0 58: D.R.Viol. (nm): 58: nr: 0 58: Orient. Rest.: 58: nr: 0 58: Ori. R. RMSD: 58: nr: 0 58: Angle Rest.: 58: nr: 0 58: Angle Rest. Z: 58: nr: 0 58: Dih. Rest.: 58: nr: 0 58: Dih. Rest. Vi.: 58: nr: 0 58: Constraint: 58: nr: 0 58: Constr. No Co.: 58: nr: 0 58: Settle: 58: nr: 0 58: Virtual site 1: 58: nr: 0 58: Virtual site 2: 58: nr: 0 58: Virt. site 2fd: 58: nr: 0 58: Virtual site 3: 58: nr: 0 58: Virt. site 3fd: 58: nr: 0 58: Vir. site 3fad: 58: nr: 0 58: Vir. site 3out: 58: nr: 0 58: Virt. site 4fd: 58: nr: 0 58: Vir. site 4fdn: 58: nr: 0 58: Virtual site N: 58: nr: 0 58: COM Pull En.: 58: nr: 0 58: Dens. fitting: 58: nr: 0 58: Quantum En.: 58: nr: 0 58: Potential: 58: nr: 0 58: Kinetic En.: 58: nr: 0 58: Total Energy: 58: nr: 0 58: Conserved En.: 58: nr: 0 58: Temperature: 58: nr: 0 58: Vir. Temp.: 58: nr: 0 58: Pres. DC: 58: nr: 0 58: Pressure: 58: nr: 0 58: dH/dl constr.: 58: nr: 0 58: dVremain/dl: 58: nr: 0 58: dEkin/dl: 58: nr: 0 58: dVcoul/dl: 58: nr: 0 58: dVvdw/dl: 58: nr: 0 58: dVbonded/dl: 58: nr: 0 58: dVrestraint/dl: 58: nr: 0 58: dVtemp/dl: 58: nr: 0 58: grp[T-Coupling ] nr=1, name=[ rest] 58: grp[Energy Mon. ] nr=1, name=[ rest] 58: grp[Acc. not used] nr=1, name=[ rest] 58: grp[Freeze ] nr=1, name=[ rest] 58: grp[User1 ] nr=1, name=[ rest] 58: grp[User2 ] nr=1, name=[ rest] 58: grp[VCM ] nr=1, name=[ rest] 58: grp[Compressed X] nr=1, name=[ rest] 58: grp[Or. Res. Fit] nr=1, name=[ rest] 58: grp[QMMM ] nr=1, name=[ rest] 58: grpname (11): 58: grpname[0]={name="System"} 58: grpname[1]={name="Protein"} 58: grpname[2]={name="Protein-H"} 58: grpname[3]={name="C-alpha"} 58: grpname[4]={name="Backbone"} 58: grpname[5]={name="MainChain"} 58: grpname[6]={name="MainChain+Cb"} 58: grpname[7]={name="MainChain+H"} 58: grpname[8]={name="SideChain"} 58: grpname[9]={name="SideChain-H"} 58: grpname[10]={name="rest"} 58: groups T-Cou Energ Acc. Freez User1 User2 VCM Compr Or. R QMMM 58: allocated 0 0 0 0 0 0 0 0 0 0 58: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0 58: box (3x3): 58: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00} 58: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00} 58: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00} 58: box_rel (3x3): 58: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: boxv (3x3): 58: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: pres_prev (3x3): 58: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: svir_prev (3x3): 58: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: fvir_prev (3x3): 58: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: nosehoover_xi: not available 58: x (156x3): 58: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00} 58: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00} 58: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00} 58: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00} 58: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00} 58: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00} 58: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00} 58: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00} 58: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01} 58: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01} 58: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01} 58: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00} 58: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01} 58: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01} 58: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01} 58: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01} 58: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01} 58: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01} 58: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01} 58: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01} 58: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01} 58: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01} 58: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00} 58: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00} 58: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00} 58: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00} 58: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00} 58: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01} 58: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00} 58: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00} 58: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00} 58: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00} 58: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01} 58: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01} 58: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00} 58: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00} 58: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00} 58: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00} 58: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01} 58: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01} 58: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01} 58: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01} 58: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01} 58: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01} 58: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01} 58: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01} 58: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01} 58: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01} 58: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01} 58: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01} 58: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01} 58: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01} 58: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01} 58: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01} 58: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01} 58: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01} 58: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01} 58: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01} 58: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01} 58: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01} 58: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01} 58: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01} 58: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01} 58: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01} 58: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01} 58: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01} 58: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01} 58: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01} 58: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01} 58: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01} 58: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01} 58: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01} 58: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01} 58: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01} 58: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02} 58: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02} 58: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02} 58: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02} 58: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02} 58: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01} 58: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02} 58: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01} 58: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02} 58: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01} 58: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01} 58: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01} 58: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02} 58: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01} 58: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02} 58: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01} 58: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02} 58: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01} 58: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01} 58: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02} 58: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02} 58: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02} 58: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01} 58: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02} 58: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02} 58: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02} 58: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02} 58: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02} 58: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01} 58: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01} 58: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01} 58: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01} 58: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01} 58: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01} 58: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01} 58: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01} 58: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01} 58: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01} 58: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01} 58: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01} 58: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01} 58: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01} 58: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01} 58: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01} 58: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01} 58: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01} 58: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01} 58: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01} 58: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01} 58: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01} 58: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01} 58: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02} 58: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01} 58: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01} 58: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01} 58: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01} 58: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01} 58: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01} 58: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01} 58: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01} 58: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02} 58: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02} 58: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02} 58: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02} 58: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01} 58: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01} 58: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01} 58: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01} 58: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01} 58: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01} 58: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01} 58: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01} 58: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01} 58: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01} 58: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01} 58: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01} 58: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01} 58: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01} 58: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01} 58: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02} 58: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01} 58: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01} 58: v (156x3): 58: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: Group statistics 58: T-Coupling : 156 (total 156 atoms) 58: Energy Mon. : 156 (total 156 atoms) 58: Acc. not used: 156 (total 156 atoms) 58: Freeze : 156 (total 156 atoms) 58: User1 : 156 (total 156 atoms) 58: User2 : 156 (total 156 atoms) 58: VCM : 156 (total 156 atoms) 58: Compressed X: 156 (total 156 atoms) 58: Or. Res. Fit: 156 (total 156 atoms) 58: QMMM : 156 (total 156 atoms) 58: [ OK ] DumpTest.WorksWithTpr (2 ms) 58: [ RUN ] DumpTest.WorksWithTprAndMdpWriting 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: [ OK ] DumpTest.WorksWithTprAndMdpWriting (0 ms) 58: [----------] 2 tests from DumpTest (3 ms total) 58: 58: [----------] 3 tests from HelpwritingTest 58: [ RUN ] HelpwritingTest.ConvertTprWritesHelp 58: [ OK ] HelpwritingTest.ConvertTprWritesHelp (5 ms) 58: [ RUN ] HelpwritingTest.DumpWritesHelp 58: [ OK ] HelpwritingTest.DumpWritesHelp (0 ms) 58: [ RUN ] HelpwritingTest.ReportMethodsWritesHelp 58: [ OK ] HelpwritingTest.ReportMethodsWritesHelp (2 ms) 58: [----------] 3 tests from HelpwritingTest (8 ms total) 58: 58: [----------] 7 tests from GmxMakeNdx 58: [ RUN ] GmxMakeNdx.WritesDefaultProteinIndexGroups 58: 58: Reading structure file 58: Going to read 0 old index file(s) 58: Analysing residue names: 58: There are: 16 Protein residues 58: Analysing Protein... 58: 58: 0 System : 256 atoms 58: 1 Protein : 256 atoms 58: 2 Protein-H : 139 atoms 58: 3 C-alpha : 16 atoms 58: 4 Backbone : 48 atoms 58: 5 MainChain : 63 atoms 58: 6 MainChain+Cb : 78 atoms 58: 7 MainChain+H : 81 atoms 58: 8 SideChain : 175 atoms 58: 9 SideChain-H : 76 atoms 58: 58: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 58: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 58: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 58: 'r': residue 'res' nr 'chain' char 58: "name": group 'case': case sensitive 'q': save and quit 58: 'ri': residue index 58: 58: > 58: [ OK ] GmxMakeNdx.WritesDefaultProteinIndexGroups (4 ms) 58: [ RUN ] GmxMakeNdx.HandlesNoStructureInput 58: Going to read 1 old index file(s) 58: Deducing 22 atoms in the system from indices in the index file 58: 58: 0 System : 22 atoms 58: 1 Protein : 22 atoms 58: 2 Protein-H : 10 atoms 58: 3 C-alpha : 1 atoms 58: 4 Backbone : 5 atoms 58: 5 MainChain : 7 atoms 58: 6 MainChain+Cb : 8 atoms 58: 7 MainChain+H : 9 atoms 58: 8 SideChain : 13 atoms 58: 9 SideChain-H : 3 atoms 58: 10 CA : 1 atoms 58: 11 C_&_r_1 : 1 atoms 58: 12 C_&_r_2 : 1 atoms 58: 13 N_&_r_2 : 1 atoms 58: 14 N_&_r_3 : 1 atoms 58: 58: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 58: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 58: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 58: 'r': residue 'res' nr 'chain' char 58: "name": group 'case': case sensitive 'q': save and quit 58: 'ri': residue index 58: 58: > 58: Copied index group 1 'Protein' 58: Copied index group 2 'Protein-H' 58: Merged two groups with OR: 22 10 -> 22 58: 58: > 58: [ OK ] GmxMakeNdx.HandlesNoStructureInput (8 ms) 58: [ RUN ] GmxMakeNdx.HandlesNotProtein 58: Going to read 1 old index file(s) 58: Deducing 6 atoms in the system from indices in the index file 58: 58: 0 System : 6 atoms 58: 58: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 58: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 58: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 58: 'r': residue 'res' nr 'chain' char 58: "name": group 'case': case sensitive 'q': save and quit 58: 'ri': residue index 58: 58: > 58: [ OK ] GmxMakeNdx.HandlesNotProtein (3 ms) 58: [ RUN ] GmxMakeNdx.HandlesEmptyIndexResult 58: Going to read 1 old index file(s) 58: Deducing 22 atoms in the system from indices in the index file 58: 58: 0 System : 22 atoms 58: 1 Protein : 22 atoms 58: 2 Protein-H : 10 atoms 58: 3 C-alpha : 1 atoms 58: 4 Backbone : 5 atoms 58: 5 MainChain : 7 atoms 58: 6 MainChain+Cb : 8 atoms 58: 7 MainChain+H : 9 atoms 58: 8 SideChain : 13 atoms 58: 9 SideChain-H : 3 atoms 58: 10 CA : 1 atoms 58: 11 C_&_r_1 : 1 atoms 58: 12 C_&_r_2 : 1 atoms 58: 13 N_&_r_2 : 1 atoms 58: 14 N_&_r_3 : 1 atoms 58: 58: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 58: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 58: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 58: 'r': residue 'res' nr 'chain' char 58: "name": group 'case': case sensitive 'q': save and quit 58: 'ri': residue index 58: 58: > 58: Copied index group 4 'Backbone' 58: Copied index group 8 'SideChain' 58: Merged two groups with AND: 5 13 -> 0 58: Group is empty 58: 58: > 58: [ OK ] GmxMakeNdx.HandlesEmptyIndexResult (0 ms) 58: [ RUN ] GmxMakeNdx.HandlesEmptyIndexFile 58: Going to read 1 old index file(s) 58: Deducing 6 atoms in the system from indices in the index file 58: 58: 0 System : 6 atoms 58: 58: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 58: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 58: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 58: 'r': residue 'res' nr 'chain' char 58: "name": group 'case': case sensitive 'q': save and quit 58: 'ri': residue index 58: 58: > 58: Removed group 0 'System' 58: 58: > 58: [ OK ] GmxMakeNdx.HandlesEmptyIndexFile (1 ms) 58: [ RUN ] GmxMakeNdx.Splitres 58: 58: Reading structure file 58: Going to read 0 old index file(s) 58: Analysing residue names: 58: There are: 2 Water residues 58: 58: 0 System : 6 atoms 58: 1 Water : 6 atoms 58: 2 SOL : 6 atoms 58: 58: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 58: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 58: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 58: 'r': residue 'res' nr 'chain' char 58: "name": group 'case': case sensitive 'q': save and quit 58: 'ri': residue index 58: 58: > 58: Splitting group 1 'Water' into residues 58: 58: > 58: [ OK ] GmxMakeNdx.Splitres (2 ms) 58: [ RUN ] GmxMakeNdx.Splitat 58: 58: Reading structure file 58: Going to read 0 old index file(s) 58: Analysing residue names: 58: There are: 2 Water residues 58: 58: 0 System : 6 atoms 58: 1 Water : 6 atoms 58: 2 SOL : 6 atoms 58: 58: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 58: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 58: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 58: 'r': residue 'res' nr 'chain' char 58: "name": group 'case': case sensitive 'q': save and quit 58: 'ri': residue index 58: 58: > 58: Splitting group 1 'Water' into atoms 58: 58: > 58: [ OK ] GmxMakeNdx.Splitat (2 ms) 58: [----------] 7 tests from GmxMakeNdx (24 ms total) 58: 58: [----------] 4 tests from ReportMethodsTest 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file lysozyme.top, line 1465]: 58: System has non-zero total charge: 2.000000 58: Total charge should normally be an integer. See 58: https://manual.gromacs.org/current/user-guide/floating-point.html 58: for discussion on how close it should be to an integer. 58: 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 465.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 58: NVE simulation with an initial temperature of zero: will use a Verlet 58: buffer of 10%. Check your energy drift! 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 4 NOTEs 58: Setting the LD random seed to -68437509 58: 58: Generated 330891 of the 330891 non-bonded parameter combinations 58: 58: Generated 330891 of the 330891 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 58: Analysing residue names: 58: There are: 10 Protein residues 58: Analysing Protein... 58: 58: This run will generate roughly 0 Mb of data 58: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated 58: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms) 58: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted 58: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms) 58: [ RUN ] ReportMethodsTest.WritesCorrectInformation 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: [ OK ] ReportMethodsTest.WritesCorrectInformation (0 ms) 58: [ RUN ] ReportMethodsTest.ToolEndToEndTest 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: section: Methods 58: subsection: Simulation system 58: A system of 1 molecules (156 atoms) was simulated. 58: 58: subsection: Simulation settings 58: A total of 0 ns were simulated with a time step of 1 fs. 58: Neighbor searching was performed every 10 steps. 58: The Cut-off algorithm was used for electrostatic interactions. 58: with a cut-off of 1 nm. 58: A single cut-off of 1.1 nm was used for Van der Waals interactions. 58: [ OK ] ReportMethodsTest.ToolEndToEndTest (0 ms) 58: [----------] 4 tests from ReportMethodsTest (1 ms total) 58: 58: [----------] 4 tests from ConvertTprTest 58: [ RUN ] ConvertTprTest.ExtendRuntimeExtensionTest 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file lysozyme.top, line 1465]: 58: System has non-zero total charge: 2.000000 58: Total charge should normally be an integer. See 58: https://manual.gromacs.org/current/user-guide/floating-point.html 58: for discussion on how close it should be to an integer. 58: 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 465.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 58: NVE simulation with an initial temperature of zero: will use a Verlet 58: buffer of 10%. Check your energy drift! 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 4 NOTEs 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended_again.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Setting the LD random seed to -408290306 58: 58: Generated 330891 of the 330891 non-bonded parameter combinations 58: 58: Generated 330891 of the 330891 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 58: Analysing residue names: 58: There are: 10 Protein residues 58: Analysing Protein... 58: 58: This run will generate roughly 0 Mb of data 58: Input file: 58: Run start step 0 58: Run start time 0 ps 58: Step to be made during run 0 58: Runtime for the run 0 ps 58: Run end step 0 58: Run end time 0 ps 58: 58: Extending remaining runtime by 100 ps 58: 58: Output file: 58: Run start step 0 58: Run start time 0 ps 58: Step to be made during run 100000 58: Runtime for the run 100 ps 58: Run end step 100000 58: Run end time 100 ps 58: 58: Input file: 58: Run start step 0 58: Run start time 0 ps 58: Step to be made during run 100000 58: Runtime for the run 100 ps 58: Run end step 100000 58: Run end time 100 ps 58: 58: Extending remaining runtime by 100 ps 58: 58: Output file: 58: Run start step 0 58: Run start time 0 ps 58: Step to be made during run 200000 58: Runtime for the run 200 ps 58: Run end step 200000 58: Run end time 200 ps 58: 58: [ OK ] ConvertTprTest.ExtendRuntimeExtensionTest (289 ms) 58: [ RUN ] ConvertTprTest.UntilRuntimeExtensionTest 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file lysozyme.top, line 1465]: 58: System has non-zero total charge: 2.000000 58: Total charge should normally be an integer. See 58: https://manual.gromacs.org/current/user-guide/floating-point.html 58: for discussion on how close it should be to an integer. 58: 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 465.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 58: NVE simulation with an initial temperature of zero: will use a Verlet 58: buffer of 10%. Check your energy drift! 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 4 NOTEs 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_extended.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Setting the LD random seed to -134973457 58: 58: Generated 330891 of the 330891 non-bonded parameter combinations 58: 58: Generated 330891 of the 330891 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 58: Analysing residue names: 58: There are: 10 Protein residues 58: Analysing Protein... 58: 58: This run will generate roughly 0 Mb of data 58: Input file: 58: Run start step 0 58: Run start time 0 ps 58: Step to be made during run 0 58: Runtime for the run 0 ps 58: Run end step 0 58: Run end time 0 ps 58: 58: Extending remaining runtime to 100 ps 58: 58: Output file: 58: Run start step 0 58: Run start time 0 ps 58: Step to be made during run 100000 58: Runtime for the run 100 ps 58: Run end step 100000 58: Run end time 100 ps 58: 58: [ OK ] ConvertTprTest.UntilRuntimeExtensionTest (266 ms) 58: [ RUN ] ConvertTprTest.nstepRuntimeExtensionTest 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file lysozyme.top, line 1465]: 58: System has non-zero total charge: 2.000000 58: Total charge should normally be an integer. See 58: https://manual.gromacs.org/current/user-guide/floating-point.html 58: for discussion on how close it should be to an integer. 58: 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 465.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 58: NVE simulation with an initial temperature of zero: will use a Verlet 58: buffer of 10%. Check your energy drift! 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 4 NOTEs 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Setting nsteps to 102 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_extended.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Setting the LD random seed to -264194 58: 58: Generated 330891 of the 330891 non-bonded parameter combinations 58: 58: Generated 330891 of the 330891 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 58: Analysing residue names: 58: There are: 10 Protein residues 58: Analysing Protein... 58: 58: This run will generate roughly 0 Mb of data 58: Input file: 58: Run start step 0 58: Run start time 0 ps 58: Step to be made during run 0 58: Runtime for the run 0 ps 58: Run end step 0 58: Run end time 0 ps 58: 58: 58: Output file: 58: Run start step 0 58: Run start time 0 ps 58: Step to be made during run 102 58: Runtime for the run 0.102 ps 58: Run end step 102 58: Run end time 0.102 ps 58: 58: [ OK ] ConvertTprTest.nstepRuntimeExtensionTest (266 ms) 58: [ RUN ] ConvertTprTest.generateVelocitiesTest 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file lysozyme.top, line 1465]: 58: System has non-zero total charge: 2.000000 58: Total charge should normally be an integer. See 58: https://manual.gromacs.org/current/user-guide/floating-point.html 58: for discussion on how close it should be to an integer. 58: 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 465.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 58: NVE simulation with an initial temperature of zero: will use a Verlet 58: buffer of 10%. Check your energy drift! 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 4 NOTEs 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_new_velocities.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Setting the LD random seed to -673185923 58: 58: Generated 330891 of the 330891 non-bonded parameter combinations 58: 58: Generated 330891 of the 330891 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 58: Analysing residue names: 58: There are: 10 Protein residues 58: Analysing Protein... 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] ConvertTprTest.generateVelocitiesTest (416 ms) 58: [----------] 4 tests from ConvertTprTest (1239 ms total) 58: 58: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: trr version: GMX_trn_file (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr (1 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 58: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng (0 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc (8 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 58: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro (0 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 58: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 58: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb (0 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 (0 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr (0 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 58: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng (0 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc (0 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 58: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro (0 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 58: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 58: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb (0 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 (0 ms) 58: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats (14 ms total) 58: 58: [----------] 30 tests from Works/TrjconvDumpTest 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 (4 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 (1 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 (4 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 58: Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 58: Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 58: Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 58: Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 58: Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 58: Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 (4 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 58: Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 58: Will write trr: Trajectory in portable xdr format 58: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 58: Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 58: Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 58: Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 58: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 58: Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 58: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 58: Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 58: Will write trr: Trajectory in portable xdr format 58: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 58: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 58: Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 58: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 58: Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 58: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 58: Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 (8 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 (0 ms) 58: [----------] 30 tests from Works/TrjconvDumpTest (33 ms total) 58: 58: [----------] Global test environment tear-down 58: [==========] 62 tests from 7 test suites ran. (1953 ms total) 58: [ PASSED ] 62 tests. 58/87 Test #58: ToolUnitTests ............................. Passed 1.98 sec test 59 Start 59: FileIOTests 59: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/fileio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/FileIOTests.xml" 59: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fileio/tests 59: Test timeout computed to be: 30 59: [==========] Running 413 tests from 15 test suites. 59: [----------] Global test environment set-up. 59: [----------] 4 tests from Checkpoint 59: [ RUN ] Checkpoint.ReadingThrowsWhenValueNotPresent 59: [ OK ] Checkpoint.ReadingThrowsWhenValueNotPresent (0 ms) 59: [ RUN ] Checkpoint.ReadingDoesNotThrowWhenValuePresent 59: [ OK ] Checkpoint.ReadingDoesNotThrowWhenValuePresent (0 ms) 59: [ RUN ] Checkpoint.KvtRoundTripInt64 59: [ OK ] Checkpoint.KvtRoundTripInt64 (0 ms) 59: [ RUN ] Checkpoint.KvtRoundTripReal 59: [ OK ] Checkpoint.KvtRoundTripReal (0 ms) 59: [----------] 4 tests from Checkpoint (0 ms total) 59: 59: [----------] 1 test from StructureIOTest 59: [ RUN ] StructureIOTest.ReadTpsConfRetainsChainids 59: [ OK ] StructureIOTest.ReadTpsConfRetainsChainids (0 ms) 59: [----------] 1 test from StructureIOTest (0 ms total) 59: 59: [----------] 2 tests from FileMD5Test 59: [ RUN ] FileMD5Test.CanComputeMD5 59: [ OK ] FileMD5Test.CanComputeMD5 (7 ms) 59: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 59: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 59: [----------] 2 tests from FileMD5Test (8 ms total) 59: 59: [----------] 4 tests from FileTypeTest 59: [ RUN ] FileTypeTest.CorrectValueForEmptyString 59: [ OK ] FileTypeTest.CorrectValueForEmptyString (0 ms) 59: [ RUN ] FileTypeTest.CorrectValueForNoExtension 59: [ OK ] FileTypeTest.CorrectValueForNoExtension (0 ms) 59: [ RUN ] FileTypeTest.CorrectValueForEmptyExtension 59: [ OK ] FileTypeTest.CorrectValueForEmptyExtension (0 ms) 59: [ RUN ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters 59: [ OK ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters (0 ms) 59: [----------] 4 tests from FileTypeTest (0 ms total) 59: 59: [----------] 3 tests from MrcSerializer 59: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet 59: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms) 59: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize 59: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms) 59: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip 59: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (0 ms) 59: [----------] 3 tests from MrcSerializer (0 ms total) 59: 59: [----------] 4 tests from MrcDensityMap 59: [ RUN ] MrcDensityMap.RoundTripIsIdempotent 59: [ OK ] MrcDensityMap.RoundTripIsIdempotent (0 ms) 59: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent 59: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms) 59: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile 59: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms) 59: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile 59: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (1 ms) 59: [----------] 4 tests from MrcDensityMap (1 ms total) 59: 59: [----------] 8 tests from MrcDensityMapHeaderTest 59: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader 59: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms) 59: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect 59: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms) 59: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid 59: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms) 59: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven 59: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms) 59: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined 59: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms) 59: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues 59: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms) 59: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents 59: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms) 59: [ RUN ] MrcDensityMapHeaderTest.IsSane 59: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms) 59: [----------] 8 tests from MrcDensityMapHeaderTest (0 ms total) 59: 59: [----------] 10 tests from ReadTest 59: [ RUN ] ReadTest.get_eint_ReadsInteger 59: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 59: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 59: 59: ERROR 1 [file unknown]: 59: Right hand side '0.8' for parameter 'test' in parameter file is not an 59: integer value 59: 59: 59: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 59: [ RUN ] ReadTest.get_eint_WarnsAboutString 59: 59: ERROR 1 [file unknown]: 59: Right hand side 'hello' for parameter 'test' in parameter file is not an 59: integer value 59: 59: 59: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 59: [ RUN ] ReadTest.get_eint64_ReadsInteger 59: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 59: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 59: 59: ERROR 1 [file unknown]: 59: Right hand side '0.8' for parameter 'test' in parameter file is not an 59: integer value 59: 59: 59: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 59: [ RUN ] ReadTest.get_eint64_WarnsAboutString 59: 59: ERROR 1 [file unknown]: 59: Right hand side 'hello' for parameter 'test' in parameter file is not an 59: integer value 59: 59: 59: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 59: [ RUN ] ReadTest.get_ereal_ReadsInteger 59: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 59: [ RUN ] ReadTest.get_ereal_ReadsFloat 59: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 59: [ RUN ] ReadTest.get_ereal_WarnsAboutString 59: 59: ERROR 1 [file unknown]: 59: Right hand side 'hello' for parameter 'test' in parameter file is not a 59: real value 59: 59: 59: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 59: [ RUN ] ReadTest.setStringEntry_ReturnsCorrectString 59: [ OK ] ReadTest.setStringEntry_ReturnsCorrectString (0 ms) 59: [----------] 10 tests from ReadTest (1 ms total) 59: 59: [----------] 3 tests from TimeControlTest 59: [ RUN ] TimeControlTest.UnSetHasNoValue 59: [ OK ] TimeControlTest.UnSetHasNoValue (0 ms) 59: [ RUN ] TimeControlTest.CanSetValue 59: [ OK ] TimeControlTest.CanSetValue (0 ms) 59: [ RUN ] TimeControlTest.CanUnsetValueAgain 59: [ OK ] TimeControlTest.CanUnsetValueAgain (0 ms) 59: [----------] 3 tests from TimeControlTest (0 ms total) 59: 59: [----------] 1 test from FileIOXdrSerializerTest 59: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect 59: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (0 ms) 59: [----------] 1 test from FileIOXdrSerializerTest (0 ms total) 59: 59: [----------] 1 test from TngTest 59: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 59: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 59: [----------] 1 test from TngTest (0 ms total) 59: 59: [----------] 4 tests from XvgioTest 59: [ RUN ] XvgioTest.readXvgIntWorks 59: [ OK ] XvgioTest.readXvgIntWorks (0 ms) 59: [ RUN ] XvgioTest.readXvgRealWorks 59: [ OK ] XvgioTest.readXvgRealWorks (0 ms) 59: [ RUN ] XvgioTest.readXvgIgnoreCommentLineWorks 59: [ OK ] XvgioTest.readXvgIgnoreCommentLineWorks (0 ms) 59: [ RUN ] XvgioTest.readXvgDeprecatedWorks 59: [ OK ] XvgioTest.readXvgDeprecatedWorks (0 ms) 59: [----------] 4 tests from XvgioTest (0 ms total) 59: 59: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 59: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 59: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (6 ms) 59: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 59: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (0 ms) 59: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 59: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (0 ms) 59: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 59: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (0 ms) 59: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (7 ms total) 59: 59: [----------] 360 tests from FileTypeMatch/FileTypeTest 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 (0 ms) 59: [----------] 360 tests from FileTypeMatch/FileTypeTest (1 ms total) 59: 59: [----------] 4 tests from XvgReadTimeSeries/XvgioTest 59: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 59: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 (9 ms) 59: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 59: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 (0 ms) 59: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 59: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 (0 ms) 59: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 59: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 (2 ms) 59: [----------] 4 tests from XvgReadTimeSeries/XvgioTest (14 ms total) 59: 59: [----------] Global test environment tear-down 59: [==========] 413 tests from 15 test suites ran. (35 ms total) 59: [ PASSED ] 413 tests. 59/87 Test #59: FileIOTests ............................... Passed 0.07 sec test 60 Start 60: SelectionUnitTests 60: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/selection-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/SelectionUnitTests.xml" 60: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/selection/tests 60: Test timeout computed to be: 30 60: [==========] Running 201 tests from 11 test suites. 60: [----------] Global test environment set-up. 60: [----------] 1 test from IndexGroupTest 60: [ RUN ] IndexGroupTest.RemovesDuplicates 60: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) 60: [----------] 1 test from IndexGroupTest (0 ms total) 60: 60: [----------] 15 tests from IndexBlockTest 60: [ RUN ] IndexBlockTest.CreatesUnknownBlock 60: [ OK ] IndexBlockTest.CreatesUnknownBlock (0 ms) 60: [ RUN ] IndexBlockTest.CreatesAtomBlock 60: [ OK ] IndexBlockTest.CreatesAtomBlock (0 ms) 60: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology 60: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (0 ms) 60: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology 60: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (0 ms) 60: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology 60: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms) 60: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology 60: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (0 ms) 60: [ RUN ] IndexBlockTest.CreatesSingleBlock 60: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms) 60: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive 60: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (1 ms) 60: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive 60: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) 60: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative 60: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) 60: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial 60: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) 60: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive 60: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) 60: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative 60: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) 60: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive 60: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) 60: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative 60: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) 60: [----------] 15 tests from IndexBlockTest (6 ms total) 60: 60: [----------] 11 tests from IndexMapTest 60: [ RUN ] IndexMapTest.InitializesAtomBlock 60: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms) 60: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom 60: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (3 ms) 60: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle 60: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms) 60: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue 60: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms) 60: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule 60: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms) 60: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll 60: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms) 60: [ RUN ] IndexMapTest.InitializesMoleculeBlock 60: [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms) 60: [ RUN ] IndexMapTest.MapsSingleBlock 60: [ OK ] IndexMapTest.MapsSingleBlock (0 ms) 60: [ RUN ] IndexMapTest.MapsResidueBlocks 60: [ OK ] IndexMapTest.MapsResidueBlocks (0 ms) 60: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask 60: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (0 ms) 60: [ RUN ] IndexMapTest.HandlesMultipleRequests 60: [ OK ] IndexMapTest.HandlesMultipleRequests (0 ms) 60: [----------] 11 tests from IndexMapTest (11 ms total) 60: 60: [----------] 3 tests from IndexGroupsAndNamesTest 60: [ RUN ] IndexGroupsAndNamesTest.containsNames 60: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms) 60: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing 60: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms) 60: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect 60: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms) 60: [----------] 3 tests from IndexGroupsAndNamesTest (0 ms total) 60: 60: [----------] 15 tests from NeighborhoodSearchTest 60: [ RUN ] NeighborhoodSearchTest.SimpleSearch 60: [ OK ] NeighborhoodSearchTest.SimpleSearch (23 ms) 60: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 60: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (22 ms) 60: [ RUN ] NeighborhoodSearchTest.GridSearchBox 60: [ OK ] NeighborhoodSearchTest.GridSearchBox (1 ms) 60: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 60: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (14 ms) 60: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 60: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (2 ms) 60: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 60: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (4 ms) 60: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 60: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (1 ms) 60: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 60: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) 60: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 60: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (55 ms) 60: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches 60: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms) 60: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC 60: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) 60: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC 60: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) 60: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs 60: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) 60: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions 60: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (6 ms) 60: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 60: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (0 ms) 60: [----------] 15 tests from NeighborhoodSearchTest (134 ms total) 60: 60: [----------] 13 tests from PositionCalculationTest 60: [ RUN ] PositionCalculationTest.ComputesAtomPositions 60: [ OK ] PositionCalculationTest.ComputesAtomPositions (1 ms) 60: [ RUN ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex 60: [ OK ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex (0 ms) 60: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions 60: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (0 ms) 60: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions 60: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (0 ms) 60: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions 60: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms) 60: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions 60: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms) 60: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole 60: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms) 60: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax 60: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (0 ms) 60: [ RUN ] PositionCalculationTest.ComputesPositionMask 60: [ OK ] PositionCalculationTest.ComputesPositionMask (0 ms) 60: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms 60: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (0 ms) 60: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 60: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms) 60: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations 60: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (0 ms) 60: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations 60: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (5 ms) 60: [----------] 13 tests from PositionCalculationTest (15 ms total) 60: 60: [----------] 33 tests from SelectionCollectionTest 60: [ RUN ] SelectionCollectionTest.HandlesNoSelections 60: [ OK ] SelectionCollectionTest.HandlesNoSelections (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType 60: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (1 ms) 60: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests 60: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry 60: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (0 ms) 60: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile 60: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace 60: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions 60: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue 60: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 60: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 60: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 60: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 60: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 60: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 60: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference 60: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed 60: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup 60: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed 60: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 60: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (0 ms) 60: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo 60: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (0 ms) 60: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes 60: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (0 ms) 60: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo 60: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (0 ms) 60: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation 60: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (0 ms) 60: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 60: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (0 ms) 60: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 60: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets 60: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 60: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 60: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 60: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (4 ms) 60: [ RUN ] SelectionCollectionTest.RetrieveValidSelection 60: [ OK ] SelectionCollectionTest.RetrieveValidSelection (0 ms) 60: [ RUN ] SelectionCollectionTest.RetrieveInvalidSelection 60: [ OK ] SelectionCollectionTest.RetrieveInvalidSelection (0 ms) 60: [ RUN ] SelectionCollectionTest.CanCopyEmptyCollection 60: [ OK ] SelectionCollectionTest.CanCopyEmptyCollection (0 ms) 60: [ RUN ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately 60: [ OK ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately (0 ms) 60: [----------] 33 tests from SelectionCollectionTest (12 ms total) 60: 60: [----------] 14 tests from SelectionCollectionInteractiveTest 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput 60: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (1 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation 60: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (0 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput 60: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (0 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput 60: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (0 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups 60: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (0 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections 60: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (6 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus 60: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (0 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus 60: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (0 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus 60: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (0 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline 60: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (0 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections 60: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (1 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine 60: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (0 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput 60: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (0 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively 60: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (0 ms) 60: [----------] 14 tests from SelectionCollectionInteractiveTest (18 ms total) 60: 60: [----------] 70 tests from SelectionCollectionDataTest 60: [ RUN ] SelectionCollectionDataTest.HandlesAllNone 60: [ OK ] SelectionCollectionDataTest.HandlesAllNone (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr 60: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesResnr 60: [ OK ] SelectionCollectionDataTest.HandlesResnr (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesResIndex 60: [ OK ] SelectionCollectionDataTest.HandlesResIndex (1 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex 60: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesAtomname 60: [ OK ] SelectionCollectionDataTest.HandlesAtomname (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname 60: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype 60: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesChain 60: [ OK ] SelectionCollectionDataTest.HandlesChain (5 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesMass 60: [ OK ] SelectionCollectionDataTest.HandlesMass (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesCharge 60: [ OK ] SelectionCollectionDataTest.HandlesCharge (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc 60: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode 60: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy 60: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesBeta 60: [ OK ] SelectionCollectionDataTest.HandlesBeta (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesResname 60: [ OK ] SelectionCollectionDataTest.HandlesResname (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords 60: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (1 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue 60: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (1 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName 60: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords 60: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (2 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 60: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (1 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword 60: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (6 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword 60: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (1 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword 60: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (4 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 60: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (8 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 60: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (2 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 60: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (5 ms) 60: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 60: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (1 ms) 60: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 60: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (4 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 60: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (1 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 60: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 60: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (1 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 60: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (1 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 60: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (1 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed 60: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions 60: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (1 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers 60: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions 60: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (3 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges 60: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges 60: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode 60: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching 60: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching 60: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 60: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (7 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 60: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (1 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions 60: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame 60: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords 60: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods 60: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions 60: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic 60: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons 60: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (1 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 60: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (1 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 60: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 60: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (1 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 60: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (1 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 60: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 60: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (1 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 60: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (5 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis 60: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables 60: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables 60: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables 60: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups 60: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups 60: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 60: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (0 ms) 60: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation 60: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation (1 ms) 60: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation 60: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation (4 ms) 60: [ RUN ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent 60: [ OK ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent (1 ms) 60: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation 60: [ OK ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation (1 ms) 60: [----------] 70 tests from SelectionCollectionDataTest (125 ms total) 60: 60: [----------] 17 tests from SelectionOptionTest 60: [ RUN ] SelectionOptionTest.ParsesSimpleSelection 60: [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired 60: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired 60: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (0 ms) 60: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired 60: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (0 ms) 60: [ RUN ] SelectionOptionTest.ChecksEmptySelections 60: [ OK ] SelectionOptionTest.ChecksEmptySelections (0 ms) 60: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections 60: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesTooManySelections 60: [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesTooFewSelections 60: [ OK ] SelectionOptionTest.HandlesTooFewSelections (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText 60: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesAdjuster 60: [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster 60: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster 60: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster 60: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection 60: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections 60: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection 60: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster 60: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms) 60: [----------] 17 tests from SelectionOptionTest (1 ms total) 60: 60: [----------] 9 tests from SelectionFileOptionTest 60: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile 60: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (0 ms) 60: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions 60: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (0 ms) 60: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile 60: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms) 60: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile 60: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (0 ms) 60: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet 60: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (0 ms) 60: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile 60: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (0 ms) 60: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile 60: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms) 60: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile 60: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (0 ms) 60: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles 60: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (0 ms) 60: [----------] 9 tests from SelectionFileOptionTest (1 ms total) 60: 60: [----------] Global test environment tear-down 60: [==========] 201 tests from 11 test suites ran. (326 ms total) 60: [ PASSED ] 201 tests. 60/87 Test #60: SelectionUnitTests ........................ Passed 0.37 sec test 61 Start 61: MdrunOutputTests 61: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunOutputTests.xml" 61: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 61: Test timeout computed to be: 600 61: [==========] Running 12 tests from 5 test suites. 61: [----------] Global test environment set-up. 61: [----------] 1 test from MdrunTest 61: [ RUN ] MdrunTest.WritesHelp 61: [ OK ] MdrunTest.WritesHelp (35 ms) 61: [----------] 1 test from MdrunTest (35 ms total) 61: 61: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput 61: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 61: Generating 1-4 interactions: fudge = 0.5 61: Number of degrees of freedom in T-Coupling group rest is 9.00 61: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 61: NVE simulation: will use the initial temperature of 2573.591 K for 61: determining the Verlet buffer size 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 2 NOTEs 61: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc2' 61: 1 steps, 0.0 ps. 61: Setting the LD random seed to -285512329 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Generated 3 of the 3 1-4 parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 61: 61: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.519 0.260 200.0 61: (ns/day) (hour/ns) 61: Performance: 0.665 36.065 61: Reading frame 0 time 0.000 61: # Atoms 6 61: Reading frame 1 time 0.001 Last frame 1 time 0.001 61: 61: 61: Item #frames Timestep (ps) 61: Step 2 0.001 61: Time 2 0.001 61: Lambda 0 61: Coords 2 0.001 61: Velocities 0 61: Forces 0 61: Box 2 0.001 61: Checking file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc 61: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (277 ms) 61: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 61: Generating 1-4 interactions: fudge = 0.5 61: Number of degrees of freedom in T-Coupling group rest is 9.00 61: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 61: NVE simulation: will use the initial temperature of 2573.591 K for 61: determining the Verlet buffer size 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 2 NOTEs 61: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc2' 61: 1 steps, 0.0 ps. 61: Setting the LD random seed to -12944529 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Generated 3 of the 3 1-4 parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 61: 61: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.664 0.332 200.0 61: (ns/day) (hour/ns) 61: Performance: 0.521 46.097 61: Reading frame 0 time 0.000 61: # Atoms 6 61: Reading frame 1 time 0.001 Last frame 1 time 0.001 61: 61: 61: Item #frames Timestep (ps) 61: Step 2 0.001 61: Time 2 0.001 61: Lambda 0 61: Coords 2 0.001 61: Velocities 0 61: Forces 0 61: Box 2 0.001 61: Checking file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc 61: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (335 ms) 61: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 61: Generating 1-4 interactions: fudge = 0.5 61: Number of degrees of freedom in T-Coupling group rest is 9.00 61: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 61: NVE simulation: will use the initial temperature of 2573.591 K for 61: determining the Verlet buffer size 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 2 NOTEs 61: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc2' 61: 1 steps, 0.0 ps. 61: Setting the LD random seed to -1073743873 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Generated 3 of the 3 1-4 parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 61: 61: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.637 0.319 200.0 61: (ns/day) (hour/ns) 61: Performance: 0.542 44.257 61: Reading frame 0 time 0.000 61: # Atoms 3 61: Reading frame 1 time 0.001 Last frame 1 time 0.001 61: 61: 61: Item #frames Timestep (ps) 61: Step 2 0.001 61: Time 2 0.001 61: Lambda 0 61: Coords 2 0.001 61: Velocities 0 61: Forces 0 61: Box 2 0.001 61: Checking file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc 61: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (322 ms) 61: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (935 ms total) 61: 61: [----------] 2 tests from Argon12/OutputFiles 61: [ RUN ] Argon12/OutputFiles.FilesArePresent/0 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Number of degrees of freedom in T-Coupling group System is 33.00 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 61: NVE simulation: will use the initial temperature of 68.810 K for 61: determining the Verlet buffer size 61: 61: 61: There were 3 NOTEs 61: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'Argon' 61: 16 steps, 0.0 ps. 61: Generated 1 of the 1 non-bonded parameter combinations 61: 61: Excluding 1 bonded neighbours molecule type 'Argon' 61: 61: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 61: 61: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.040 0.020 199.5 61: (ns/day) (hour/ns) 61: Performance: 73.278 0.328 61: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (86 ms) 61: [ RUN ] Argon12/OutputFiles.FilesArePresent/1 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Number of degrees of freedom in T-Coupling group System is 33.00 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 61: NVE simulation: will use the initial temperature of 68.810 K for 61: determining the Verlet buffer size 61: 61: 61: There were 3 NOTEs 61: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'Argon' 61: 16 steps, 0.0 ps. 61: Generated 1 of the 1 non-bonded parameter combinations 61: 61: Excluding 1 bonded neighbours molecule type 'Argon' 61: 61: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 61: 61: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.072 0.036 199.3 61: (ns/day) (hour/ns) 61: Performance: 40.468 0.593 61: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (63 ms) 61: [----------] 2 tests from Argon12/OutputFiles (150 ms total) 61: 61: [----------] 3 tests from MdrunCanWrite/Trajectories 61: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 61: Number of degrees of freedom in T-Coupling group System is 12.00 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There was 1 NOTE 61: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 61: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 61: 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc-and-methanol' 61: 6 steps, 0.0 ps. 61: Setting the LD random seed to 2115239863 61: 61: Generated 8 of the 10 non-bonded parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'Methanol' 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 61: 61: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.116 0.058 199.8 61: (ns/day) (hour/ns) 61: Performance: 10.409 2.306 61: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (69 ms) 61: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 61: Number of degrees of freedom in T-Coupling group System is 12.00 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There was 1 NOTE 61: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 61: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 61: 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc-and-methanol' 61: 6 steps, 0.0 ps. 61: Setting the LD random seed to -272837697 61: 61: Generated 8 of the 10 non-bonded parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'Methanol' 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 61: 61: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.038 0.019 199.6 61: (ns/day) (hour/ns) 61: Performance: 31.436 0.763 61: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (35 ms) 61: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 61: Number of degrees of freedom in T-Coupling group System is 12.00 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There was 1 NOTE 61: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 61: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 61: 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc-and-methanol' 61: 6 steps, 0.0 ps. 61: Setting the LD random seed to -637541665 61: 61: Generated 8 of the 10 non-bonded parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'Methanol' 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 61: 61: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.057 0.030 190.5 61: (ns/day) (hour/ns) 61: Performance: 20.068 1.196 61: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (37 ms) 61: [----------] 3 tests from MdrunCanWrite/Trajectories (143 ms total) 61: 61: [----------] 3 tests from MdrunCanWrite/NptTrajectories 61: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 61: Number of degrees of freedom in T-Coupling group System is 12.00 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There was 1 NOTE 61: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 61: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 61: 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc-and-methanol' 61: 2 steps, 0.0 ps. 61: Setting the LD random seed to 1056306143 61: 61: Generated 8 of the 10 non-bonded parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'Methanol' 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 61: 61: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.036 0.018 199.5 61: (ns/day) (hour/ns) 61: Performance: 14.334 1.674 61: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (26 ms) 61: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 61: 61: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 61: The Berendsen barostat does not generate any strictly correct ensemble, 61: and should not be used for new production simulations (in our opinion). 61: We recommend using the C-rescale barostat instead. 61: 61: Number of degrees of freedom in T-Coupling group System is 12.00 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There was 1 NOTE 61: 61: There was 1 WARNING 61: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 61: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 61: 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc-and-methanol' 61: 2 steps, 0.0 ps. 61: Setting the LD random seed to -1178084405 61: 61: Generated 8 of the 10 non-bonded parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'Methanol' 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 61: 61: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.023 0.012 199.4 61: (ns/day) (hour/ns) 61: Performance: 22.149 1.084 61: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (25 ms) 61: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 61: Number of degrees of freedom in T-Coupling group System is 12.00 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There was 1 NOTE 61: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 61: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 61: 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc-and-methanol' 61: 2 steps, 0.0 ps. 61: Setting the LD random seed to -551687283 61: 61: Generated 8 of the 10 non-bonded parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'Methanol' 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 61: 61: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.030 0.015 199.3 61: (ns/day) (hour/ns) 61: Performance: 17.292 1.388 61: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (101 ms) 61: [----------] 3 tests from MdrunCanWrite/NptTrajectories (153 ms total) 61: 61: [----------] Global test environment tear-down 61: [==========] 12 tests from 5 test suites ran. (1547 ms total) 61: [ PASSED ] 12 tests. 61/87 Test #61: MdrunOutputTests .......................... Passed 1.58 sec test 62 Start 62: MdrunModulesTests 62: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunModulesTests.xml" 62: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 62: Test timeout computed to be: 600 62: [==========] Running 15 tests from 3 test suites. 62: [----------] Global test environment set-up. 62: [----------] 9 tests from DensityFittingTest 62: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct 62: Number of degrees of freedom in T-Coupling group rest is 33.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: 62: Steepest Descents: 62: Tolerance (Fmax) = 1.00000e+01 62: Number of steps = 2 62: 62: Energy minimization reached the maximum number of steps before the forces 62: reached the requested precision Fmax < 10. 62: 62: writing lowest energy coordinates. 62: 62: Steepest Descents did not converge to Fmax < 10 in 3 steps. 62: Potential Energy = -3.8565254e+03 62: Maximum force = 4.5099883e+03 on atom 3 62: Norm of force = 1.6816849e+03 62: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as single precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -1082425361 62: 62: Generated 1 of the 1 non-bonded parameter combinations 62: 62: Excluding 1 bonded neighbours molecule type 'Argon' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (59 ms) 62: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation 62: Number of degrees of freedom in T-Coupling group rest is 33.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: 62: Steepest Descents: 62: Tolerance (Fmax) = 1.00000e+01 62: Number of steps = 2 62: 62: Energy minimization reached the maximum number of steps before the forces 62: reached the requested precision Fmax < 10. 62: 62: writing lowest energy coordinates. 62: 62: Steepest Descents did not converge to Fmax < 10 in 3 steps. 62: Potential Energy = -9.8207725e+03 62: Maximum force = 7.3954834e+03 on atom 2 62: Norm of force = 2.7825089e+03 62: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.edr as single precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to 1874837368 62: 62: Generated 1 of the 1 non-bonded parameter combinations 62: 62: Excluding 1 bonded neighbours molecule type 'Argon' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation (18 ms) 62: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff 62: 62: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 62: [ OK ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff (10 ms) 62: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix 62: Number of degrees of freedom in T-Coupling group rest is 33.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 62: Overriding nsteps with value passed on the command line: 4 steps 62: 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: 62: Steepest Descents: 62: Tolerance (Fmax) = 1.00000e+01 62: Number of steps = 4 62: 62: Energy minimization reached the maximum number of steps before the forces 62: reached the requested precision Fmax < 10. 62: 62: writing lowest energy coordinates. 62: 62: Steepest Descents did not converge to Fmax < 10 in 5 steps. 62: Potential Energy = -1.0954993e+04 62: Maximum force = 7.4724790e+03 on atom 2 62: Norm of force = 2.7758003e+03 62: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.edr as single precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Setting the LD random seed to 2013248435 62: 62: Generated 1 of the 1 non-bonded parameter combinations 62: 62: Excluding 1 bonded neighbours molecule type 'Argon' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix (11 ms) 62: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff 62: 62: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 62: [ OK ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff (7 ms) 62: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix 62: Number of degrees of freedom in T-Coupling group rest is 33.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: 62: Steepest Descents: 62: Tolerance (Fmax) = 1.00000e+01 62: Number of steps = 2 62: 62: Energy minimization reached the maximum number of steps before the forces 62: reached the requested precision Fmax < 10. 62: 62: writing lowest energy coordinates. 62: 62: Steepest Descents did not converge to Fmax < 10 in 3 steps. 62: Potential Energy = -3.8565254e+03 62: Maximum force = 4.5099883e+03 on atom 3 62: Norm of force = 1.6816849e+03 62: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.edr as single precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to 2140716911 62: 62: Generated 1 of the 1 non-bonded parameter combinations 62: 62: Excluding 1 bonded neighbours molecule type 'Argon' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix (8 ms) 62: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy 62: Number of degrees of freedom in T-Coupling group rest is 33.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: 62: Steepest Descents: 62: Tolerance (Fmax) = 1.00000e+01 62: Number of steps = 2 62: 62: Energy minimization reached the maximum number of steps before the forces 62: reached the requested precision Fmax < 10. 62: 62: writing lowest energy coordinates. 62: 62: Steepest Descents did not converge to Fmax < 10 in 3 steps. 62: Potential Energy = -2.7138664e+04 62: Maximum force = 6.7827656e+03 on atom 2 62: Norm of force = 1.9608866e+03 62: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as single precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -380294148 62: 62: Generated 1 of the 1 non-bonded parameter combinations 62: 62: Excluding 1 bonded neighbours molecule type 'Argon' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (8 ms) 62: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch 62: 62: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 62: Setting the LD random seed to -621029697 62: 62: Generated 1 of the 1 non-bonded parameter combinations 62: 62: Excluding 1 bonded neighbours molecule type 'Argon' 62: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (11 ms) 62: [ RUN ] DensityFittingTest.CheckpointWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstenergy (2) 62: 62: Number of degrees of freedom in T-Coupling group rest is 33.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 62: NVE simulation: will use the initial temperature of 68.810 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'Argon' 62: 2 steps, 0.0 ps. 62: Setting the LD random seed to 2012196095 62: 62: Generated 1 of the 1 non-bonded parameter combinations 62: 62: Excluding 1 bonded neighbours molecule type 'Argon' 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.075 0.037 199.6 62: (ns/day) (hour/ns) 62: Performance: 6.937 3.460 62: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 62: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps 62: Can not increase nstlist because an NVE ensemble is used 62: 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'Argon' 62: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps). 62: 62: Writing final coordinates. 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.017 0.009 199.2 62: (ns/day) (hour/ns) 62: Performance: 49.596 0.484 62: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as single precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (87 ms) 62: [----------] 9 tests from DensityFittingTest (224 ms total) 62: 62: [----------] 4 tests from MimicTest 62: [ RUN ] MimicTest.OneQuantumMol 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 3 NOTEs 62: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/4water.gro' 62: 62: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: 62: NOTE: 15 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.000 0.000 184.2 62: (ns/day) (hour/ns) 62: Performance: 470.023 0.051 62: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file 62: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -67453025 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] MimicTest.OneQuantumMol (7 ms) 62: [ RUN ] MimicTest.AllQuantumMol 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 3 NOTEs 62: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/4water.gro' 62: 62: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.000 0.000 187.1 62: (ns/day) (hour/ns) 62: Performance: 344.148 0.070 62: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file 62: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 2045967359 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] MimicTest.AllQuantumMol (18 ms) 62: [ RUN ] MimicTest.TwoQuantumMol 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 3 NOTEs 62: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/4water.gro' 62: 62: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.014 0.007 199.0 62: (ns/day) (hour/ns) 62: Performance: 12.039 1.994 62: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file 62: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 2071965463 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] MimicTest.TwoQuantumMol (30 ms) 62: [ RUN ] MimicTest.BondCuts 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: Number of degrees of freedom in T-Coupling group rest is 66.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 62: NVE simulation: will use the initial temperature of 300.368 K for 62: determining the Verlet buffer size 62: 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 3 NOTEs 62: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/ala.gro' 62: 62: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: 62: NOTE: 40 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.160 0.080 199.9 62: (ns/day) (hour/ns) 62: Performance: 1.078 22.260 62: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file 62: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -622862401 62: 62: Generated 2211 of the 2211 non-bonded parameter combinations 62: 62: Generated 2211 of the 2211 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] MimicTest.BondCuts (119 ms) 62: [----------] 4 tests from MimicTest (176 ms total) 62: 62: [----------] 2 tests from WithIntegrator/ImdTest 62: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0 62: Generating 1-4 interactions: fudge = 1 62: 62: NOTE 1 [file glycine_vacuo.top, line 12]: 62: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an 62: estimated oscillational period of 1.0e-02 ps, which is less than 10 times 62: the time step of 2.0e-03 ps. 62: Maybe you forgot to change the constraints mdp option. 62: 62: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 62: Number of degrees of freedom in T-Coupling group System is 27.00 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 2 NOTEs 62: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 62: Changing nstlist from 10 to 25, rlist from 1.071 to 1.232 62: 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: 62: IMD: Enabled. This simulation will accept incoming IMD connections. 62: IMD: Pulling from IMD remote is enabled (-imdpull). 62: IMD: Setting port for connection requests to 0. 62: IMD: Setting up incoming socket. 62: IMD: Listening for IMD connection on port 43713. 62: IMD: -imdwait not set, starting simulation. 62: starting mdrun 'Glycine' 62: 2 steps, 0.0 ps. 62: Setting the LD random seed to -536875265 62: 62: Generated 20503 of the 20503 non-bonded parameter combinations 62: 62: Generated 17396 of the 20503 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Glycine' 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.071 nm, buffer size 0.071 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.050 0.025 199.6 62: (ns/day) (hour/ns) 62: Performance: 20.514 1.170 62: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (163 ms) 62: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 62: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not 62: apply to steep. 62: 62: Generating 1-4 interactions: fudge = 1 62: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 62: Number of degrees of freedom in T-Coupling group System is 27.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 2 NOTEs 62: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: 62: IMD: Enabled. This simulation will accept incoming IMD connections. 62: IMD: Pulling from IMD remote is enabled (-imdpull). 62: IMD: Setting port for connection requests to 0. 62: IMD: Setting up incoming socket. 62: IMD: Listening for IMD connection on port 53521. 62: IMD: -imdwait not set, starting simulation. 62: 62: Steepest Descents: 62: Tolerance (Fmax) = 1.00000e+01 62: Number of steps = 2 62: 62: Energy minimization reached the maximum number of steps before the forces 62: reached the requested precision Fmax < 10. 62: 62: writing lowest energy coordinates. 62: 62: Steepest Descents did not converge to Fmax < 10 in 3 steps. 62: Potential Energy = 1.1977064e+03 62: Maximum force = 1.7794877e+04 on atom 9 62: Norm of force = 7.8732901e+03 62: Setting the LD random seed to -1413582977 62: 62: Generated 20503 of the 20503 non-bonded parameter combinations 62: 62: Generated 17396 of the 20503 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Glycine' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (59 ms) 62: [----------] 2 tests from WithIntegrator/ImdTest (223 ms total) 62: 62: [----------] Global test environment tear-down 62: [==========] 15 tests from 3 test suites ran. (721 ms total) 62: [ PASSED ] 15 tests. 62/87 Test #62: MdrunModulesTests ......................... Passed 0.75 sec test 63 Start 63: MdrunIOTests 63: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunIOTests.xml" 63: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 63: Test timeout computed to be: 600 63: [==========] Running 76 tests from 13 test suites. 63: [----------] Global test environment set-up. 63: [----------] 9 tests from GromppTest 63: [ RUN ] GromppTest.EmptyMdpFileWorks 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 63: NVE simulation: will use the initial temperature of 1046.791 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Setting the LD random seed to -50921721 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] GromppTest.EmptyMdpFileWorks (7 ms) 63: [ RUN ] GromppTest.SimulatedAnnealingWorks 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: Simulated annealing for group rest: Periodic, 4 timepoints 63: Time (ps) Temperature (K) 63: 0.0 298.0 63: 2.0 320.0 63: 4.0 320.0 63: 6.0 298.0 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 63: NVE simulation: will use the initial temperature of 1046.791 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Setting the LD random seed to -1678582871 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] GromppTest.SimulatedAnnealingWorks (5 ms) 63: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: Simulated annealing for group Methanol: Single, 3 timepoints 63: Time (ps) Temperature (K) 63: 0.0 298.0 63: 3.0 280.0 63: 6.0- 270.0 63: Simulated annealing for group SOL: Periodic, 4 timepoints 63: Time (ps) Temperature (K) 63: 0.0 298.0 63: 2.0 320.0 63: 4.0 320.0 63: 6.0 298.0 63: Number of degrees of freedom in T-Coupling group Methanol is 7.20 63: Number of degrees of freedom in T-Coupling group SOL is 4.80 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 63: NVE simulation: will use the initial temperature of 1046.791 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Setting the LD random seed to -13109761 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (7 ms) 63: [ RUN ] GromppTest.DeathTestHandlesNoMaxwarnError 63: Setting the LD random seed to 918545245 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] GromppTest.DeathTestHandlesNoMaxwarnError (11 ms) 63: [ RUN ] GromppTest.HandlesMaxwarn 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: 63: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 63: The Berendsen thermostat does not generate the correct kinetic energy 63: distribution, and should not be used for new production simulations (in 63: our opinion). We would recommend the V-rescale thermostat. 63: 63: Number of degrees of freedom in T-Coupling group System is 12.00 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 2 NOTEs 63: 63: There was 1 WARNING 63: Setting the LD random seed to -1900036325 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] GromppTest.HandlesMaxwarn (2 ms) 63: [ RUN ] GromppTest.MaxwarnShouldBePositive 63: [ OK ] GromppTest.MaxwarnShouldBePositive (0 ms) 63: [ RUN ] GromppTest.ValidTransformationCoord 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: Pull group 1 'SOL' has 3 atoms 63: Pull group 2 'Methanol' has 3 atoms 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 63: NVE simulation: will use the initial temperature of 1046.791 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: Pull group natoms pbc atom distance at start reference at t=0 63: 1 3 5 63: 2 3 2 0.613 nm 0.000 nm 63: 1 3 5 63: 2 3 2 0.613 nm 0.000 nm 63: 63: There were 3 NOTEs 63: Setting the LD random seed to -1218578697 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] GromppTest.ValidTransformationCoord (12 ms) 63: [ RUN ] GromppTest.InvalidTransformationCoord 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: Pull group 1 'SOL' has 3 atoms 63: Pull group 2 'Methanol' has 3 atoms 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 63: NVE simulation: will use the initial temperature of 1046.791 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: Pull group natoms pbc atom distance at start reference at t=0 63: 1 3 5 63: 2 3 2 0.613 nm 0.000 nm 63: 1 3 5 63: 2 3 2 Setting the LD random seed to -68175629 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: [ OK ] GromppTest.InvalidTransformationCoord (13 ms) 63: [ RUN ] GromppTest.RejectCRescaleAndAnisotropic 63: Setting the LD random seed to 1879031419 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: [ OK ] GromppTest.RejectCRescaleAndAnisotropic (13 ms) 63: [----------] 9 tests from GromppTest (76 ms total) 63: 63: [----------] 6 tests from MdrunTerminationTest 63: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There was 1 NOTE 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 2 steps, 0.0 ps. 63: Setting the LD random seed to 1008560591 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.072 0.036 199.7 63: (ns/day) (hour/ns) 63: Performance: 7.225 3.322 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Setting nsteps to 4 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 63: Input file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 2 63: Runtime for the run 0.002 ps 63: Run end step 2 63: Run end time 0.002 ps 63: 63: 63: Output file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 4 63: Runtime for the run 0.004 ps 63: Run end step 4 63: Run end time 0.004 ps 63: 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.019 0.010 199.4 63: (ns/day) (hour/ns) 63: Performance: 26.735 0.898 63: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (77 ms) 63: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There was 1 NOTE 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 10 to 1, rlist from 1.032 to 1 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 100 steps, 0.1 ps. 63: 63: Step 26: Run time exceeded 0.000 hours, will terminate the run within 200 steps 63: Setting the LD random seed to -33820673 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.029 0.015 199.6 63: (ns/day) (hour/ns) 63: Performance: 592.636 0.040 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Setting nsteps to 102 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). 63: Input file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 100 63: Runtime for the run 0.1 ps 63: Run end step 100 63: Run end time 0.1 ps 63: 63: 63: Output file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 102 63: Runtime for the run 0.102 ps 63: Run end step 102 63: Run end time 0.102 ps 63: 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.030 0.015 199.5 63: (ns/day) (hour/ns) 63: Performance: 17.357 1.383 63: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (37 ms) 63: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There was 1 NOTE 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 2 steps, 0.0 ps. 63: Setting the LD random seed to -826377251 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.028 0.014 199.3 63: (ns/day) (hour/ns) 63: Performance: 18.139 1.323 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Setting nsteps to 4 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 63: Input file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 2 63: Runtime for the run 0.002 ps 63: Run end step 2 63: Run end time 0.002 ps 63: 63: 63: Output file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 4 63: Runtime for the run 0.004 ps 63: Run end step 4 63: Run end time 0.004 ps 63: 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.029 0.014 199.5 63: (ns/day) (hour/ns) 63: Performance: 17.973 1.335 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Setting nsteps to 6 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps). 63: Input file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 4 63: Runtime for the run 0.004 ps 63: Run end step 4 63: Run end time 0.004 ps 63: 63: 63: Output file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 6 63: Runtime for the run 0.006 ps 63: Run end step 6 63: Run end time 0.006 ps 63: 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.019 0.010 199.6 63: (ns/day) (hour/ns) 63: Performance: 27.073 0.886 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Setting nsteps to 8 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). 63: Input file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 6 63: Runtime for the run 0.006 ps 63: Run end step 6 63: Run end time 0.006 ps 63: 63: 63: Output file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 8 63: Runtime for the run 0.008 ps 63: Run end step 8 63: Run end time 0.008 ps 63: 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.041 0.020 199.7 63: (ns/day) (hour/ns) 63: Performance: 12.648 1.898 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: NOTE: 28 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.000 0.000 174.4 63: (ns/day) (hour/ns) 63: Performance: 798.211 0.030 63: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (156 ms) 63: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There was 1 NOTE 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 2 steps, 0.0 ps. 63: Setting the LD random seed to -103051753 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.033 0.016 199.4 63: (ns/day) (hour/ns) 63: Performance: 15.870 1.512 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Setting nsteps to 4 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 4 steps, 0.0 ps. 63: Input file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 2 63: Runtime for the run 0.002 ps 63: Run end step 2 63: Run end time 0.002 ps 63: 63: 63: Output file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 4 63: Runtime for the run 0.004 ps 63: Run end step 4 63: Run end time 0.004 ps 63: 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.020 0.010 199.1 63: (ns/day) (hour/ns) 63: Performance: 43.241 0.555 63: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (97 ms) 63: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There was 1 NOTE 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 2 steps, 0.0 ps. 63: Setting the LD random seed to 1945349795 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.016 0.008 199.2 63: (ns/day) (hour/ns) 63: Performance: 31.800 0.755 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Setting nsteps to 4 63: Input file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 2 63: Runtime for the run 0.002 ps 63: Run end step 2 63: Run end time 0.002 ps 63: 63: 63: Output file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 4 63: Runtime for the run 0.004 ps 63: Run end step 4 63: Run end time 0.004 ps 63: 63: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (22 ms) 63: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There was 1 NOTE 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 2 steps, 0.0 ps. 63: Setting the LD random seed to -1590537 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.017 0.009 199.3 63: (ns/day) (hour/ns) 63: Performance: 30.424 0.789 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Setting nsteps to 4 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 63: Input file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 2 63: Runtime for the run 0.002 ps 63: Run end step 2 63: Run end time 0.002 ps 63: 63: 63: Output file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 4 63: Runtime for the run 0.004 ps 63: Run end step 4 63: Run end time 0.004 ps 63: 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.030 0.015 199.4 63: (ns/day) (hour/ns) 63: Performance: 17.134 1.401 63: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (42 ms) 63: [----------] 6 tests from MdrunTerminationTest (434 ms total) 63: 63: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks 63: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 15 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.440 0.220 199.9 63: (ns/day) (hour/ns) 63: Performance: 6.673 3.597 63: trr version: GMX_trn_file (single precision) 63: 63: 63: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (300 ms) 63: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.059 0.030 199.8 63: (ns/day) (hour/ns) 63: Performance: 49.493 0.485 63: 63: 63: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (49 ms) 63: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (350 ms total) 63: 63: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.041 0.020 199.5 63: (ns/day) (hour/ns) 63: Performance: 71.755 0.334 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.029 0.014 199.3 63: (ns/day) (hour/ns) 63: Performance: 54.312 0.442 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.029 0.015 199.6 63: (ns/day) (hour/ns) 63: Performance: 53.183 0.451 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (68 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.120 0.060 199.8 63: (ns/day) (hour/ns) 63: Performance: 24.527 0.979 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: NOTE: 30 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.216 0.108 199.9 63: (ns/day) (hour/ns) 63: Performance: 7.193 3.336 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.028 0.014 199.6 63: (ns/day) (hour/ns) 63: Performance: 54.930 0.437 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (251 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.027 0.014 199.4 63: (ns/day) (hour/ns) 63: Performance: 108.064 0.222 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.044 0.022 199.7 63: (ns/day) (hour/ns) 63: Performance: 35.078 0.684 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.028 0.014 199.7 63: (ns/day) (hour/ns) 63: Performance: 55.875 0.430 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (104 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.038 0.019 199.6 63: (ns/day) (hour/ns) 63: Performance: 77.170 0.311 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.053 0.027 199.7 63: (ns/day) (hour/ns) 63: Performance: 29.152 0.823 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.068 0.034 199.6 63: (ns/day) (hour/ns) 63: Performance: 22.742 1.055 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (96 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.049 0.025 199.7 63: (ns/day) (hour/ns) 63: Performance: 59.640 0.402 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.042 0.021 199.6 63: (ns/day) (hour/ns) 63: Performance: 36.754 0.653 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.107 0.053 199.8 63: (ns/day) (hour/ns) 63: Performance: 14.584 1.646 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (139 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.029 0.015 199.6 63: (ns/day) (hour/ns) 63: Performance: 99.865 0.240 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.046 0.023 199.6 63: (ns/day) (hour/ns) 63: Performance: 33.883 0.708 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.074 0.037 199.8 63: (ns/day) (hour/ns) 63: Performance: 20.934 1.146 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (95 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.070 0.035 199.8 63: (ns/day) (hour/ns) 63: Performance: 42.189 0.569 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.059 0.030 195.2 63: (ns/day) (hour/ns) 63: Performance: 25.723 0.933 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 53 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.122 0.061 199.9 63: (ns/day) (hour/ns) 63: Performance: 12.767 1.880 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (178 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.059 0.029 199.7 63: (ns/day) (hour/ns) 63: Performance: 49.868 0.481 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.030 0.015 199.6 63: (ns/day) (hour/ns) 63: Performance: 51.331 0.468 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.052 0.026 199.6 63: (ns/day) (hour/ns) 63: Performance: 29.821 0.805 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (93 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.039 0.020 199.6 63: (ns/day) (hour/ns) 63: Performance: 74.252 0.323 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.020 0.010 199.4 63: (ns/day) (hour/ns) 63: Performance: 77.877 0.308 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.031 0.015 199.2 63: (ns/day) (hour/ns) 63: Performance: 50.236 0.478 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (72 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.037 0.019 199.6 63: (ns/day) (hour/ns) 63: Performance: 79.053 0.304 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.066 0.033 199.7 63: (ns/day) (hour/ns) 63: Performance: 23.499 1.021 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.097 0.049 199.8 63: (ns/day) (hour/ns) 63: Performance: 16.007 1.499 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (111 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 21 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.304 0.152 200.0 63: (ns/day) (hour/ns) 63: Performance: 9.664 2.484 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.075 0.038 199.8 63: (ns/day) (hour/ns) 63: Performance: 20.667 1.161 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 29 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.083 0.042 199.7 63: (ns/day) (hour/ns) 63: Performance: 18.604 1.290 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (289 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.029 0.014 199.5 63: (ns/day) (hour/ns) 63: Performance: 102.475 0.234 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.062 0.031 199.7 63: (ns/day) (hour/ns) 63: Performance: 25.163 0.954 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.039 0.020 199.5 63: (ns/day) (hour/ns) 63: Performance: 39.723 0.604 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (96 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.037 0.018 199.5 63: (ns/day) (hour/ns) 63: Performance: 79.487 0.302 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.073 0.037 199.7 63: (ns/day) (hour/ns) 63: Performance: 21.286 1.127 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.059 0.030 199.7 63: (ns/day) (hour/ns) 63: Performance: 26.240 0.915 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 (123 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.161 0.081 199.9 63: (ns/day) (hour/ns) 63: Performance: 18.201 1.319 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: NOTE: 15 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.216 0.108 199.9 63: (ns/day) (hour/ns) 63: Performance: 7.195 3.336 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.066 0.033 199.7 63: (ns/day) (hour/ns) 63: Performance: 23.491 1.022 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 (316 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.143 0.072 199.9 63: (ns/day) (hour/ns) 63: Performance: 20.470 1.172 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.061 0.031 199.7 63: (ns/day) (hour/ns) 63: Performance: 25.430 0.944 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.645 0.322 200.0 63: (ns/day) (hour/ns) 63: Performance: 2.411 9.953 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 (449 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.053 0.027 199.7 63: (ns/day) (hour/ns) 63: Performance: 55.249 0.434 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.061 0.030 199.6 63: (ns/day) (hour/ns) 63: Performance: 25.635 0.936 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.057 0.029 199.7 63: (ns/day) (hour/ns) 63: Performance: 27.028 0.888 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 (115 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 63: NVE simulation: will use the initial temperature of 456.887 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 6 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 63: NVE simulation: will use the initial temperature of 456.887 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 6 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps. 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.489 0.245 199.9 63: (ns/day) (hour/ns) 63: Performance: 6.006 3.996 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.066 0.033 199.5 63: (ns/day) (hour/ns) 63: Performance: 23.348 1.028 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.037 0.019 199.0 63: (ns/day) (hour/ns) 63: Performance: 41.956 0.572 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 (365 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 63: NVE simulation: will use the initial temperature of 456.887 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 6 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 63: NVE simulation: will use the initial temperature of 456.887 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 6 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps. 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.056 0.028 199.6 63: (ns/day) (hour/ns) 63: Performance: 52.049 0.461 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.138 0.069 199.8 63: (ns/day) (hour/ns) 63: Performance: 11.281 2.127 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.034 0.017 199.6 63: (ns/day) (hour/ns) 63: Performance: 45.613 0.526 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 (162 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 63: NVE simulation: will use the initial temperature of 456.887 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 6 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 63: NVE simulation: will use the initial temperature of 456.887 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 6 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps. 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.042 0.021 199.3 63: (ns/day) (hour/ns) 63: Performance: 69.908 0.343 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.057 0.028 199.6 63: (ns/day) (hour/ns) 63: Performance: 27.444 0.875 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.055 0.028 199.5 63: (ns/day) (hour/ns) 63: Performance: 28.157 0.852 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 (129 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 63: NVE simulation: will use the initial temperature of 456.887 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 6 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 63: NVE simulation: will use the initial temperature of 456.887 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 6 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps. 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.092 0.046 199.7 63: (ns/day) (hour/ns) 63: Performance: 31.837 0.754 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.082 0.041 199.6 63: (ns/day) (hour/ns) 63: Performance: 18.872 1.272 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.124 0.062 199.8 63: (ns/day) (hour/ns) 63: Performance: 12.504 1.919 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 (201 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 5 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 5 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps. 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.038 0.019 199.5 63: (ns/day) (hour/ns) 63: Performance: 77.842 0.308 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.119 0.060 199.7 63: (ns/day) (hour/ns) 63: Performance: 13.009 1.845 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.055 0.027 199.3 63: (ns/day) (hour/ns) 63: Performance: 28.285 0.848 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 (231 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 5 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 5 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 63: 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps. 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.510 0.255 200.0 63: (ns/day) (hour/ns) 63: Performance: 5.754 4.171 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 63: 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.039 0.020 199.5 63: (ns/day) (hour/ns) 63: Performance: 39.607 0.606 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 63: 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.048 0.024 199.6 63: (ns/day) (hour/ns) 63: Performance: 32.071 0.748 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 (749 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 5 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 5 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps. 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.032 0.016 199.5 63: (ns/day) (hour/ns) 63: Performance: 91.986 0.261 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.045 0.023 199.5 63: (ns/day) (hour/ns) 63: Performance: 34.502 0.696 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.039 0.020 199.5 63: (ns/day) (hour/ns) 63: Performance: 39.303 0.611 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 (287 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 5 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 5 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 63: 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps. 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.038 0.019 199.5 63: (ns/day) (hour/ns) 63: Performance: 76.199 0.315 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 63: 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.038 0.019 199.5 63: (ns/day) (hour/ns) 63: Performance: 41.141 0.583 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 63: 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 1.059 0.529 200.0 63: (ns/day) (hour/ns) 63: Performance: 1.469 16.339 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 (1157 ms) 63: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (5895 ms total) 63: 63: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact 63: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 293.480 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 293.480 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps. 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.051 0.026 199.5 63: (ns/day) (hour/ns) 63: Performance: 57.458 0.418 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.038 0.019 199.0 63: (ns/day) (hour/ns) 63: Performance: 40.255 0.596 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 42 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.188 0.094 199.8 63: (ns/day) (hour/ns) 63: Performance: 8.244 2.911 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (186 ms) 63: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 293.480 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 293.480 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps. 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 293.48 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 293.48 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.042 0.021 199.5 63: (ns/day) (hour/ns) 63: Performance: 69.840 0.344 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.062 0.031 199.2 63: (ns/day) (hour/ns) 63: Performance: 25.131 0.955 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.181 0.090 199.8 63: (ns/day) (hour/ns) 63: Performance: 8.602 2.790 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (173 ms) 63: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: NVE simulation: will use the initial temperature of 293.480 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: NVE simulation: will use the initial temperature of 293.480 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps. 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.120 0.060 199.8 63: (ns/day) (hour/ns) 63: Performance: 24.416 0.983 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: NOTE: 12 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.068 0.034 199.8 63: (ns/day) (hour/ns) 63: Performance: 22.871 1.049 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.073 0.036 199.5 63: (ns/day) (hour/ns) 63: Performance: 21.379 1.123 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (212 ms) 63: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: NVE simulation: will use the initial temperature of 293.480 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: NVE simulation: will use the initial temperature of 293.480 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps. 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 293.48 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 293.48 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.053 0.027 199.7 63: (ns/day) (hour/ns) 63: Performance: 55.315 0.434 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: NOTE: 20 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.080 0.040 199.8 63: (ns/day) (hour/ns) 63: Performance: 19.336 1.241 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.131 0.066 199.6 63: (ns/day) (hour/ns) 63: Performance: 11.806 2.033 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (160 ms) 63: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps. 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 1.132 0.566 200.0 63: (ns/day) (hour/ns) 63: Performance: 2.595 9.248 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.038 0.019 199.2 63: (ns/day) (hour/ns) 63: Performance: 40.509 0.592 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.036 0.018 199.5 63: (ns/day) (hour/ns) 63: Performance: 43.152 0.556 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (717 ms) 63: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps. 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.045 0.023 199.5 63: (ns/day) (hour/ns) 63: Performance: 64.938 0.370 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.048 0.024 199.2 63: (ns/day) (hour/ns) 63: Performance: 32.372 0.741 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 26 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.248 0.124 199.9 63: (ns/day) (hour/ns) 63: Performance: 6.265 3.831 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (353 ms) 63: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps. 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.073 0.036 199.4 63: (ns/day) (hour/ns) 63: Performance: 40.359 0.595 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.052 0.026 199.2 63: (ns/day) (hour/ns) 63: Performance: 29.963 0.801 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.074 0.037 199.7 63: (ns/day) (hour/ns) 63: Performance: 21.061 1.140 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (228 ms) 63: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 20, rlist from 0.749 to 0.843 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps. 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.177 0.088 199.8 63: (ns/day) (hour/ns) 63: Performance: 16.608 1.445 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 20, rlist from 0.749 to 0.843 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.064 0.032 199.4 63: (ns/day) (hour/ns) 63: Performance: 24.237 0.990 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 20, rlist from 0.749 to 0.843 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 13 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.062 0.031 199.6 63: (ns/day) (hour/ns) 63: Performance: 25.181 0.953 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (218 ms) 63: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (2251 ms total) 63: 63: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact 63: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.058 0.029 199.7 63: (ns/day) (hour/ns) 63: Performance: 50.861 0.472 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.051 0.026 199.6 63: (ns/day) (hour/ns) 63: Performance: 30.399 0.790 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.065 0.033 199.7 63: (ns/day) (hour/ns) 63: Performance: 23.887 1.005 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (126 ms) 63: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.131 0.065 199.8 63: (ns/day) (hour/ns) 63: Performance: 22.425 1.070 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.074 0.037 199.5 63: (ns/day) (hour/ns) 63: Performance: 21.041 1.141 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.338 0.169 199.9 63: (ns/day) (hour/ns) 63: Performance: 4.600 5.217 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (296 ms) 63: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 63: 1 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 63: 1 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.054 0.027 199.7 63: (ns/day) (hour/ns) 63: Performance: 53.873 0.445 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.051 0.026 199.7 63: (ns/day) (hour/ns) 63: Performance: 30.428 0.789 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.087 0.043 199.8 63: (ns/day) (hour/ns) 63: Performance: 17.941 1.338 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (110 ms) 63: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 63: 1 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 63: 1 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.050 0.025 199.6 63: (ns/day) (hour/ns) 63: Performance: 58.887 0.408 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.065 0.032 199.6 63: (ns/day) (hour/ns) 63: Performance: 23.964 1.001 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.067 0.033 199.6 63: (ns/day) (hour/ns) 63: Performance: 23.237 1.033 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (115 ms) 63: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 21 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.299 0.149 199.9 63: (ns/day) (hour/ns) 63: Performance: 9.827 2.442 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.039 0.020 199.4 63: (ns/day) (hour/ns) 63: Performance: 39.777 0.603 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.052 0.026 199.5 63: (ns/day) (hour/ns) 63: Performance: 29.973 0.801 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (231 ms) 63: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.032 0.016 199.5 63: (ns/day) (hour/ns) 63: Performance: 92.037 0.261 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.038 0.019 199.6 63: (ns/day) (hour/ns) 63: Performance: 41.196 0.583 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.212 0.106 199.9 63: (ns/day) (hour/ns) 63: Performance: 7.331 3.274 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (164 ms) 63: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 17 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.373 0.187 199.9 63: (ns/day) (hour/ns) 63: Performance: 7.863 3.052 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.051 0.025 199.5 63: (ns/day) (hour/ns) 63: Performance: 30.531 0.786 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.039 0.020 199.2 63: (ns/day) (hour/ns) 63: Performance: 39.575 0.606 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (383 ms) 63: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.037 0.019 199.6 63: (ns/day) (hour/ns) 63: Performance: 78.299 0.307 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.047 0.024 199.6 63: (ns/day) (hour/ns) 63: Performance: 32.941 0.729 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.173 0.087 199.8 63: (ns/day) (hour/ns) 63: Performance: 8.982 2.672 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (157 ms) 63: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact (1587 ms total) 63: 63: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact 63: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.378 0.189 200.0 63: (ns/day) (hour/ns) 63: Performance: 7.769 3.089 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.070 0.035 199.7 63: (ns/day) (hour/ns) 63: Performance: 22.233 1.079 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.073 0.037 199.7 63: (ns/day) (hour/ns) 63: Performance: 21.206 1.132 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (387 ms) 63: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.050 0.025 199.5 63: (ns/day) (hour/ns) 63: Performance: 58.843 0.408 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.080 0.040 199.7 63: (ns/day) (hour/ns) 63: Performance: 19.527 1.229 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.085 0.043 199.4 63: (ns/day) (hour/ns) 63: Performance: 18.221 1.317 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (154 ms) 63: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact (542 ms total) 63: 63: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact 63: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.235 0.118 199.9 63: (ns/day) (hour/ns) 63: Performance: 12.492 1.921 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.223 0.112 199.9 63: (ns/day) (hour/ns) 63: Performance: 6.974 3.441 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.095 0.048 199.8 63: (ns/day) (hour/ns) 63: Performance: 16.289 1.473 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (364 ms) 63: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.034 0.017 199.4 63: (ns/day) (hour/ns) 63: Performance: 85.124 0.282 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.082 0.041 199.8 63: (ns/day) (hour/ns) 63: Performance: 19.009 1.263 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.075 0.038 199.7 63: (ns/day) (hour/ns) 63: Performance: 20.642 1.163 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (115 ms) 63: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 63: 1 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 63: 1 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.044 0.022 199.4 63: (ns/day) (hour/ns) 63: Performance: 66.986 0.358 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.033 0.016 199.6 63: (ns/day) (hour/ns) 63: Performance: 47.215 0.508 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.064 0.032 199.3 63: (ns/day) (hour/ns) 63: Performance: 24.092 0.996 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (97 ms) 63: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 63: 1 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 63: 1 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.038 0.019 199.5 63: (ns/day) (hour/ns) 63: Performance: 77.913 0.308 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.040 0.020 199.5 63: (ns/day) (hour/ns) 63: Performance: 38.505 0.623 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.045 0.022 199.5 63: (ns/day) (hour/ns) 63: Performance: 34.858 0.688 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (78 ms) 63: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 14 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.057 0.029 199.6 63: (ns/day) (hour/ns) 63: Performance: 51.397 0.467 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: NOTE: 30 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.211 0.106 199.9 63: (ns/day) (hour/ns) 63: Performance: 7.349 3.266 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 43 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.084 0.042 199.6 63: (ns/day) (hour/ns) 63: Performance: 18.560 1.293 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (218 ms) 63: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.045 0.022 199.7 63: (ns/day) (hour/ns) 63: Performance: 65.894 0.364 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.192 0.096 199.9 63: (ns/day) (hour/ns) 63: Performance: 8.081 2.970 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.058 0.029 199.5 63: (ns/day) (hour/ns) 63: Performance: 26.963 0.890 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (161 ms) 63: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 63: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (0 ms) 63: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.235 0.117 199.9 63: (ns/day) (hour/ns) 63: Performance: 12.522 1.917 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.077 0.039 199.8 63: (ns/day) (hour/ns) 63: Performance: 20.051 1.197 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.075 0.037 199.6 63: (ns/day) (hour/ns) 63: Performance: 20.795 1.154 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (244 ms) 63: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact (1280 ms total) 63: 63: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact 63: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 15 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.339 0.170 199.9 63: (ns/day) (hour/ns) 63: Performance: 8.650 2.775 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.055 0.028 199.7 63: (ns/day) (hour/ns) 63: Performance: 28.006 0.857 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.132 0.066 199.7 63: (ns/day) (hour/ns) 63: Performance: 11.743 2.044 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (302 ms) 63: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (302 ms total) 63: 63: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact 63: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Pull group 1 'FirstWaterMolecule' has 3 atoms 63: Pull group 2 'SecondWaterMolecule' has 3 atoms 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: Pull group natoms pbc atom distance at start reference at t=0 63: 1 3 2 63: 2 3 5 1.112 nm 1.000 nm 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Pull group 1 'FirstWaterMolecule' has 3 atoms 63: Pull group 2 'SecondWaterMolecule' has 3 atoms 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: Pull group natoms pbc atom distance at start reference at t=0 63: 1 3 2 63: 2 3 5 1.112 nm 1.000 nm 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.187 0.094 199.8 63: (ns/day) (hour/ns) 63: Performance: 15.694 1.529 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.225 0.112 199.8 63: (ns/day) (hour/ns) 63: Performance: 6.915 3.471 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 21 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.152 0.076 199.6 63: (ns/day) (hour/ns) 63: Performance: 10.212 2.350 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (367 ms) 63: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Pull group 1 'FirstWaterMolecule' has 3 atoms 63: Pull group 2 'SecondWaterMolecule' has 3 atoms 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: Pull group natoms pbc atom distance at start reference at t=0 63: 1 3 2 63: 2 3 5 1.112 nm 1.000 nm 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Pull group 1 'FirstWaterMolecule' has 3 atoms 63: Pull group 2 'SecondWaterMolecule' has 3 atoms 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: Pull group natoms pbc atom distance at start reference at t=0 63: 1 3 2 63: 2 3 5 1.112 nm 1.000 nm 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.120 0.060 199.7 63: (ns/day) (hour/ns) 63: Performance: 24.425 0.983 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.052 0.026 199.5 63: (ns/day) (hour/ns) 63: Performance: 29.865 0.804 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 43 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.131 0.065 199.8 63: (ns/day) (hour/ns) 63: Performance: 11.873 2.021 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (181 ms) 63: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact (548 ms total) 63: 63: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact 63: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 63: Setting the AWH bias MC random seed to -1147273618 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Pull group 1 'C_&_r_1' has 1 atoms 63: Pull group 2 'N_&_r_2' has 1 atoms 63: Pull group 3 'CA' has 1 atoms 63: Pull group 4 'C_&_r_2' has 1 atoms 63: Pull group 5 'N_&_r_3' has 1 atoms 63: Number of degrees of freedom in T-Coupling group System is 51.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: Pull group natoms pbc atom distance at start reference at t=0 63: 1 1 0 63: 2 1 0 179.098 deg 0.000 deg 63: 2 1 0 63: 3 1 0 158.667 deg 0.000 deg 63: 63: There were 3 NOTEs 63: Setting the AWH bias MC random seed to -80359580 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Pull group 1 'C_&_r_1' has 1 atoms 63: Pull group 2 'N_&_r_2' has 1 atoms 63: Pull group 3 'CA' has 1 atoms 63: Pull group 4 'C_&_r_2' has 1 atoms 63: Pull group 5 'N_&_r_3' has 1 atoms 63: Number of degrees of freedom in T-Coupling group System is 51.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: Pull group natoms pbc atom distance at start reference at t=0 63: 1 1 0 63: 2 1 0 179.098 deg 0.000 deg 63: 2 1 0 63: 3 1 0 158.667 deg 0.000 deg 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine-dipeptide' 63: 16 steps, 0.0 ps. 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.072 0.036 199.3 63: (ns/day) (hour/ns) 63: Performance: 40.800 0.588 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine-dipeptide' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.624 0.312 199.9 63: (ns/day) (hour/ns) 63: Performance: 2.490 9.638 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine-dipeptide' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.096 0.048 199.7 63: (ns/day) (hour/ns) 63: Performance: 16.239 1.478 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (562 ms) 63: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 63: Setting the AWH bias MC random seed to -235407889 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Pull group 1 'C_&_r_1' has 1 atoms 63: Pull group 2 'N_&_r_2' has 1 atoms 63: Pull group 3 'CA' has 1 atoms 63: Pull group 4 'C_&_r_2' has 1 atoms 63: Pull group 5 'N_&_r_3' has 1 atoms 63: Number of degrees of freedom in T-Coupling group System is 51.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: Pull group natoms pbc atom distance at start reference at t=0 63: 1 1 0 63: 2 1 0 179.098 deg 0.000 deg 63: 2 1 0 63: 3 1 0 158.667 deg 0.000 deg 63: 63: There were 3 NOTEs 63: Setting the AWH bias MC random seed to -277988885 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Pull group 1 'C_&_r_1' has 1 atoms 63: Pull group 2 'N_&_r_2' has 1 atoms 63: Pull group 3 'CA' has 1 atoms 63: Pull group 4 'C_&_r_2' has 1 atoms 63: Pull group 5 'N_&_r_3' has 1 atoms 63: Number of degrees of freedom in T-Coupling group System is 51.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: Pull group natoms pbc atom distance at start reference at t=0 63: 1 1 0 63: 2 1 0 179.098 deg 0.000 deg 63: 2 1 0 63: 3 1 0 158.667 deg 0.000 deg 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine-dipeptide' 63: 16 steps, 0.0 ps. 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 12 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.130 0.065 199.5 63: (ns/day) (hour/ns) 63: Performance: 22.492 1.067 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine-dipeptide' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.309 0.154 199.9 63: (ns/day) (hour/ns) 63: Performance: 5.037 4.765 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine-dipeptide' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.132 0.066 199.7 63: (ns/day) (hour/ns) 63: Performance: 11.736 2.045 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (451 ms) 63: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact (1013 ms total) 63: 63: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact 63: [ RUN ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps. 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.869 0.434 200.0 63: (ns/day) (hour/ns) 63: Performance: 3.381 7.099 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.095 0.047 199.8 63: (ns/day) (hour/ns) 63: Performance: 16.423 1.461 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 23 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.105 0.052 199.6 63: (ns/day) (hour/ns) 63: Performance: 14.812 1.620 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (657 ms) 63: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact (657 ms total) 63: 63: [----------] 3 tests from Checking/InitialConstraintsTest 63: [ RUN ] Checking/InitialConstraintsTest.Works/0 63: Number of degrees of freedom in T-Coupling group rest is 11.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 1141.954 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc-and-methanol' 63: 1 steps, 0.0 ps. 63: Setting the LD random seed to -604512321 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 40 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.112 0.056 199.7 63: (ns/day) (hour/ns) 63: Performance: 3.079 7.794 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (179 ms) 63: [ RUN ] Checking/InitialConstraintsTest.Works/1 63: Number of degrees of freedom in T-Coupling group rest is 11.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 1141.954 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc-and-methanol' 63: 1 steps, 0.0 ps. 63: Setting the LD random seed to -876619841 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.025 0.013 199.3 63: (ns/day) (hour/ns) 63: Performance: 13.543 1.772 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (24 ms) 63: [ RUN ] Checking/InitialConstraintsTest.Works/2 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 63: Integrator method md-vv-avek is implemented primarily for validation 63: purposes; for molecular dynamics, you should probably be using md or 63: md-vv 63: 63: Number of degrees of freedom in T-Coupling group rest is 11.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 63: NVE simulation: will use the initial temperature of 1141.954 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc-and-methanol' 63: 1 steps, 0.0 ps. 63: Setting the LD random seed to -286296081 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.022 0.011 199.0 63: (ns/day) (hour/ns) 63: Performance: 15.527 1.546 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (19 ms) 63: [----------] 3 tests from Checking/InitialConstraintsTest (222 ms total) 63: 63: [----------] Global test environment tear-down 63: [==========] 76 tests from 13 test suites ran. (15567 ms total) 63: [ PASSED ] 76 tests. 63/87 Test #63: MdrunIOTests .............................. Passed 15.58 sec test 64 Start 64: MdrunTestsOneRank 64: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunTestsOneRank.xml" 64: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 64: Test timeout computed to be: 600 64: [==========] Running 28 tests from 7 test suites. 64: [----------] Global test environment set-up. 64: [----------] 1 test from CompelTest 64: [ RUN ] CompelTest.SwapCanRun 64: Generating 1-4 interactions: fudge = 0.5 64: Split0 group 'Ch0' contains 83 atoms. 64: Split1 group 'Ch1' contains 83 atoms. 64: Solvent group 'SOL' contains 11931 atoms. 64: Swap group 'NA+' contains 19 atoms. 64: Swap group 'CL-' contains 19 atoms. 64: Number of degrees of freedom in T-Coupling group System is 27869.00 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 64: Removing center of mass motion in the presence of position restraints 64: might cause artifacts. When you are using position restraints to 64: equilibrate a macro-molecule, the artifacts are usually negligible. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 2 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Update groups can not be used for this system because there are three or more consecutively coupled constraints 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: SWAP: Determining initial numbers of ions per compartment. 64: SWAP: Setting pointers for checkpoint writing 64: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 64: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 64: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 64: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 64: starting mdrun 'Channel_coco in octane membrane' 64: 2 steps, 0.0 ps. 64: Setting the LD random seed to -1394021071 64: 64: Generated 330891 of the 330891 non-bonded parameter combinations 64: 64: Generated 330891 of the 330891 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Protein' 64: 64: turning all bonds into constraints... 64: 64: Excluding 3 bonded neighbours molecule type 'OCT' 64: 64: turning all bonds into constraints... 64: 64: Excluding 1 bonded neighbours molecule type 'NA' 64: 64: turning all bonds into constraints... 64: 64: Excluding 1 bonded neighbours molecule type 'CL' 64: 64: turning all bonds into constraints... 64: 64: Excluding 3 bonded neighbours molecule type 'Protein' 64: 64: Excluding 3 bonded neighbours molecule type 'OCT' 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning all bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.316 nm, buffer size 0.316 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.262 nm, buffer size 0.262 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 1 Mb of data 64: 64: Writing final coordinates. 64: 64: NOTE: 31 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.330 0.165 199.9 64: (ns/day) (hour/ns) 64: Performance: 7.857 3.055 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 64: 64: Update groups can not be used for this system because there are three or more consecutively coupled constraints 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: SWAP: Setting pointers for checkpoint writing 64: SWAP: Copying channel fluxes from checkpoint file data 64: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 64: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 64: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 64: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 64: starting mdrun 'Channel_coco in octane membrane' 64: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 64: 64: Writing final coordinates. 64: 64: NOTE: 26 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.247 0.124 199.8 64: (ns/day) (hour/ns) 64: Performance: 10.481 2.290 64: [ OK ] CompelTest.SwapCanRun (942 ms) 64: [----------] 1 test from CompelTest (943 ms total) 64: 64: [----------] 6 tests from BondedInteractionsTest 64: [ RUN ] BondedInteractionsTest.NormalBondWorks 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: 64: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 64: In moleculetype 'butane' 2 atoms are not bound by a potential or 64: constraint to any other atom in the same moleculetype. Although 64: technically this might not cause issues in a simulation, this often means 64: that the user forgot to add a bond/potential/constraint or put multiple 64: molecules in the same moleculetype definition by mistake. Run with -v to 64: get information for each atom. 64: 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 64: NVE simulation with an initial temperature of zero: will use a Verlet 64: buffer of 10%. Check your energy drift! 64: 64: 64: There were 3 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 64: 64: Reading frames from gro file 'A single butane', 4 atoms. 64: Reading frame 0 time 0.000 Last frame 0 time 0.000 64: 64: NOTE: 59 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.041 0.021 199.5 64: (ns/day) (hour/ns) 64: Performance: 4.201 5.713 64: Setting the LD random seed to 2079579003 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'butane' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] BondedInteractionsTest.NormalBondWorks (64 ms) 64: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: 64: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 64: In moleculetype 'butane' 2 atoms are not bound by a potential or 64: constraint to any other atom in the same moleculetype. Although 64: technically this might not cause issues in a simulation, this often means 64: that the user forgot to add a bond/potential/constraint or put multiple 64: molecules in the same moleculetype definition by mistake. Run with -v to 64: get information for each atom. 64: 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 64: NVE simulation with an initial temperature of zero: will use a Verlet 64: buffer of 10%. Check your energy drift! 64: 64: 64: There were 3 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 64: 64: Reading frames from gro file 'A single butane', 4 atoms. 64: Reading frame 0 time 0.000 Last frame 0 time 0.000 64: 64: NOTE: 16 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.001 0.000 183.9 64: (ns/day) (hour/ns) 64: Performance: 272.677 0.088 64: Setting the LD random seed to -236060770 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'butane' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] BondedInteractionsTest.TabulatedBondWorks (35 ms) 64: [ RUN ] BondedInteractionsTest.NormalAngleWorks 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: 64: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 64: In moleculetype 'butane' 4 atoms are not bound by a potential or 64: constraint to any other atom in the same moleculetype. Although 64: technically this might not cause issues in a simulation, this often means 64: that the user forgot to add a bond/potential/constraint or put multiple 64: molecules in the same moleculetype definition by mistake. Run with -v to 64: get information for each atom. 64: 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 64: NVE simulation with an initial temperature of zero: will use a Verlet 64: buffer of 10%. Check your energy drift! 64: 64: 64: There were 3 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 64: 64: Reading frames from gro file 'A single butane', 4 atoms. 64: Reading frame 0 time 0.000 Last frame 0 time 0.000 64: 64: NOTE: 15 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.000 0.000 184.1 64: (ns/day) (hour/ns) 64: Performance: 465.196 0.052 64: Setting the LD random seed to 2146410357 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'butane' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] BondedInteractionsTest.NormalAngleWorks (12 ms) 64: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: 64: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 64: In moleculetype 'butane' 4 atoms are not bound by a potential or 64: constraint to any other atom in the same moleculetype. Although 64: technically this might not cause issues in a simulation, this often means 64: that the user forgot to add a bond/potential/constraint or put multiple 64: molecules in the same moleculetype definition by mistake. Run with -v to 64: get information for each atom. 64: 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 64: NVE simulation with an initial temperature of zero: will use a Verlet 64: buffer of 10%. Check your energy drift! 64: 64: 64: There were 3 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 64: 64: Reading frames from gro file 'A single butane', 4 atoms. 64: Reading frame 0 time 0.000 Last frame 0 time 0.000 64: 64: NOTE: 15 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.000 0.000 184.3 64: (ns/day) (hour/ns) 64: Performance: 458.719 0.052 64: Setting the LD random seed to -327704869 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'butane' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (12 ms) 64: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: 64: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 64: In moleculetype 'butane' 4 atoms are not bound by a potential or 64: constraint to any other atom in the same moleculetype. Although 64: technically this might not cause issues in a simulation, this often means 64: that the user forgot to add a bond/potential/constraint or put multiple 64: molecules in the same moleculetype definition by mistake. Run with -v to 64: get information for each atom. 64: 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 64: NVE simulation with an initial temperature of zero: will use a Verlet 64: buffer of 10%. Check your energy drift! 64: 64: 64: There were 3 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 64: 64: Reading frames from gro file 'A single butane', 4 atoms. 64: Reading frame 0 time 0.000 Last frame 0 time 0.000 64: 64: NOTE: 37 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.172 0.086 199.9 64: (ns/day) (hour/ns) 64: Performance: 1.003 23.922 64: Setting the LD random seed to 1605368807 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'butane' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] BondedInteractionsTest.NormalDihedralWorks (120 ms) 64: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: 64: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 64: In moleculetype 'butane' 4 atoms are not bound by a potential or 64: constraint to any other atom in the same moleculetype. Although 64: technically this might not cause issues in a simulation, this often means 64: that the user forgot to add a bond/potential/constraint or put multiple 64: molecules in the same moleculetype definition by mistake. Run with -v to 64: get information for each atom. 64: 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 64: NVE simulation with an initial temperature of zero: will use a Verlet 64: buffer of 10%. Check your energy drift! 64: 64: 64: There were 3 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 64: 64: Reading frames from gro file 'A single butane', 4 atoms. 64: Reading frame 0 time 0.000 Last frame 0 time 0.000 64: 64: NOTE: 40 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.160 0.080 199.9 64: (ns/day) (hour/ns) 64: Performance: 1.078 22.256 64: Setting the LD random seed to 1860336638 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'butane' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (123 ms) 64: [----------] 6 tests from BondedInteractionsTest (371 ms total) 64: 64: [----------] 2 tests from BoxDeformationTest 64: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (10) 64: 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: Number of degrees of freedom in T-Coupling group rest is 33.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: There were 3 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Argon' 64: 0 steps, 0.0 ps. 64: 64: NOTE: 25 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.000 0.000 168.8 64: (ns/day) (hour/ns) 64: Performance: 808.901 0.030 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 1375171451 64: 64: Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: Setting gen_seed to -49169 64: 64: Velocities were taken from a Maxwell distribution at 0 K 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (13 ms) 64: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (10) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group rest is 1293.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: There were 2 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 20 steps, 0.0 ps. 64: Setting the LD random seed to 1996468216 64: 64: Generated 330891 of the 330891 non-bonded parameter combinations 64: 64: Generated 330891 of the 330891 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 64: Calculating fourier grid dimensions for X Y Z 64: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 64: 64: Estimate for the relative computational load of the PME mesh part: 0.20 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.977 0.488 200.0 64: (ns/day) (hour/ns) 64: Performance: 7.431 3.230 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (1065 ms) 64: [----------] 2 tests from BoxDeformationTest (1078 ms total) 64: 64: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 64: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 2 [file ala.top, line 256]: 64: For energy conservation with LINCS, lincs_iter should be 2 or larger. 64: 64: 64: Number of degrees of freedom in T-Coupling group rest is 54.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 64: The optimal PME mesh load for parallel simulations is below 0.5 64: and for highly parallel simulations between 0.25 and 0.33, 64: for higher performance, increase the cut-off and the PME grid spacing. 64: 64: 64: 64: There were 3 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'UNNAMED in water' 64: 4 steps, 0.0 ps. 64: Setting the LD random seed to -1092617366 64: 64: Generated 2211 of the 2211 non-bonded parameter combinations 64: 64: Generated 2211 of the 2211 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 64: 64: turning H bonds into constraints... 64: 64: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 64: Calculating fourier grid dimensions for X Y Z 64: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 64: 64: Estimate for the relative computational load of the PME mesh part: 0.94 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: NOTE: 71 % of the run time was spent in domain decomposition, 64: 0 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.112 0.056 199.8 64: (ns/day) (hour/ns) 64: Performance: 7.688 3.122 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 2 [file ala.top, line 256]: 64: For energy conservation with LINCS, lincs_iter should be 2 or larger. 64: 64: 64: Number of degrees of freedom in T-Coupling group rest is 54.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 64: The optimal PME mesh load for parallel simulations is below 0.5 64: and for highly parallel simulations between 0.25 and 0.33, 64: for higher performance, increase the cut-off and the PME grid spacing. 64: 64: 64: 64: There were 3 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'UNNAMED in water' 64: 4 steps, 0.0 ps. 64: Setting the LD random seed to -339823002 64: 64: Generated 2211 of the 2211 non-bonded parameter combinations 64: 64: Generated 2211 of the 2211 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 64: 64: turning H bonds into constraints... 64: 64: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 64: Calculating fourier grid dimensions for X Y Z 64: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 64: 64: Estimate for the relative computational load of the PME mesh part: 0.94 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.053 0.027 198.9 64: (ns/day) (hour/ns) 64: Performance: 16.076 1.493 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) 64: 64: 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (807 ms) 64: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 2 [file ala.top, line 256]: 64: For energy conservation with LINCS, lincs_iter should be 2 or larger. 64: 64: 64: Number of degrees of freedom in T-Coupling group rest is 54.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 64: The optimal PME mesh load for parallel simulations is below 0.5 64: and for highly parallel simulations between 0.25 and 0.33, 64: for higher performance, increase the cut-off and the PME grid spacing. 64: 64: 64: 64: There were 3 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'UNNAMED in water' 64: 4 steps, 0.0 ps. 64: Setting the LD random seed to 2080290750 64: 64: Generated 2211 of the 2211 non-bonded parameter combinations 64: 64: Generated 2211 of the 2211 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 64: 64: turning H bonds into constraints... 64: 64: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 64: Calculating fourier grid dimensions for X Y Z 64: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 64: 64: Estimate for the relative computational load of the PME mesh part: 0.94 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.057 0.028 199.1 64: (ns/day) (hour/ns) 64: Performance: 15.194 1.580 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 2 [file ala.top, line 256]: 64: For energy conservation with LINCS, lincs_iter should be 2 or larger. 64: 64: 64: Number of degrees of freedom in T-Coupling group rest is 54.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 64: The optimal PME mesh load for parallel simulations is below 0.5 64: and for highly parallel simulations between 0.25 and 0.33, 64: for higher performance, increase the cut-off and the PME grid spacing. 64: 64: 64: 64: There were 3 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 64: Can not increase nstlist because an NVE ensemble is used 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'UNNAMED in water' 64: 4 steps, 0.0 ps. 64: Setting the LD random seed to -134514 64: 64: Generated 2211 of the 2211 non-bonded parameter combinations 64: 64: Generated 2211 of the 2211 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 64: 64: turning H bonds into constraints... 64: 64: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 64: Calculating fourier grid dimensions for X Y Z 64: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 64: 64: Estimate for the relative computational load of the PME mesh part: 0.94 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.068 0.034 199.2 64: (ns/day) (hour/ns) 64: Performance: 12.577 1.908 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 64: 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (142 ms) 64: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (950 ms total) 64: 64: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 64: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Pull group 1 'FirstWaterMolecule' has 3 atoms 64: Pull group 2 'SecondWaterMolecule' has 3 atoms 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: Pull group natoms pbc atom distance at start reference at t=0 64: 1 3 2 64: 2 3 5 1.112 nm 1.000 nm 64: 64: There was 1 NOTE 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 4 steps, 0.0 ps. 64: Setting the LD random seed to -893502733 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Generated 3 of the 3 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: NOTE: 10 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.616 0.308 200.0 64: (ns/day) (hour/ns) 64: Performance: 1.403 17.103 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Pull group 1 'FirstWaterMolecule' has 3 atoms 64: Pull group 2 'SecondWaterMolecule' has 3 atoms 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: Pull group natoms pbc atom distance at start reference at t=0 64: 1 3 2 64: 2 3 5 1.112 nm 1.000 nm 64: 64: There was 1 NOTE 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 64: Can not increase nstlist because an NVE ensemble is used 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 4 steps, 0.0 ps. 64: Setting the LD random seed to -637829126 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Generated 3 of the 3 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.059 0.030 199.5 64: (ns/day) (hour/ns) 64: Performance: 14.539 1.651 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 64: 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (450 ms) 64: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (451 ms total) 64: 64: [----------] 12 tests from FreezeWorks/FreezeGroupTest 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 64: NVE simulation: will use the initial temperature of 318.937 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 5 NOTEs 64: 64: There was 1 WARNING 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.029 0.015 199.2 64: (ns/day) (hour/ns) 64: Performance: 53.272 0.451 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (38 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 64: NVE simulation: will use the initial temperature of 318.937 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 5 NOTEs 64: 64: There was 1 WARNING 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.099 0.049 199.7 64: (ns/day) (hour/ns) 64: Performance: 15.754 1.523 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (67 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 64: NVE simulation: will use the initial temperature of 318.937 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 5 NOTEs 64: 64: There was 1 WARNING 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.259 0.129 199.9 64: (ns/day) (hour/ns) 64: Performance: 6.013 3.991 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (191 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 64: NVE simulation: will use the initial temperature of 318.937 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 5 NOTEs 64: 64: There was 1 WARNING 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: NOTE: 24 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.264 0.132 199.9 64: (ns/day) (hour/ns) 64: Performance: 5.886 4.077 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (249 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 64: NVE simulation: will use the initial temperature of 318.937 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 5 NOTEs 64: 64: There was 1 WARNING 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.040 0.020 199.4 64: (ns/day) (hour/ns) 64: Performance: 38.663 0.621 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (89 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 64: ./src/programs/mdrun/tests/freezegroups.cpp:194: Skipped 64: Parrinello-Rahman is not implemented in md-vv. 64: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 NOTEs 64: 64: There was 1 WARNING 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.077 0.038 199.6 64: (ns/day) (hour/ns) 64: Performance: 20.275 1.184 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (144 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 NOTEs 64: 64: There was 1 WARNING 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.044 0.022 199.6 64: (ns/day) (hour/ns) 64: Performance: 35.406 0.678 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (48 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 NOTEs 64: 64: There was 1 WARNING 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.045 0.023 199.7 64: (ns/day) (hour/ns) 64: Performance: 34.163 0.703 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (36 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 NOTEs 64: 64: There was 1 WARNING 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.144 0.072 199.8 64: (ns/day) (hour/ns) 64: Performance: 10.761 2.230 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (106 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 NOTEs 64: 64: There was 1 WARNING 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.057 0.029 199.5 64: (ns/day) (hour/ns) 64: Performance: 27.126 0.885 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (77 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 NOTEs 64: 64: There was 1 WARNING 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.163 0.081 199.9 64: (ns/day) (hour/ns) 64: Performance: 9.549 2.513 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (149 ms) 64: [----------] 12 tests from FreezeWorks/FreezeGroupTest (1206 ms total) 64: 64: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 64: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 64: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: Net Acceleration in X direction, will not be corrected 64: Net Acceleration in Y direction, will not be corrected 64: Net Acceleration in Z direction, will not be corrected 64: 64: There were 3 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 8 steps, 0.0 ps. 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Generated 3 of the 3 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Setting gen_seed to -1375742753 64: 64: Velocities were taken from a Maxwell distribution at 0 K 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.077 0.039 199.5 64: (ns/day) (hour/ns) 64: Performance: 40.227 0.597 64: 64: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (64 ms) 64: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 64: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 64: Net Acceleration in X direction, will not be corrected 64: Net Acceleration in Y direction, will not be corrected 64: Net Acceleration in Z direction, will not be corrected 64: 64: There were 3 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because verlet-buffer-tolerance is not set or used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 8 steps, 0.0 ps. 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Generated 3 of the 3 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Setting gen_seed to 1668540667 64: 64: Velocities were taken from a Maxwell distribution at 0 K 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.070 0.035 199.5 64: (ns/day) (hour/ns) 64: Performance: 44.047 0.545 64: 64: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (43 ms) 64: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 64: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: Net Acceleration in X direction, will not be corrected 64: Net Acceleration in Y direction, will not be corrected 64: Net Acceleration in Z direction, will not be corrected 64: 64: There were 3 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 8 steps, 0.0 ps. 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Generated 3 of the 3 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Setting gen_seed to -134316601 64: 64: Velocities were taken from a Maxwell distribution at 0 K 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.095 0.047 199.6 64: (ns/day) (hour/ns) 64: Performance: 32.767 0.732 64: 64: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (63 ms) 64: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 64: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 64: Net Acceleration in X direction, will not be corrected 64: Net Acceleration in Y direction, will not be corrected 64: Net Acceleration in Z direction, will not be corrected 64: 64: There were 3 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because verlet-buffer-tolerance is not set or used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 8 steps, 0.0 ps. 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Generated 3 of the 3 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Setting gen_seed to 2077196092 64: 64: Velocities were taken from a Maxwell distribution at 0 K 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: NOTE: 22 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.285 0.143 199.9 64: (ns/day) (hour/ns) 64: Performance: 10.910 2.200 64: 64: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (236 ms) 64: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (408 ms total) 64: 64: [----------] Global test environment tear-down 64: [==========] 28 tests from 7 test suites ran. (5658 ms total) 64: [ PASSED ] 27 tests. 64: [ SKIPPED ] 1 test, listed below: 64: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 64/87 Test #64: MdrunTestsOneRank ......................... Passed 5.70 sec test 65 Start 65: MdrunTestsTwoRanks 65: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunTestsTwoRanks.xml" 65: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 65: Test timeout computed to be: 600 65: [==========] Running 28 tests from 7 test suites. 65: [----------] Global test environment set-up. 65: [----------] 1 test from CompelTest 65: [ RUN ] CompelTest.SwapCanRun 65: Generating 1-4 interactions: fudge = 0.5 65: Split0 group 'Ch0' contains 83 atoms. 65: Split1 group 'Ch1' contains 83 atoms. 65: Solvent group 'SOL' contains 11931 atoms. 65: Swap group 'NA+' contains 19 atoms. 65: Swap group 'CL-' contains 19 atoms. 65: Number of degrees of freedom in T-Coupling group System is 27869.00 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 65: Removing center of mass motion in the presence of position restraints 65: might cause artifacts. When you are using position restraints to 65: equilibrate a macro-molecule, the artifacts are usually negligible. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 2 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Update groups can not be used for this system because there are three or more consecutively coupled constraints 65: 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: SWAP: Determining initial numbers of ions per compartment. 65: SWAP: Setting pointers for checkpoint writing 65: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 65: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 65: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 65: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 65: starting mdrun 'Channel_coco in octane membrane' 65: 2 steps, 0.0 ps. 65: Setting the LD random seed to 2107584381 65: 65: Generated 330891 of the 330891 non-bonded parameter combinations 65: 65: Generated 330891 of the 330891 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Protein' 65: 65: turning all bonds into constraints... 65: 65: Excluding 3 bonded neighbours molecule type 'OCT' 65: 65: turning all bonds into constraints... 65: 65: Excluding 1 bonded neighbours molecule type 'NA' 65: 65: turning all bonds into constraints... 65: 65: Excluding 1 bonded neighbours molecule type 'CL' 65: 65: turning all bonds into constraints... 65: 65: Excluding 3 bonded neighbours molecule type 'Protein' 65: 65: Excluding 3 bonded neighbours molecule type 'OCT' 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning all bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.316 nm, buffer size 0.316 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.262 nm, buffer size 0.262 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 1 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 2.3%. 65: The balanceable part of the MD step is 8%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 0.2%. 65: 65: 65: NOTE: 14 % of the run time was spent in domain decomposition, 65: 6 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 3.254 0.814 399.9 65: (ns/day) (hour/ns) 65: Performance: 1.593 15.069 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 65: 65: Update groups can not be used for this system because there are three or more consecutively coupled constraints 65: 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: SWAP: Setting pointers for checkpoint writing 65: SWAP: Copying channel fluxes from checkpoint file data 65: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 65: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 65: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 65: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 65: starting mdrun 'Channel_coco in octane membrane' 65: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: NOTE: 18 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.720 0.180 399.8 65: (ns/day) (hour/ns) 65: Performance: 7.196 3.335 65: [ OK ] CompelTest.SwapCanRun (1877 ms) 65: [----------] 1 test from CompelTest (1877 ms total) 65: 65: [----------] 6 tests from BondedInteractionsTest 65: [ RUN ] BondedInteractionsTest.NormalBondWorks 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: 65: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 65: In moleculetype 'butane' 2 atoms are not bound by a potential or 65: constraint to any other atom in the same moleculetype. Although 65: technically this might not cause issues in a simulation, this often means 65: that the user forgot to add a bond/potential/constraint or put multiple 65: molecules in the same moleculetype definition by mistake. Run with -v to 65: get information for each atom. 65: 65: Number of degrees of freedom in T-Coupling group rest is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 65: NVE simulation with an initial temperature of zero: will use a Verlet 65: buffer of 10%. Check your energy drift! 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 65: 65: Reading frames from gro file 'A single butane', 4 atoms. 65: Reading frame 0 time 0.000 Last frame 0 time 0.000 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.029 0.007 397.7 65: (ns/day) (hour/ns) 65: Performance: 11.847 2.026 65: Setting the LD random seed to -270069761 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'butane' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] BondedInteractionsTest.NormalBondWorks (29 ms) 65: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: 65: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 65: In moleculetype 'butane' 2 atoms are not bound by a potential or 65: constraint to any other atom in the same moleculetype. Although 65: technically this might not cause issues in a simulation, this often means 65: that the user forgot to add a bond/potential/constraint or put multiple 65: molecules in the same moleculetype definition by mistake. Run with -v to 65: get information for each atom. 65: 65: Number of degrees of freedom in T-Coupling group rest is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 65: NVE simulation with an initial temperature of zero: will use a Verlet 65: buffer of 10%. Check your energy drift! 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 65: 65: Reading frames from gro file 'A single butane', 4 atoms. 65: Reading frame 0 time 0.000 Last frame 0 time 0.000 65: 65: NOTE: 23 % of the run time was spent in domain decomposition, 65: 0 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.074 0.018 399.4 65: (ns/day) (hour/ns) 65: Performance: 4.688 5.119 65: Setting the LD random seed to 2146941347 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'butane' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] BondedInteractionsTest.TabulatedBondWorks (129 ms) 65: [ RUN ] BondedInteractionsTest.NormalAngleWorks 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: 65: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 65: In moleculetype 'butane' 4 atoms are not bound by a potential or 65: constraint to any other atom in the same moleculetype. Although 65: technically this might not cause issues in a simulation, this often means 65: that the user forgot to add a bond/potential/constraint or put multiple 65: molecules in the same moleculetype definition by mistake. Run with -v to 65: get information for each atom. 65: 65: Number of degrees of freedom in T-Coupling group rest is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 65: NVE simulation with an initial temperature of zero: will use a Verlet 65: buffer of 10%. Check your energy drift! 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 65: 65: Reading frames from gro file 'A single butane', 4 atoms. 65: Reading frame 0 time 0.000 Last frame 0 time 0.000 65: 65: NOTE: 35 % of the run time was spent in domain decomposition, 65: 16 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.593 0.148 399.9 65: (ns/day) (hour/ns) 65: Performance: 0.583 41.164 65: Setting the LD random seed to -641040387 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'butane' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] BondedInteractionsTest.NormalAngleWorks (244 ms) 65: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: 65: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 65: In moleculetype 'butane' 4 atoms are not bound by a potential or 65: constraint to any other atom in the same moleculetype. Although 65: technically this might not cause issues in a simulation, this often means 65: that the user forgot to add a bond/potential/constraint or put multiple 65: molecules in the same moleculetype definition by mistake. Run with -v to 65: get information for each atom. 65: 65: Number of degrees of freedom in T-Coupling group rest is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 65: NVE simulation with an initial temperature of zero: will use a Verlet 65: buffer of 10%. Check your energy drift! 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 65: 65: Reading frames from gro file 'A single butane', 4 atoms. 65: Reading frame 0 time 0.000 Last frame 0 time 0.000 65: 65: NOTE: 52 % of the run time was spent in domain decomposition, 65: 13 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.291 0.073 399.8 65: (ns/day) (hour/ns) 65: Performance: 1.188 20.204 65: Setting the LD random seed to -419466634 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'butane' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (367 ms) 65: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: 65: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 65: In moleculetype 'butane' 4 atoms are not bound by a potential or 65: constraint to any other atom in the same moleculetype. Although 65: technically this might not cause issues in a simulation, this often means 65: that the user forgot to add a bond/potential/constraint or put multiple 65: molecules in the same moleculetype definition by mistake. Run with -v to 65: get information for each atom. 65: 65: Number of degrees of freedom in T-Coupling group rest is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 65: NVE simulation with an initial temperature of zero: will use a Verlet 65: buffer of 10%. Check your energy drift! 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 65: 65: Reading frames from gro file 'A single butane', 4 atoms. 65: Reading frame 0 time 0.000 Last frame 0 time 0.000 65: 65: NOTE: 32 % of the run time was spent in domain decomposition, 65: 12 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 7 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.664 0.170 390.9 65: (ns/day) (hour/ns) 65: Performance: 0.509 47.175 65: Setting the LD random seed to 2080103038 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'butane' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] BondedInteractionsTest.NormalDihedralWorks (278 ms) 65: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: 65: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 65: In moleculetype 'butane' 4 atoms are not bound by a potential or 65: constraint to any other atom in the same moleculetype. Although 65: technically this might not cause issues in a simulation, this often means 65: that the user forgot to add a bond/potential/constraint or put multiple 65: molecules in the same moleculetype definition by mistake. Run with -v to 65: get information for each atom. 65: 65: Number of degrees of freedom in T-Coupling group rest is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 65: NVE simulation with an initial temperature of zero: will use a Verlet 65: buffer of 10%. Check your energy drift! 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 65: 65: Reading frames from gro file 'A single butane', 4 atoms. 65: Reading frame 0 time 0.000 Last frame 0 time 0.000 65: 65: NOTE: 64 % of the run time was spent in domain decomposition, 65: 0 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 7 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.112 0.028 399.5 65: (ns/day) (hour/ns) 65: Performance: 3.072 7.812 65: Setting the LD random seed to -1242054722 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'butane' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (250 ms) 65: [----------] 6 tests from BondedInteractionsTest (1300 ms total) 65: 65: [----------] 2 tests from BoxDeformationTest 65: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (10) 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: Number of degrees of freedom in T-Coupling group rest is 33.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 0 steps, 0.0 ps. 65: 65: NOTE: 21 % of the run time was spent in domain decomposition, 65: 14 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 5 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.001 0.000 282.3 65: (ns/day) (hour/ns) 65: Performance: 540.071 0.044 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 450805535 65: 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Setting gen_seed to 2105540603 65: 65: Velocities were taken from a Maxwell distribution at 0 K 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (119 ms) 65: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (10) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group rest is 1293.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: There were 2 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 20 steps, 0.0 ps. 65: Setting the LD random seed to -1355972742 65: 65: Generated 330891 of the 330891 non-bonded parameter combinations 65: 65: Generated 330891 of the 330891 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 65: Calculating fourier grid dimensions for X Y Z 65: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 65: 65: Estimate for the relative computational load of the PME mesh part: 0.20 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB got disabled because it was unsuitable to use. 65: Average load imbalance: 17.4%. 65: The balanceable part of the MD step is 15%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 2.7%. 65: 65: 65: Core t (s) Wall t (s) (%) 65: Time: 2.664 0.666 399.9 65: (ns/day) (hour/ns) 65: Performance: 5.447 4.406 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (1212 ms) 65: [----------] 2 tests from BoxDeformationTest (1332 ms total) 65: 65: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 65: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 2 [file ala.top, line 256]: 65: For energy conservation with LINCS, lincs_iter should be 2 or larger. 65: 65: 65: Number of degrees of freedom in T-Coupling group rest is 54.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 65: The optimal PME mesh load for parallel simulations is below 0.5 65: and for highly parallel simulations between 0.25 and 0.33, 65: for higher performance, increase the cut-off and the PME grid spacing. 65: 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'UNNAMED in water' 65: 4 steps, 0.0 ps. 65: Setting the LD random seed to -541065603 65: 65: Generated 2211 of the 2211 non-bonded parameter combinations 65: 65: Generated 2211 of the 2211 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 65: 65: turning H bonds into constraints... 65: 65: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 65: Calculating fourier grid dimensions for X Y Z 65: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 65: 65: Estimate for the relative computational load of the PME mesh part: 0.94 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 23 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.575 0.144 399.6 65: (ns/day) (hour/ns) 65: Performance: 3.001 7.996 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 2 [file ala.top, line 256]: 65: For energy conservation with LINCS, lincs_iter should be 2 or larger. 65: 65: 65: Number of degrees of freedom in T-Coupling group rest is 54.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 65: The optimal PME mesh load for parallel simulations is below 0.5 65: and for highly parallel simulations between 0.25 and 0.33, 65: for higher performance, increase the cut-off and the PME grid spacing. 65: 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'UNNAMED in water' 65: 4 steps, 0.0 ps. 65: Setting the LD random seed to -8471085 65: 65: Generated 2211 of the 2211 non-bonded parameter combinations 65: 65: Generated 2211 of the 2211 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 65: 65: turning H bonds into constraints... 65: 65: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 65: Calculating fourier grid dimensions for X Y Z 65: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 65: 65: Estimate for the relative computational load of the PME mesh part: 0.94 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 18 % of the run time was spent in domain decomposition, 65: 2 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 19 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 1.566 0.392 399.6 65: (ns/day) (hour/ns) 65: Performance: 1.102 21.778 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) 65: 65: 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (1693 ms) 65: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 2 [file ala.top, line 256]: 65: For energy conservation with LINCS, lincs_iter should be 2 or larger. 65: 65: 65: Number of degrees of freedom in T-Coupling group rest is 54.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 65: The optimal PME mesh load for parallel simulations is below 0.5 65: and for highly parallel simulations between 0.25 and 0.33, 65: for higher performance, increase the cut-off and the PME grid spacing. 65: 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'UNNAMED in water' 65: 4 steps, 0.0 ps. 65: Setting the LD random seed to -4826625 65: 65: Generated 2211 of the 2211 non-bonded parameter combinations 65: 65: Generated 2211 of the 2211 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 65: 65: turning H bonds into constraints... 65: 65: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 65: Calculating fourier grid dimensions for X Y Z 65: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 65: 65: Estimate for the relative computational load of the PME mesh part: 0.94 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 53 % of the run time was spent in domain decomposition, 65: 0 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 22 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.308 0.077 399.5 65: (ns/day) (hour/ns) 65: Performance: 5.610 4.278 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 2 [file ala.top, line 256]: 65: For energy conservation with LINCS, lincs_iter should be 2 or larger. 65: 65: 65: Number of degrees of freedom in T-Coupling group rest is 54.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 65: The optimal PME mesh load for parallel simulations is below 0.5 65: and for highly parallel simulations between 0.25 and 0.33, 65: for higher performance, increase the cut-off and the PME grid spacing. 65: 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 65: Can not increase nstlist because an NVE ensemble is used 65: 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'UNNAMED in water' 65: 4 steps, 0.0 ps. 65: Setting the LD random seed to 1739583231 65: 65: Generated 2211 of the 2211 non-bonded parameter combinations 65: 65: Generated 2211 of the 2211 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 65: 65: turning H bonds into constraints... 65: 65: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 65: Calculating fourier grid dimensions for X Y Z 65: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 65: 65: Estimate for the relative computational load of the PME mesh part: 0.94 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 6 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 3.646 0.918 397.1 65: (ns/day) (hour/ns) 65: Performance: 0.470 51.014 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 65: 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (1591 ms) 65: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (3285 ms total) 65: 65: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 65: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Pull group 1 'FirstWaterMolecule' has 3 atoms 65: Pull group 2 'SecondWaterMolecule' has 3 atoms 65: Number of degrees of freedom in T-Coupling group rest is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: Pull group natoms pbc atom distance at start reference at t=0 65: 1 3 2 65: 2 3 5 1.112 nm 1.000 nm 65: 65: There was 1 NOTE 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 4 steps, 0.0 ps. 65: Setting the LD random seed to -1143455762 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 19 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 1.008 0.252 399.9 65: (ns/day) (hour/ns) 65: Performance: 1.714 14.006 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Pull group 1 'FirstWaterMolecule' has 3 atoms 65: Pull group 2 'SecondWaterMolecule' has 3 atoms 65: Number of degrees of freedom in T-Coupling group rest is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: Pull group natoms pbc atom distance at start reference at t=0 65: 1 3 2 65: 2 3 5 1.112 nm 1.000 nm 65: 65: There was 1 NOTE 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 65: Can not increase nstlist because an NVE ensemble is used 65: 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 4 steps, 0.0 ps. 65: Setting the LD random seed to -580124969 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 15 % of the run time was spent in domain decomposition, 65: 0 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 42 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.724 0.181 399.8 65: (ns/day) (hour/ns) 65: Performance: 2.386 10.058 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 65: 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (749 ms) 65: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (749 ms total) 65: 65: [----------] 12 tests from FreezeWorks/FreezeGroupTest 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 65: NVE simulation: will use the initial temperature of 318.937 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 5 NOTEs 65: 65: There was 1 WARNING 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 39.9%. 65: The balanceable part of the MD step is 50%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 19.7%. 65: 65: NOTE: 19.7 % of the available CPU time was lost due to load imbalance 65: in the domain decomposition. 65: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 65: You can also consider manually changing the decomposition (option -dd); 65: e.g. by using fewer domains along the box dimension in which there is 65: considerable inhomogeneity in the simulated system. 65: 65: NOTE: 12 % of the run time was spent in domain decomposition, 65: 2 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 6 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 3.684 0.922 399.6 65: (ns/day) (hour/ns) 65: Performance: 0.844 28.449 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (1009 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 65: NVE simulation: will use the initial temperature of 318.937 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 5 NOTEs 65: 65: There was 1 WARNING 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 30.2%. 65: The balanceable part of the MD step is 13%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 4.0%. 65: 65: 65: NOTE: 23 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.750 0.196 382.6 65: (ns/day) (hour/ns) 65: Performance: 3.968 6.048 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (461 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 65: NVE simulation: will use the initial temperature of 318.937 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 5 NOTEs 65: 65: There was 1 WARNING 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 0.3%. 65: The balanceable part of the MD step is 11%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 0.0%. 65: 65: 65: NOTE: 38 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.206 0.062 332.2 65: (ns/day) (hour/ns) 65: Performance: 12.564 1.910 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (102 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 65: NVE simulation: will use the initial temperature of 318.937 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 5 NOTEs 65: 65: There was 1 WARNING 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 8.4%. 65: The balanceable part of the MD step is 38%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 3.2%. 65: 65: 65: NOTE: 49 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.156 0.039 399.2 65: (ns/day) (hour/ns) 65: Performance: 19.948 1.203 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (282 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 65: NVE simulation: will use the initial temperature of 318.937 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 5 NOTEs 65: 65: There was 1 WARNING 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 5.0%. 65: The balanceable part of the MD step is 0%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 0.0%. 65: 65: 65: NOTE: 51 % of the run time was spent in domain decomposition, 65: 2 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 14 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.784 0.198 396.0 65: (ns/day) (hour/ns) 65: Performance: 3.927 6.112 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (611 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 65: ./src/programs/mdrun/tests/freezegroups.cpp:194: Skipped 65: Parrinello-Rahman is not implemented in md-vv. 65: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: 65: There was 1 WARNING 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 65: 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 52 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.456 0.126 362.1 65: (ns/day) (hour/ns) 65: Performance: 6.175 3.887 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (249 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: 65: There was 1 WARNING 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 65: 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 49 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.127 0.032 399.2 65: (ns/day) (hour/ns) 65: Performance: 24.451 0.982 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (124 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: 65: There was 1 WARNING 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 65: 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 23 % of the run time was spent in domain decomposition, 65: 7 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 11 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 1.202 0.301 399.4 65: (ns/day) (hour/ns) 65: Performance: 2.583 9.291 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (423 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: 65: There was 1 WARNING 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 65: 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 3.212 0.806 398.5 65: (ns/day) (hour/ns) 65: Performance: 0.965 24.878 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (1001 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: 65: There was 1 WARNING 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 65: 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 11 % of the run time was spent in domain decomposition, 65: 0 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 19 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.647 0.164 395.2 65: (ns/day) (hour/ns) 65: Performance: 4.746 5.057 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (289 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: 65: There was 1 WARNING 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 65: 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 16 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.448 0.112 399.8 65: (ns/day) (hour/ns) 65: Performance: 6.939 3.459 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (560 ms) 65: [----------] 12 tests from FreezeWorks/FreezeGroupTest (5116 ms total) 65: 65: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 65: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 65: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: Net Acceleration in X direction, will not be corrected 65: Net Acceleration in Y direction, will not be corrected 65: Net Acceleration in Z direction, will not be corrected 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 8 steps, 0.0 ps. 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Setting gen_seed to 1576988155 65: 65: Velocities were taken from a Maxwell distribution at 0 K 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 17.6%. 65: The balanceable part of the MD step is 45%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 8.0%. 65: 65: NOTE: 8.0 % of the available CPU time was lost due to load imbalance 65: in the domain decomposition. 65: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 65: You can also consider manually changing the decomposition (option -dd); 65: e.g. by using fewer domains along the box dimension in which there is 65: considerable inhomogeneity in the simulated system. 65: 65: NOTE: 15 % of the run time was spent in domain decomposition, 65: 0 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 18 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.946 0.253 374.7 65: (ns/day) (hour/ns) 65: Performance: 6.158 3.897 65: 65: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (688 ms) 65: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 65: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 65: Net Acceleration in X direction, will not be corrected 65: Net Acceleration in Y direction, will not be corrected 65: Net Acceleration in Z direction, will not be corrected 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because verlet-buffer-tolerance is not set or used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 8 steps, 0.0 ps. 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Setting gen_seed to -1893762193 65: 65: Velocities were taken from a Maxwell distribution at 0 K 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 8.8%. 65: The balanceable part of the MD step is 45%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 4.0%. 65: 65: 65: NOTE: 13 % of the run time was spent in domain decomposition, 65: 2 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 13 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 1.552 0.388 399.9 65: (ns/day) (hour/ns) 65: Performance: 4.008 5.989 65: 65: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (647 ms) 65: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 65: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: Net Acceleration in X direction, will not be corrected 65: Net Acceleration in Y direction, will not be corrected 65: Net Acceleration in Z direction, will not be corrected 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 8 steps, 0.0 ps. 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Setting gen_seed to 1598807933 65: 65: Velocities were taken from a Maxwell distribution at 0 K 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 1.7%. 65: The balanceable part of the MD step is 67%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 1.1%. 65: 65: 65: NOTE: 12 % of the run time was spent in domain decomposition, 65: 6 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 4.280 1.070 400.0 65: (ns/day) (hour/ns) 65: Performance: 1.453 16.513 65: 65: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (1192 ms) 65: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 65: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 65: Net Acceleration in X direction, will not be corrected 65: Net Acceleration in Y direction, will not be corrected 65: Net Acceleration in Z direction, will not be corrected 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because verlet-buffer-tolerance is not set or used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 8 steps, 0.0 ps. 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Setting gen_seed to -1886390549 65: 65: Velocities were taken from a Maxwell distribution at 0 K 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 6.4%. 65: The balanceable part of the MD step is 29%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 1.8%. 65: 65: 65: NOTE: 15 % of the run time was spent in domain decomposition, 65: 7 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 13 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 1.199 0.302 397.3 65: (ns/day) (hour/ns) 65: Performance: 5.152 4.659 65: 65: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (627 ms) 65: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (3156 ms total) 65: 65: [----------] Global test environment tear-down 65: [==========] 28 tests from 7 test suites ran. (17087 ms total) 65: [ PASSED ] 27 tests. 65: [ SKIPPED ] 1 test, listed below: 65: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 65/87 Test #65: MdrunTestsTwoRanks ........................ Passed 17.13 sec test 66 Start 66: MdrunSingleRankAlgorithmsTests 66: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-single-rank-algorithms-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunSingleRankAlgorithmsTests.xml" 66: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 66: Test timeout computed to be: 600 66: [==========] Running 5 tests from 3 test suites. 66: [----------] Global test environment set-up. 66: [----------] 1 test from DispersionCorrectionTest 66: [ RUN ] DispersionCorrectionTest.DispersionCorrectionCanRun 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 30.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Changing nstlist from 10 to 40, rlist from 1.023 to 1.158 66: 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 200 steps, 0.4 ps. 66: Setting the LD random seed to -16974097 66: 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning H bonds into constraints... 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Converted 3 Bonds with virtual sites to connections, 7 left 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 12 Constraints with virtual sites to connections, 0 left 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.038 nm, buffer size 0.038 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.023 nm, buffer size 0.023 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.260 0.130 199.9 66: (ns/day) (hour/ns) 66: Performance: 267.397 0.090 66: [ OK ] DispersionCorrectionTest.DispersionCorrectionCanRun (199 ms) 66: [----------] 1 test from DispersionCorrectionTest (199 ms total) 66: 66: [----------] 1 test from OriresTest 66: [ RUN ] OriresTest.OriresCanRun 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 518.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank. 66: Changing nstlist from 10 to 25, rlist from 1.07 to 1.203 66: 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1' 66: 10 steps, 0.0 ps. 66: Setting the LD random seed to -170424597 66: 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.070 nm, buffer size 0.070 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.189 0.095 199.9 66: (ns/day) (hour/ns) 66: Performance: 20.082 1.195 66: [ OK ] OriresTest.OriresCanRun (803 ms) 66: [----------] 1 test from OriresTest (803 ms total) 66: 66: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest 66: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 66: Number of degrees of freedom in T-Coupling group rest is 10.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 66: NVE simulation with an initial temperature of zero: will use a Verlet 66: buffer of 10%. Check your energy drift! 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 66: The optimal PME mesh load for parallel simulations is below 0.5 66: and for highly parallel simulations between 0.25 and 0.33, 66: for higher performance, increase the cut-off and the PME grid spacing. 66: 66: 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Dipoles' 66: 20 steps, 0.1 ps. 66: Setting the LD random seed to -604115042 66: 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Dipole' 66: 66: Searching the wall atom type(s) 66: 66: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 66: Calculating fourier grid dimensions for X Y Z 66: Using a fourier grid of 20x20x40, spacing 0.200 0.200 0.200 66: 66: Estimate for the relative computational load of the PME mesh part: 1.00 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.101 0.051 199.6 66: (ns/day) (hour/ns) 66: Performance: 89.772 0.267 66: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 trr version: GMX_trn_file (single precision) 66: 66: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 (957 ms) 66: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 66: Test system 'epsilon-surface-constraint' cannot run with 1 ranks. 66: The supported numbers are > 1. 66: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 (0 ms) 66: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 66: With epsilon_surface > 0 all molecules should be neutral. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 66: With epsilon_surface > 0 you can only use domain decomposition when there 66: are only small molecules with all bonds constrained (mdrun will check for 66: this). 66: 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 66: NVE simulation with an initial temperature of zero: will use a Verlet 66: buffer of 10%. Check your energy drift! 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 66: The optimal PME mesh load for parallel simulations is below 0.5 66: and for highly parallel simulations between 0.25 and 0.33, 66: for higher performance, increase the cut-off and the PME grid spacing. 66: 66: 66: 66: There were 4 NOTEs 66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Dipoles' 66: 20 steps, 0.1 ps. 66: Setting the LD random seed to -1209812129 66: 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Dipole' 66: 66: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 66: Calculating fourier grid dimensions for X Y Z 66: Using a fourier grid of 20x20x20, spacing 0.200 0.200 0.200 66: 66: Estimate for the relative computational load of the PME mesh part: 1.00 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.087 0.044 199.6 66: (ns/day) (hour/ns) 66: Performance: 103.520 0.232 66: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 66: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 (362 ms) 66: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest (1320 ms total) 66: 66: [----------] Global test environment tear-down 66: [==========] 5 tests from 3 test suites ran. (2416 ms total) 66: [ PASSED ] 5 tests. 66/87 Test #66: MdrunSingleRankAlgorithmsTests ............ Passed 2.44 sec test 67 Start 67: Minimize1RankTests 67: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/minimize-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/Minimize1RankTests.xml" 67: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 67: Test timeout computed to be: 600 67: [==========] Running 12 tests from 2 test suites. 67: [----------] Global test environment set-up. 67: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 67: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group System is 27.00 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 4 NOTEs 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 5 steps. 67: Potential Energy = -4.7991035e+01 67: Maximum force = 1.8629774e+02 on atom 13 67: Norm of force = 8.7722025e+01 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 67: 67: Generated 330891 of the 330891 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (374 ms) 67: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group System is 27.00 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 4 NOTEs 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Polak-Ribiere Conjugate Gradients: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: F-max = 3.02331e+02 on atom 3 67: F-Norm = 1.18024e+02 67: 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 67: Potential Energy = -5.5862438e+01 67: Maximum force = 4.2726288e+02 on atom 13 67: Norm of force = 1.8452569e+02 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 67: 67: Generated 330891 of the 330891 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (309 ms) 67: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: Generating 1-4 interactions: fudge = 1 67: Number of degrees of freedom in T-Coupling group System is 22.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 4 NOTEs 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 5 steps. 67: Potential Energy = 3.1937726e+02 67: Maximum force = 9.9988652e+03 on atom 9 67: Norm of force = 4.6166996e+03 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 67: 67: Generated 17396 of the 20503 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Glycine' 67: 67: turning H bonds into constraints... 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (101 ms) 67: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: Generating 1-4 interactions: fudge = 1 67: 67: NOTE 3 [file glycine_vacuo.top, line 12]: 67: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 67: 67: Number of degrees of freedom in T-Coupling group System is 22.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 5 NOTEs 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Polak-Ribiere Conjugate Gradients: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: F-max = 2.41575e+04 on atom 10 67: F-Norm = 1.18451e+04 67: 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 67: Potential Energy = 1.5174292e+02 67: Maximum force = 7.4208784e+03 on atom 9 67: Norm of force = 3.5692952e+03 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 67: 67: Generated 17396 of the 20503 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Glycine' 67: 67: turning H bonds into constraints... 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (78 ms) 67: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file unknown]: 67: You are using constraints on all bonds, whereas the forcefield has been 67: parametrized only with constraints involving hydrogen atoms. We suggest 67: using constraints = h-bonds instead, this will also improve performance. 67: 67: Number of degrees of freedom in T-Coupling group System is 23.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 5 NOTEs 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Update groups can not be used for this system because an incompatible virtual site type is used 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 5 steps. 67: Potential Energy = -1.5698425e+02 67: Maximum force = 4.5703290e+02 on atom 17 67: Norm of force = 1.8327769e+02 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 67: 67: turning all bonds into constraints... 67: 67: Cleaning up constraints and constant bonded interactions with virtual sites 67: 67: Removed 18 Angles with virtual sites, 21 left 67: 67: Removed 10 Proper Dih.s with virtual sites, 44 left 67: 67: Converted 15 Constraints with virtual sites to connections, 7 left 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (26 ms) 67: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file unknown]: 67: You are using constraints on all bonds, whereas the forcefield has been 67: parametrized only with constraints involving hydrogen atoms. We suggest 67: using constraints = h-bonds instead, this will also improve performance. 67: 67: 67: NOTE 4 [file unknown]: 67: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 67: 67: Number of degrees of freedom in T-Coupling group System is 23.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 6 NOTEs 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Update groups can not be used for this system because an incompatible virtual site type is used 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Polak-Ribiere Conjugate Gradients: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: F-max = 1.06801e+03 on atom 28 67: F-Norm = 4.26916e+02 67: 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 67: Potential Energy = -1.6941193e+02 67: Maximum force = 2.1831454e+02 on atom 17 67: Norm of force = 7.9220636e+01 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 67: 67: turning all bonds into constraints... 67: 67: Cleaning up constraints and constant bonded interactions with virtual sites 67: 67: Removed 18 Angles with virtual sites, 21 left 67: 67: Removed 10 Proper Dih.s with virtual sites, 44 left 67: 67: Converted 15 Constraints with virtual sites to connections, 7 left 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (235 ms) 67: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (1127 ms total) 67: 67: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 67: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents converged to Fmax < 10 in 1 steps 67: Potential Energy = -9.7425687e-01 67: Maximum force = 4.0132279e+00 on atom 1 67: Norm of force = 1.6383933e+00 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (20 ms) 67: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Polak-Ribiere Conjugate Gradients: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: F-max = 4.01323e+00 on atom 1 67: F-Norm = 1.63839e+00 67: 67: 67: writing lowest energy coordinates. 67: 67: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 67: Potential Energy = -9.9064195e-01 67: Maximum force = 2.5781672e+00 on atom 1 67: Norm of force = 1.0525324e+00 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (26 ms) 67: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 67: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 3 NOTEs 67: 67: There was 1 WARNING 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Low-Memory BFGS Minimizer: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: Using 10 BFGS correction steps. 67: 67: F-max = 4.01323e+00 on atom 1 67: F-Norm = 1.63839e+00 67: 67: 67: writing lowest energy coordinates. 67: 67: Low-Memory BFGS Minimizer converged to Fmax < 10 in -1 steps 67: Potential Energy = -9.9064195e-01 67: Maximum force = 2.5781672e+00 on atom 1 67: Norm of force = 1.0525324e+00 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (14 ms) 67: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: Generating 1-4 interactions: fudge = 1 67: Number of degrees of freedom in T-Coupling group System is 27.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 4 NOTEs 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 5 steps. 67: Potential Energy = 3.1939697e+02 67: Maximum force = 9.9704248e+03 on atom 9 67: Norm of force = 4.6227540e+03 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 67: 67: Generated 17396 of the 20503 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Glycine' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (104 ms) 67: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: Generating 1-4 interactions: fudge = 1 67: Number of degrees of freedom in T-Coupling group System is 27.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 4 NOTEs 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Polak-Ribiere Conjugate Gradients: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: F-max = 2.41672e+04 on atom 10 67: F-Norm = 1.19357e+04 67: 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 67: Potential Energy = 1.5625757e+02 67: Maximum force = 7.5018242e+03 on atom 9 67: Norm of force = 3.6139019e+03 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 67: 67: Generated 17396 of the 20503 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Glycine' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (62 ms) 67: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 67: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 67: 67: Generating 1-4 interactions: fudge = 1 67: Number of degrees of freedom in T-Coupling group System is 27.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Low-Memory BFGS Minimizer: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: Using 10 BFGS correction steps. 67: 67: F-max = 2.41672e+04 on atom 10 67: F-Norm = 1.19357e+04 67: 67: 67: Energy minimization has stopped, but the forces have not converged to the 67: requested precision Fmax < 10 (which may not be possible for your system). It 67: stopped because the algorithm tried to make a new step whose size was too 67: small, or there was no change in the energy since last step. Either way, we 67: regard the minimization as converged to within the available machine 67: precision, given your starting configuration and EM parameters. 67: 67: Double precision normally gives you higher accuracy, but this is often not 67: needed for preparing to run molecular dynamics. 67: 67: writing lowest energy coordinates. 67: 67: Low-Memory BFGS Minimizer converged to machine precision in 0 steps, 67: but did not reach the requested Fmax < 10. 67: Potential Energy = 5.6111725e+02 67: Maximum force = 1.2685491e+04 on atom 10 67: Norm of force = 6.0643622e+03 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 67: 67: Generated 17396 of the 20503 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Glycine' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (57 ms) 67: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (286 ms total) 67: 67: [----------] Global test environment tear-down 67: [==========] 12 tests from 2 test suites ran. (1502 ms total) 67: [ PASSED ] 12 tests. 67/87 Test #67: Minimize1RankTests ........................ Passed 1.52 sec test 68 Start 68: Minimize2RankTests 68: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/minimize-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/Minimize2RankTests.xml" 68: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 68: Test timeout computed to be: 600 68: [==========] Running 12 tests from 2 test suites. 68: [----------] Global test environment set-up. 68: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 68: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 27.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 4 NOTEs 68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: Steepest Descents: 68: Tolerance (Fmax) = 1.00000e+01 68: Number of steps = 4 68: 68: Energy minimization reached the maximum number of steps before the forces 68: reached the requested precision Fmax < 10. 68: 68: writing lowest energy coordinates. 68: 68: Steepest Descents did not converge to Fmax < 10 in 5 steps. 68: Potential Energy = -4.7991009e+01 68: Maximum force = 1.8629736e+02 on atom 13 68: Norm of force = 8.7722017e+01 68: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 68: 68: Generated 330891 of the 330891 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (420 ms) 68: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 27.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 4 NOTEs 68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: Polak-Ribiere Conjugate Gradients: 68: Tolerance (Fmax) = 1.00000e+01 68: Number of steps = 4 68: F-max = 3.02331e+02 on atom 3 68: F-Norm = 1.18024e+02 68: 68: 68: Energy minimization reached the maximum number of steps before the forces 68: reached the requested precision Fmax < 10. 68: 68: writing lowest energy coordinates. 68: 68: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 68: Potential Energy = -5.5862362e+01 68: Maximum force = 4.2726562e+02 on atom 13 68: Norm of force = 1.8452687e+02 68: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 68: 68: Generated 330891 of the 330891 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (824 ms) 68: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: Generating 1-4 interactions: fudge = 1 68: Number of degrees of freedom in T-Coupling group System is 22.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 4 NOTEs 68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: Steepest Descents: 68: Tolerance (Fmax) = 1.00000e+01 68: Number of steps = 4 68: 68: Energy minimization reached the maximum number of steps before the forces 68: reached the requested precision Fmax < 10. 68: 68: writing lowest energy coordinates. 68: 68: Steepest Descents did not converge to Fmax < 10 in 5 steps. 68: Potential Energy = 3.1937708e+02 68: Maximum force = 9.9988643e+03 on atom 9 68: Norm of force = 4.6166993e+03 68: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 68: 68: Generated 17396 of the 20503 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Glycine' 68: 68: turning H bonds into constraints... 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (259 ms) 68: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: Generating 1-4 interactions: fudge = 1 68: 68: NOTE 3 [file glycine_vacuo.top, line 12]: 68: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 68: 68: Number of degrees of freedom in T-Coupling group System is 22.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 5 NOTEs 68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: Polak-Ribiere Conjugate Gradients: 68: Tolerance (Fmax) = 1.00000e+01 68: Number of steps = 4 68: F-max = 2.41575e+04 on atom 10 68: F-Norm = 1.18451e+04 68: 68: 68: Energy minimization reached the maximum number of steps before the forces 68: reached the requested precision Fmax < 10. 68: 68: writing lowest energy coordinates. 68: 68: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 68: Potential Energy = 1.5174438e+02 68: Maximum force = 7.4208867e+03 on atom 9 68: Norm of force = 3.5692995e+03 68: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 68: 68: Generated 17396 of the 20503 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Glycine' 68: 68: turning H bonds into constraints... 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (987 ms) 68: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 5 NOTEs 68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: Steepest Descents: 68: Tolerance (Fmax) = 1.00000e+01 68: Number of steps = 4 68: 68: Energy minimization reached the maximum number of steps before the forces 68: reached the requested precision Fmax < 10. 68: 68: writing lowest energy coordinates. 68: 68: Steepest Descents did not converge to Fmax < 10 in 5 steps. 68: Potential Energy = -1.5698413e+02 68: Maximum force = 4.5703293e+02 on atom 17 68: Norm of force = 1.8327771e+02 68: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (1138 ms) 68: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: 68: NOTE 4 [file unknown]: 68: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 6 NOTEs 68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: Polak-Ribiere Conjugate Gradients: 68: Tolerance (Fmax) = 1.00000e+01 68: Number of steps = 4 68: F-max = 1.06801e+03 on atom 28 68: F-Norm = 4.26916e+02 68: 68: 68: Energy minimization reached the maximum number of steps before the forces 68: reached the requested precision Fmax < 10. 68: 68: writing lowest energy coordinates. 68: 68: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 68: Potential Energy = -1.6941205e+02 68: Maximum force = 2.1833974e+02 on atom 17 68: Norm of force = 7.9218953e+01 68: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (653 ms) 68: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (4283 ms total) 68: 68: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 68: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: Steepest Descents: 68: Tolerance (Fmax) = 1.00000e+01 68: Number of steps = 4 68: 68: writing lowest energy coordinates. 68: 68: Steepest Descents converged to Fmax < 10 in 1 steps 68: Potential Energy = -9.7425687e-01 68: Maximum force = 4.0132279e+00 on atom 3 68: Norm of force = 1.6383933e+00 68: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (188 ms) 68: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: Polak-Ribiere Conjugate Gradients: 68: Tolerance (Fmax) = 1.00000e+01 68: Number of steps = 4 68: F-max = 4.01323e+00 on atom 3 68: F-Norm = 1.63839e+00 68: 68: 68: writing lowest energy coordinates. 68: 68: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 68: Potential Energy = -9.9064195e-01 68: Maximum force = 2.5781672e+00 on atom 3 68: Norm of force = 1.0525324e+00 68: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (480 ms) 68: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 68: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 3 NOTEs 68: 68: There was 1 WARNING 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (2 ms) 68: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: Generating 1-4 interactions: fudge = 1 68: Number of degrees of freedom in T-Coupling group System is 27.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 4 NOTEs 68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: Steepest Descents: 68: Tolerance (Fmax) = 1.00000e+01 68: Number of steps = 4 68: 68: Energy minimization reached the maximum number of steps before the forces 68: reached the requested precision Fmax < 10. 68: 68: writing lowest energy coordinates. 68: 68: Steepest Descents did not converge to Fmax < 10 in 5 steps. 68: Potential Energy = 3.1939685e+02 68: Maximum force = 9.9704248e+03 on atom 9 68: Norm of force = 4.6227568e+03 68: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 68: 68: Generated 17396 of the 20503 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Glycine' 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (138 ms) 68: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: Generating 1-4 interactions: fudge = 1 68: Number of degrees of freedom in T-Coupling group System is 27.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 4 NOTEs 68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: Polak-Ribiere Conjugate Gradients: 68: Tolerance (Fmax) = 1.00000e+01 68: Number of steps = 4 68: F-max = 2.41672e+04 on atom 10 68: F-Norm = 1.19357e+04 68: 68: 68: Energy minimization reached the maximum number of steps before the forces 68: reached the requested precision Fmax < 10. 68: 68: writing lowest energy coordinates. 68: 68: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 68: Potential Energy = 1.5625764e+02 68: Maximum force = 7.5018237e+03 on atom 9 68: Norm of force = 3.6139019e+03 68: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 68: 68: Generated 17396 of the 20503 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Glycine' 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (596 ms) 68: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 68: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 68: 68: Generating 1-4 interactions: fudge = 1 68: Number of degrees of freedom in T-Coupling group System is 27.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 4 NOTEs 68: 68: There was 1 WARNING 68: Generated 20503 of the 20503 non-bonded parameter combinations 68: 68: Generated 17396 of the 20503 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Glycine' 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (84 ms) 68: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (1497 ms total) 68: 68: [----------] Global test environment tear-down 68: [==========] 12 tests from 2 test suites ran. (5837 ms total) 68: [ PASSED ] 12 tests. 68/87 Test #68: Minimize2RankTests ........................ Passed 5.87 sec test 69 Start 69: MdrunNonIntegratorTests 69: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunNonIntegratorTests.xml" 69: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 69: Test timeout computed to be: 600 69: [==========] Running 46 tests from 3 test suites. 69: [----------] Global test environment set-up. 69: [----------] 1 test from NonbondedBenchTest 69: [ RUN ] NonbondedBenchTest.BasicEndToEndTest 69: SIMD width: 4 69: System size: 3000 atoms 69: Cut-off radius: 1 nm 69: Number of threads: 1 69: Number of iterations: 1 69: Compute energies: no 69: Ewald excl. corr.: analytical 69: 69: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle 69: total useful 69: Ewald all geom. 4xM 14.722 14.7219 0.0809 0.0428 69: [ OK ] NonbondedBenchTest.BasicEndToEndTest (30 ms) 69: [----------] 1 test from NonbondedBenchTest (30 ms total) 69: 69: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 69: NVE simulation: will use the initial temperature of 68.810 K for 69: determining the Verlet buffer size 69: 69: 69: There were 3 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Argon' 69: 16 steps, 0.0 ps. 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Argon' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 44 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.144 0.072 199.8 69: (ns/day) (hour/ns) 69: Performance: 20.373 1.178 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr' 69: 69: trr version: GMX_trn_file (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 20 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.000 192.2 69: (ns/day) (hour/ns) 69: Performance: 3180.482 0.008 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (141 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 69: NVE simulation: will use the initial temperature of 68.810 K for 69: determining the Verlet buffer size 69: 69: 69: There were 3 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Argon' 69: 16 steps, 0.0 ps. 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Argon' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.054 0.027 199.8 69: (ns/day) (hour/ns) 69: Performance: 54.312 0.442 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 20 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.000 192.2 69: (ns/day) (hour/ns) 69: Performance: 3190.364 0.008 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (46 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: There were 2 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 100, rlist from 0.712 to 0.744 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Argon' 69: 16 steps, 0.0 ps. 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Argon' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.038 0.019 199.6 69: (ns/day) (hour/ns) 69: Performance: 76.532 0.314 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 100, rlist from 0.712 to 0.744 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 20 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.000 191.7 69: (ns/day) (hour/ns) 69: Performance: 3324.659 0.007 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (54 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: There were 2 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Argon' 69: 16 steps, 0.0 ps. 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Argon' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.160 0.080 199.9 69: (ns/day) (hour/ns) 69: Performance: 18.308 1.311 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 21 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.000 192.1 69: (ns/day) (hour/ns) 69: Performance: 3198.647 0.008 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (93 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 69: NVE simulation: will use the initial temperature of 398.997 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.056 0.028 199.6 69: (ns/day) (hour/ns) 69: Performance: 52.826 0.454 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.009 0.004 199.4 69: (ns/day) (hour/ns) 69: Performance: 334.288 0.072 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (448 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 69: NVE simulation: will use the initial temperature of 398.997 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.104 0.052 199.9 69: (ns/day) (hour/ns) 69: Performance: 28.226 0.850 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.005 0.002 198.0 69: (ns/day) (hour/ns) 69: Performance: 643.673 0.037 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (312 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 100, rlist from 0.735 to 0.831 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.738 nm, buffer size 0.038 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.158 0.079 199.9 69: (ns/day) (hour/ns) 69: Performance: 18.555 1.293 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 100, rlist from 0.735 to 0.831 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 49 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.505 0.252 200.0 69: (ns/day) (hour/ns) 69: Performance: 5.822 4.122 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (614 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.043 0.022 199.6 69: (ns/day) (hour/ns) 69: Performance: 68.013 0.353 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 17 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.001 194.4 69: (ns/day) (hour/ns) 69: Performance: 2829.855 0.008 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (256 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file unknown]: 69: You are using constraints on all bonds, whereas the forcefield has been 69: parametrized only with constraints involving hydrogen atoms. We suggest 69: using constraints = h-bonds instead, this will also improve performance. 69: 69: Number of degrees of freedom in T-Coupling group System is 23.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 69: NVE simulation: will use the initial temperature of 456.887 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 69: There are 9 non-linear virtual site constructions. Their contribution to 69: the energy error is approximated. In most cases this does not affect the 69: error significantly. 69: 69: 69: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 6 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine dipeptide in vacuo' 69: 16 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: turning all bonds into constraints... 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Converted 15 Constraints with virtual sites to connections, 7 left 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.063 0.031 199.6 69: (ns/day) (hour/ns) 69: Performance: 46.653 0.514 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 23 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.001 193.6 69: (ns/day) (hour/ns) 69: Performance: 2447.594 0.010 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (59 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file unknown]: 69: You are using constraints on all bonds, whereas the forcefield has been 69: parametrized only with constraints involving hydrogen atoms. We suggest 69: using constraints = h-bonds instead, this will also improve performance. 69: 69: Number of degrees of freedom in T-Coupling group System is 23.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 69: NVE simulation: will use the initial temperature of 456.887 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 69: There are 9 non-linear virtual site constructions. Their contribution to 69: the energy error is approximated. In most cases this does not affect the 69: error significantly. 69: 69: 69: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 6 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine dipeptide in vacuo' 69: 16 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: turning all bonds into constraints... 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Converted 15 Constraints with virtual sites to connections, 7 left 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.344 0.172 199.9 69: (ns/day) (hour/ns) 69: Performance: 8.523 2.816 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 17 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 193.4 69: (ns/day) (hour/ns) 69: Performance: 1619.079 0.015 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (275 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file unknown]: 69: You are using constraints on all bonds, whereas the forcefield has been 69: parametrized only with constraints involving hydrogen atoms. We suggest 69: using constraints = h-bonds instead, this will also improve performance. 69: 69: Number of degrees of freedom in T-Coupling group System is 23.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 69: There are 9 non-linear virtual site constructions. Their contribution to 69: the energy error is approximated. In most cases this does not affect the 69: error significantly. 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 80, rlist from 0.748 to 0.865 69: 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine dipeptide in vacuo' 69: 16 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: turning all bonds into constraints... 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Converted 15 Constraints with virtual sites to connections, 7 left 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.039 0.019 199.4 69: (ns/day) (hour/ns) 69: Performance: 75.703 0.317 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 80, rlist from 0.748 to 0.865 69: 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 18 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 194.4 69: (ns/day) (hour/ns) 69: Performance: 1789.310 0.013 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (215 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file unknown]: 69: You are using constraints on all bonds, whereas the forcefield has been 69: parametrized only with constraints involving hydrogen atoms. We suggest 69: using constraints = h-bonds instead, this will also improve performance. 69: 69: Number of degrees of freedom in T-Coupling group System is 23.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 69: There are 9 non-linear virtual site constructions. Their contribution to 69: the energy error is approximated. In most cases this does not affect the 69: error significantly. 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 25, rlist from 0.729 to 0.81 69: 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine dipeptide in vacuo' 69: 16 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: turning all bonds into constraints... 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Converted 15 Constraints with virtual sites to connections, 7 left 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.040 0.020 199.5 69: (ns/day) (hour/ns) 69: Performance: 73.506 0.327 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 25, rlist from 0.729 to 0.81 69: 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 20 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.001 192.7 69: (ns/day) (hour/ns) 69: Performance: 1989.856 0.012 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (110 ms) 69: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (2630 ms total) 69: 69: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.043 0.022 199.5 69: (ns/day) (hour/ns) 69: Performance: 67.420 0.356 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 22 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.001 177.8 69: (ns/day) (hour/ns) 69: Performance: 2296.159 0.010 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (57 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.067 0.033 199.6 69: (ns/day) (hour/ns) 69: Performance: 44.014 0.545 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 13 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.001 177.2 69: (ns/day) (hour/ns) 69: Performance: 2291.888 0.010 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (47 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.170 0.085 199.8 69: (ns/day) (hour/ns) 69: Performance: 17.244 1.392 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.020 0.010 197.8 69: (ns/day) (hour/ns) 69: Performance: 142.057 0.169 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (164 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.134 0.067 199.7 69: (ns/day) (hour/ns) 69: Performance: 21.823 1.100 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 20 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.001 176.7 69: (ns/day) (hour/ns) 69: Performance: 2047.389 0.012 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (91 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.065 0.033 199.6 69: (ns/day) (hour/ns) 69: Performance: 45.089 0.532 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 20 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.001 181.2 69: (ns/day) (hour/ns) 69: Performance: 2144.307 0.011 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (47 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.032 0.016 199.3 69: (ns/day) (hour/ns) 69: Performance: 91.808 0.261 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 20 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.001 182.2 69: (ns/day) (hour/ns) 69: Performance: 2157.826 0.011 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (60 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.046 0.023 199.4 69: (ns/day) (hour/ns) 69: Performance: 63.465 0.378 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 20 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.001 183.0 69: (ns/day) (hour/ns) 69: Performance: 2050.797 0.012 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (43 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.046 0.023 199.4 69: (ns/day) (hour/ns) 69: Performance: 63.278 0.379 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 19 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.001 183.1 69: (ns/day) (hour/ns) 69: Performance: 1879.376 0.013 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (147 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.054 0.027 199.5 69: (ns/day) (hour/ns) 69: Performance: 54.547 0.440 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 23 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.001 181.4 69: (ns/day) (hour/ns) 69: Performance: 2236.150 0.011 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (51 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.072 0.036 199.5 69: (ns/day) (hour/ns) 69: Performance: 40.580 0.591 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.016 0.008 197.9 69: (ns/day) (hour/ns) 69: Performance: 186.498 0.129 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (73 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.081 0.042 195.1 69: (ns/day) (hour/ns) 69: Performance: 35.180 0.682 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.004 0.002 169.9 69: (ns/day) (hour/ns) 69: Performance: 606.238 0.040 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (85 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.067 0.034 199.8 69: (ns/day) (hour/ns) 69: Performance: 43.838 0.547 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 20 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.001 181.7 69: (ns/day) (hour/ns) 69: Performance: 2101.157 0.011 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (52 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.319 0.159 199.9 69: (ns/day) (hour/ns) 69: Performance: 9.214 2.605 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 19 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.001 182.2 69: (ns/day) (hour/ns) 69: Performance: 2188.488 0.011 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (180 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.062 0.031 199.8 69: (ns/day) (hour/ns) 69: Performance: 47.643 0.504 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 24 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.001 184.5 69: (ns/day) (hour/ns) 69: Performance: 2042.637 0.012 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (47 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 24 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.336 0.168 199.9 69: (ns/day) (hour/ns) 69: Performance: 8.745 2.744 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 22 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.001 174.4 69: (ns/day) (hour/ns) 69: Performance: 1980.262 0.012 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (196 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.063 0.031 199.7 69: (ns/day) (hour/ns) 69: Performance: 46.700 0.514 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 21 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.001 182.8 69: (ns/day) (hour/ns) 69: Performance: 2193.944 0.011 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (51 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 11 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.074 0.037 199.8 69: (ns/day) (hour/ns) 69: Performance: 39.589 0.606 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 21 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.001 175.2 69: (ns/day) (hour/ns) 69: Performance: 1960.724 0.012 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (82 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.049 0.024 199.7 69: (ns/day) (hour/ns) 69: Performance: 60.282 0.398 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 12 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.009 0.005 195.4 69: (ns/day) (hour/ns) 69: Performance: 304.844 0.079 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (59 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.052 0.026 199.7 69: (ns/day) (hour/ns) 69: Performance: 55.927 0.429 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 21 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.001 182.2 69: (ns/day) (hour/ns) 69: Performance: 2332.675 0.010 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (46 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 1.092 0.546 200.0 69: (ns/day) (hour/ns) 69: Performance: 2.691 8.920 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 20 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 178.3 69: (ns/day) (hour/ns) 69: Performance: 1694.799 0.014 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (576 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 1.255 0.627 200.0 69: (ns/day) (hour/ns) 69: Performance: 2.341 10.252 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 19 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 169.9 69: (ns/day) (hour/ns) 69: Performance: 1657.856 0.014 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (685 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.083 0.041 199.7 69: (ns/day) (hour/ns) 69: Performance: 35.419 0.678 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 34 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.142 0.071 199.6 69: (ns/day) (hour/ns) 69: Performance: 20.663 1.161 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (141 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.116 0.058 199.7 69: (ns/day) (hour/ns) 69: Performance: 25.308 0.948 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.002 88.4 69: (ns/day) (hour/ns) 69: Performance: 641.461 0.037 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (114 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.080 0.040 199.6 69: (ns/day) (hour/ns) 69: Performance: 36.550 0.657 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 12 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.002 89.7 69: (ns/day) (hour/ns) 69: Performance: 641.461 0.037 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (84 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.115 0.057 199.7 69: (ns/day) (hour/ns) 69: Performance: 25.545 0.940 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.010 0.006 159.3 69: (ns/day) (hour/ns) 69: Performance: 229.086 0.105 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (109 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.128 0.064 199.7 69: (ns/day) (hour/ns) 69: Performance: 23.005 1.043 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.005 39.1 69: (ns/day) (hour/ns) 69: Performance: 286.686 0.084 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (121 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 11 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.728 0.364 200.0 69: (ns/day) (hour/ns) 69: Performance: 4.033 5.951 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 19 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 182.2 69: (ns/day) (hour/ns) 69: Performance: 1771.813 0.014 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (528 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.064 0.032 199.6 69: (ns/day) (hour/ns) 69: Performance: 45.771 0.524 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 21 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.001 176.4 69: (ns/day) (hour/ns) 69: Performance: 2157.071 0.011 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (107 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 26 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.304 0.152 199.9 69: (ns/day) (hour/ns) 69: Performance: 9.657 2.485 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.012 0.006 197.7 69: (ns/day) (hour/ns) 69: Performance: 241.687 0.099 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (308 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.309 0.154 199.9 69: (ns/day) (hour/ns) 69: Performance: 9.513 2.523 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.002 77.5 69: (ns/day) (hour/ns) 69: Performance: 798.315 0.030 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (185 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.067 0.034 199.7 69: (ns/day) (hour/ns) 69: Performance: 43.782 0.548 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.016 0.008 197.3 69: (ns/day) (hour/ns) 69: Performance: 178.661 0.134 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (83 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 14 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.565 0.282 200.0 69: (ns/day) (hour/ns) 69: Performance: 5.201 4.614 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 22 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.001 182.4 69: (ns/day) (hour/ns) 69: Performance: 2320.374 0.010 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (444 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.052 0.026 199.6 69: (ns/day) (hour/ns) 69: Performance: 56.601 0.424 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 21 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.001 183.6 69: (ns/day) (hour/ns) 69: Performance: 2009.982 0.012 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (60 ms) 69: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (5146 ms total) 69: 69: [----------] Global test environment tear-down 69: [==========] 46 tests from 3 test suites ran. (7874 ms total) 69: [ PASSED ] 46 tests. 69/87 Test #69: MdrunNonIntegratorTests ................... Passed 7.90 sec test 70 Start 70: MdrunTpiTests 70: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-tpi-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunTpiTests.xml" 70: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 70: Test timeout computed to be: 600 70: [==========] Running 2 tests from 1 test suite. 70: [----------] Global test environment set-up. 70: [----------] 2 tests from Simple/TpiTest 70: [ RUN ] Simple/TpiTest.ReproducesOutput/0 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 1308.00 70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 70: TPI is not implemented for GPUs. 70: 70: Using 1 MPI thread 70: Using 1 OpenMP thread 70: 70: 70: NOTE: Thread affinity was not set. 70: Reading frames from gro file '216 water molecules', 648 atoms. 70: Reading frame 0 time 0.000 mu 6.291e+01 6.291e+01 70: Last frame 0 time 0.000 70: Generated 331705 of the 331705 non-bonded parameter combinations 70: 70: Generated 331705 of the 331705 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Excluding 3 bonded neighbours molecule type 'methane' 70: Analysing residue names: 70: There are: 216 Water residues 70: There are: 1 Other residues 70: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] Simple/TpiTest.ReproducesOutput/0 (367 ms) 70: [ RUN ] Simple/TpiTest.ReproducesOutput/1 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 1308.00 70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 70: TPI is not implemented for GPUs. 70: 70: Using 1 MPI thread 70: Using 1 OpenMP thread 70: 70: 70: NOTE: Thread affinity was not set. 70: Reading frames from gro file '216 water molecules', 648 atoms. 70: Reading frame 0 time 0.000 mu 4.535e+01 4.535e+01 70: Last frame 0 time 0.000 70: Generated 331705 of the 331705 non-bonded parameter combinations 70: 70: Generated 331705 of the 331705 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Excluding 3 bonded neighbours molecule type 'methane' 70: Analysing residue names: 70: There are: 216 Water residues 70: There are: 1 Other residues 70: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] Simple/TpiTest.ReproducesOutput/1 (420 ms) 70: [----------] 2 tests from Simple/TpiTest (788 ms total) 70: 70: [----------] Global test environment tear-down 70: [==========] 2 tests from 1 test suite ran. (820 ms total) 70: [ PASSED ] 2 tests. 70/87 Test #70: MdrunTpiTests ............................. Passed 0.84 sec test 71 Start 71: MdrunMpiTests 71: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunMpiTests.xml" 71: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 71: Test timeout computed to be: 600 71: [==========] Running 16 tests from 2 test suites. 71: [----------] Global test environment set-up. 71: [----------] 4 tests from MimicTest 71: [ RUN ] MimicTest.OneQuantumMol 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 71: For a correct single-point energy evaluation with nsteps = 0, use 71: continuation = yes to avoid constraining the input coordinates. 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group rest is 21.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/4water.gro' 71: 71: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 71: Reading frame 0 time 0.000 Last frame 0 time 0.000 71: 71: NOTE: 42 % of the run time was spent in domain decomposition, 71: 13 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.490 0.122 399.9 71: (ns/day) (hour/ns) 71: Performance: 0.706 34.012 71: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -58770989 71: 71: Generated 10 of the 10 non-bonded parameter combinations 71: 71: Generated 10 of the 10 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MimicTest.OneQuantumMol (228 ms) 71: [ RUN ] MimicTest.AllQuantumMol 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 71: For a correct single-point energy evaluation with nsteps = 0, use 71: continuation = yes to avoid constraining the input coordinates. 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group rest is 21.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/4water.gro' 71: 71: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 71: Reading frame 0 time 0.000 Last frame 0 time 0.000 71: 71: NOTE: 34 % of the run time was spent in domain decomposition, 71: 8 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.002 0.000 381.9 71: (ns/day) (hour/ns) 71: Performance: 181.375 0.132 71: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -25708603 71: 71: Generated 10 of the 10 non-bonded parameter combinations 71: 71: Generated 10 of the 10 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MimicTest.AllQuantumMol (44 ms) 71: [ RUN ] MimicTest.TwoQuantumMol 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 71: For a correct single-point energy evaluation with nsteps = 0, use 71: continuation = yes to avoid constraining the input coordinates. 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group rest is 21.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/4water.gro' 71: 71: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 71: Reading frame 0 time 0.000 Last frame 0 time 0.000 71: 71: NOTE: 15 % of the run time was spent in domain decomposition, 71: 8 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.001 0.000 376.0 71: (ns/day) (hour/ns) 71: Performance: 260.243 0.092 71: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -843071489 71: 71: Generated 10 of the 10 non-bonded parameter combinations 71: 71: Generated 10 of the 10 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MimicTest.TwoQuantumMol (158 ms) 71: [ RUN ] MimicTest.BondCuts 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 71: For a correct single-point energy evaluation with nsteps = 0, use 71: continuation = yes to avoid constraining the input coordinates. 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group rest is 66.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 71: NVE simulation: will use the initial temperature of 300.368 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/ala.gro' 71: 71: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 71: Reading frame 0 time 0.000 Last frame 0 time 0.000 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.011 0.003 394.9 71: (ns/day) (hour/ns) 71: Performance: 30.341 0.791 71: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -2025853249 71: 71: Generated 2211 of the 2211 non-bonded parameter combinations 71: 71: Generated 2211 of the 2211 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 71: 71: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 71: 71: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MimicTest.BondCuts (66 ms) 71: [----------] 4 tests from MimicTest (502 ms total) 71: 71: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group rest is 9.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: There was 1 NOTE 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 9.00 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group rest is 9.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 71: The optimal PME mesh load for parallel simulations is below 0.5 71: and for highly parallel simulations between 0.25 and 0.33, 71: for higher performance, increase the cut-off and the PME grid spacing. 71: 71: 71: 71: There were 2 NOTEs 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 9.00 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 71: The optimal PME mesh load for parallel simulations is below 0.5 71: and for highly parallel simulations between 0.25 and 0.33, 71: for higher performance, increase the cut-off and the PME grid spacing. 71: 71: 71: 71: There was 1 NOTE 71: Setting the LD random seed to 2025637247 71: 71: Generated 3 of the 3 non-bonded parameter combinations 71: 71: Generated 3 of the 3 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: This run will generate roughly 0 Mb of data 71: Setting the LD random seed to 263315327 71: 71: Generated 3 of the 3 non-bonded parameter combinations 71: 71: Generated 3 of the 3 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 1.017 nm, buffer size 0.017 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 1.005 nm, buffer size 0.005 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: Setting the LD random seed to -537919557 71: 71: Generated 3 of the 3 non-bonded parameter combinations 71: 71: Generated 3 of the 3 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 71: Calculating fourier grid dimensions for X Y Z 71: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 71: 71: Estimate for the relative computational load of the PME mesh part: 1.00 71: 71: This run will generate roughly 0 Mb of data 71: Setting the LD random seed to -1679820041 71: 71: Generated 3 of the 3 non-bonded parameter combinations 71: 71: Generated 3 of the 3 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 71: 71: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: Calculating fourier grid dimensions for X Y Z 71: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 71: 71: Estimate for the relative computational load of the PME mesh part: 1.00 71: 71: This run will generate roughly 0 Mb of data 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_No.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc2' 71: 20 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: 71: Dynamic load balancing report: 71: DLB was turned on during the run due to measured imbalance. 71: Average load imbalance: 43.4%. 71: The balanceable part of the MD step is 22%, load imbalance is computed from this. 71: Part of the total run time spent waiting due to load imbalance: 9.7%. 71: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 71: 71: NOTE: 9.7 % of the available CPU time was lost due to load imbalance 71: in the domain decomposition. 71: You can consider manually changing the decomposition (option -dd); 71: e.g. by using fewer domains along the box dimension in which there is 71: considerable inhomogeneity in the simulated system. 71: 71: NOTE: 14 % of the run time was spent in domain decomposition, 71: 7 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: NOTE: 6 % of the run time was spent communicating energies, 71: you might want to increase some nst* mdp options 71: 71: Core t (s) Wall t (s) (%) 71: Time: 1.215 0.304 399.5 71: (ns/day) (hour/ns) 71: Performance: 5.968 4.021 71: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (413 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 71: ./src/programs/mdrun/tests/domain_decomposition.cpp:372: Skipped 71: Test configuration is invalid: 71: Cannot have separate PME ranks when PME is not used 71: 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 71: ./src/programs/mdrun/tests/domain_decomposition.cpp:372: Skipped 71: Test configuration is invalid: 71: Cannot have separate PME ranks when PME is not used 71: Cannot use two separate PME ranks when there are only two ranks total 71: 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_TemperatureAndPressure.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 10 to 50, rlist from 1.005 to 1.136 71: 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc2' 71: 20 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: NOTE: 10 % of the run time was spent communicating energies, 71: you might want to increase some nst* mdp options 71: 71: Core t (s) Wall t (s) (%) 71: Time: 1.223 0.310 394.8 71: (ns/day) (hour/ns) 71: Performance: 5.855 4.099 71: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (403 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 71: ./src/programs/mdrun/tests/domain_decomposition.cpp:372: Skipped 71: Test configuration is invalid: 71: Cannot have separate PME ranks when PME is not used 71: 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 71: ./src/programs/mdrun/tests/domain_decomposition.cpp:372: Skipped 71: Test configuration is invalid: 71: Cannot have separate PME ranks when PME is not used 71: Cannot use two separate PME ranks when there are only two ranks total 71: 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc2' 71: 20 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: 71: Dynamic load balancing report: 71: DLB was turned on during the run due to measured imbalance. 71: Average load imbalance: 44.5%. 71: The balanceable part of the MD step is 7%, load imbalance is computed from this. 71: Part of the total run time spent waiting due to load imbalance: 3.3%. 71: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 71: 71: 71: Core t (s) Wall t (s) (%) 71: Time: 2.487 0.626 397.4 71: (ns/day) (hour/ns) 71: Performance: 2.899 8.278 71: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (843 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc2' 71: 20 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 2.070 0.517 399.9 71: (ns/day) (hour/ns) 71: Performance: 3.506 6.845 71: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (739 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 71: ./src/programs/mdrun/tests/domain_decomposition.cpp:372: Skipped 71: Test configuration is invalid: 71: Cannot use two separate PME ranks when there are only two ranks total 71: 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 10 to 100, rlist from 1 to 1 71: 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc2' 71: 20 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 2.536 0.640 396.3 71: (ns/day) (hour/ns) 71: Performance: 2.835 8.465 71: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (1004 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 10 to 100, rlist from 1 to 1 71: 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc2' 71: 20 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.107 0.027 397.9 71: (ns/day) (hour/ns) 71: Performance: 67.300 0.357 71: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (200 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 71: ./src/programs/mdrun/tests/domain_decomposition.cpp:372: Skipped 71: Test configuration is invalid: 71: Cannot use two separate PME ranks when there are only two ranks total 71: 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 71: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest (3605 ms total) 71: 71: [----------] Global test environment tear-down 71: [==========] 16 tests from 2 test suites ran. (4331 ms total) 71: [ PASSED ] 10 tests. 71: [ SKIPPED ] 6 tests, listed below: 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 71/87 Test #71: MdrunMpiTests ............................. Passed 4.35 sec test 72 Start 72: MdrunMultiSimTests 72: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-multisim-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunMultiSimTests.xml" 72: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 72: Test timeout computed to be: 600 72: [==========] Running 2 tests from 1 test suite. 72: [----------] Global test environment set-up. 72: [----------] 2 tests from InNvt/MultiSimTerminationTest 72: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 72: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (5 ms) 72: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 72: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 (0 ms) 72: [----------] 2 tests from InNvt/MultiSimTerminationTest (5 ms total) 72: 72: [----------] Global test environment tear-down 72: [==========] 2 tests from 1 test suite ran. (34 ms total) 72: [ PASSED ] 2 tests. 72: 72: YOU HAVE 4 DISABLED TESTS 72: 72/87 Test #72: MdrunMultiSimTests ........................ Passed 0.05 sec test 73 Start 73: MdrunMultiSimReplexTests 73: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-multisim-replex-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunMultiSimReplexTests.xml" 73: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 73: Test timeout computed to be: 600 73: [==========] Running 1 test from 1 test suite. 73: [----------] Global test environment set-up. 73: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest 73: [ RUN ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 73: [ OK ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) 73: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest (0 ms total) 73: 73: [----------] Global test environment tear-down 73: [==========] 1 test from 1 test suite ran. (27 ms total) 73: [ PASSED ] 1 test. 73: 73: YOU HAVE 4 DISABLED TESTS 73: 73/87 Test #73: MdrunMultiSimReplexTests .................. Passed 0.05 sec test 74 Start 74: MdrunMultiSimReplexEquivalenceTests 74: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-multisim-replex-equivalence-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunMultiSimReplexEquivalenceTests.xml" 74: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 74: Test timeout computed to be: 600 74: [==========] Running 0 tests from 0 test suites. 74: [==========] 0 tests from 0 test suites ran. (0 ms total) 74: [ PASSED ] 0 tests. 74: 74: YOU HAVE 10 DISABLED TESTS 74: 74/87 Test #74: MdrunMultiSimReplexEquivalenceTests ....... Passed 0.02 sec test 75 Start 75: MdrunMpi1RankPmeTests 75: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunMpi1RankPmeTests.xml" 75: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 75: Test timeout computed to be: 600 75: [==========] Running 19 tests from 1 test suite. 75: [----------] Global test environment set-up. 75: [----------] 19 tests from ReproducesEnergies/PmeTest 75: Number of degrees of freedom in T-Coupling group rest is 12.00 75: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 75: NVE simulation: will use the initial temperature of 1046.791 K for 75: determining the Verlet buffer size 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 75: The optimal PME mesh load for parallel simulations is below 0.5 75: and for highly parallel simulations between 0.25 and 0.33, 75: for higher performance, increase the cut-off and the PME grid spacing. 75: 75: 75: 75: There were 2 NOTEs 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 75: For a correct single-point energy evaluation with nsteps = 0, use 75: continuation = yes to avoid constraining the input coordinates. 75: 75: Number of degrees of freedom in T-Coupling group rest is 13.00 75: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 75: NVE simulation: will use the initial temperature of 966.268 K for 75: determining the Verlet buffer size 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 75: The optimal PME mesh load for parallel simulations is below 0.5 75: and for highly parallel simulations between 0.25 and 0.33, 75: for higher performance, increase the cut-off and the PME grid spacing. 75: 75: 75: 75: There were 3 NOTEs 75: Setting the LD random seed to -6238353 75: 75: Generated 8 of the 10 non-bonded parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'Methanol' 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 75: 75: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 75: 75: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: Calculating fourier grid dimensions for X Y Z 75: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 75: 75: Estimate for the relative computational load of the PME mesh part: 1.00 75: 75: This run will generate roughly 0 Mb of data 75: Setting the LD random seed to -4984867 75: 75: Generated 8 of the 10 non-bonded parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'Methanol' 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Searching the wall atom type(s) 75: 75: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 75: 75: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 75: 75: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: Calculating fourier grid dimensions for X Y Z 75: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 75: 75: Estimate for the relative computational load of the PME mesh part: 1.00 75: 75: This run will generate roughly 0 Mb of data 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu 75: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 75: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 1 MPI thread 75: Using 2 OpenMP threads 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'spc-and-methanol' 75: 20 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.187 0.094 199.8 75: (ns/day) (hour/ns) 75: Performance: 19.340 1.241 75: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_0_pme_cpu.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu (287 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto 75: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 75: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 1 MPI thread 75: Using 2 OpenMP threads 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'spc-and-methanol' 75: 20 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.054 0.027 199.5 75: (ns/day) (hour/ns) 75: Performance: 67.190 0.357 75: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_0_pme_auto.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto (36 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu 75: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 75: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 1 MPI thread 75: Using 2 OpenMP threads 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'spc-and-methanol' 75: 0 steps, 0.0 ps. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.002 0.001 193.0 75: (ns/day) (hour/ns) 75: Performance: 71.618 0.335 75: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls_mdrun_notunepme_npme_0_pme_cpu.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu (735 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets using PME rank(s) but the simulation is using only one rank 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets using PME rank(s) but the simulation is using only one rank 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets using PME rank(s) but the simulation is using only one rank 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets using PME rank(s) but the simulation is using only one rank 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets using PME rank(s) but the simulation is using only one rank 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets using PME rank(s) but the simulation is using only one rank 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets using PME rank(s) but the simulation is using only one rank 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets using PME rank(s) but the simulation is using only one rank 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu 75: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 75: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 1 MPI thread 75: Using 2 OpenMP threads 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'spc-and-methanol' 75: 20 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.059 0.030 199.8 75: (ns/day) (hour/ns) 75: Performance: 61.500 0.390 75: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_tunepme_npme_0_pme_cpu.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu (38 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 75: [----------] 19 tests from ReproducesEnergies/PmeTest (1099 ms total) 75: 75: [----------] Global test environment tear-down 75: [==========] 19 tests from 1 test suite ran. (1133 ms total) 75: [ PASSED ] 4 tests. 75: [ SKIPPED ] 15 tests, listed below: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu 75/87 Test #75: MdrunMpi1RankPmeTests ..................... Passed 1.15 sec test 76 Start 76: MdrunMpi2RankPmeTests 76: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunMpi2RankPmeTests.xml" 76: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 76: Test timeout computed to be: 600 76: [==========] Running 19 tests from 1 test suite. 76: [----------] Global test environment set-up. 76: [----------] 19 tests from ReproducesEnergies/PmeTest 76: Number of degrees of freedom in T-Coupling group rest is 12.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 76: NVE simulation: will use the initial temperature of 1046.791 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 76: The optimal PME mesh load for parallel simulations is below 0.5 76: and for highly parallel simulations between 0.25 and 0.33, 76: for higher performance, increase the cut-off and the PME grid spacing. 76: 76: 76: 76: There were 2 NOTEs 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 76: For a correct single-point energy evaluation with nsteps = 0, use 76: continuation = yes to avoid constraining the input coordinates. 76: 76: Number of degrees of freedom in T-Coupling group rest is 13.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 76: NVE simulation: will use the initial temperature of 966.268 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 76: The optimal PME mesh load for parallel simulations is below 0.5 76: and for highly parallel simulations between 0.25 and 0.33, 76: for higher performance, increase the cut-off and the PME grid spacing. 76: 76: 76: 76: There were 3 NOTEs 76: Setting the LD random seed to -1103702308 76: 76: Generated 8 of the 10 non-bonded parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'Methanol' 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: Calculating fourier grid dimensions for X Y Z 76: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 76: 76: Estimate for the relative computational load of the PME mesh part: 1.00 76: 76: This run will generate roughly 0 Mb of data 76: Setting the LD random seed to -349196315 76: 76: Generated 8 of the 10 non-bonded parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'Methanol' 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Searching the wall atom type(s) 76: 76: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: Calculating fourier grid dimensions for X Y Z 76: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 76: 76: Estimate for the relative computational load of the PME mesh part: 1.00 76: 76: This run will generate roughly 0 Mb of data 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu 76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 76: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc-and-methanol' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: 76: Dynamic load balancing report: 76: DLB was off during the run due to low measured imbalance. 76: Average load imbalance: 51.6%. 76: The balanceable part of the MD step is 3%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 1.3%. 76: 76: 76: NOTE: 48 % of the run time was spent in domain decomposition, 76: 0 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: NOTE: 12 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.272 0.068 399.6 76: (ns/day) (hour/ns) 76: Performance: 26.666 0.900 76: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_0_pme_cpu.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu (572 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto 76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 76: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc-and-methanol' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: 76: Dynamic load balancing report: 76: DLB was turned on during the run due to measured imbalance. 76: Average load imbalance: 19.1%. 76: The balanceable part of the MD step is 15%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 2.9%. 76: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 76: 76: 76: NOTE: 6 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: 76: Core t (s) Wall t (s) (%) 76: Time: 3.305 0.826 400.0 76: (ns/day) (hour/ns) 76: Performance: 2.195 10.932 76: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_0_pme_auto.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto (1039 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: it targets PME decomposition, but that is not supported 76: PME GPU does not support: 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: it targets PME decomposition, but that is not supported 76: PME GPU does not support: 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: it targets PME decomposition, but that is not supported 76: PME GPU does not support: 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu 76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 76: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc-and-methanol' 76: 0 steps, 0.0 ps. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.004 0.001 370.6 76: (ns/day) (hour/ns) 76: Performance: 84.296 0.285 76: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls_mdrun_notunepme_npme_0_pme_cpu.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu (795 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: it targets PME decomposition, but that is not supported 76: PME GPU does not support: 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: it targets PME decomposition, but that is not supported 76: PME GPU does not support: 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu 76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 76: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc-and-methanol' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: NOTE: 14 % of the run time was spent in domain decomposition, 76: 0 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.520 0.130 399.7 76: (ns/day) (hour/ns) 76: Performance: 13.944 1.721 76: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_1_pme_cpu.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu (398 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto 76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 76: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc-and-methanol' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 3.688 0.922 399.9 76: (ns/day) (hour/ns) 76: Performance: 1.968 12.196 76: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_1_pme_auto.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto (1333 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: PME GPU does not support: 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: PME GPU does not support: 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: PME GPU does not support: 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu 76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 76: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc-and-methanol' 76: 0 steps, 0.0 ps. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.003 0.001 372.3 76: (ns/day) (hour/ns) 76: Performance: 96.329 0.249 76: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls_mdrun_notunepme_npme_1_pme_cpu.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu (887 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: PME GPU does not support: 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: PME GPU does not support: 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu 76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 76: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc-and-methanol' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: 76: Dynamic load balancing report: 76: DLB was off during the run due to low measured imbalance. 76: Average load imbalance: 17.8%. 76: The balanceable part of the MD step is 0%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 0.1%. 76: 76: 76: NOTE: 23 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.814 0.204 399.8 76: (ns/day) (hour/ns) 76: Performance: 8.908 2.694 76: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_tunepme_npme_0_pme_cpu.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu (386 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: it targets PME decomposition, but that is not supported 76: PME GPU does not support: 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: it targets PME decomposition, but that is not supported 76: PME GPU does not support: 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 76: [----------] 19 tests from ReproducesEnergies/PmeTest (5416 ms total) 76: 76: [----------] Global test environment tear-down 76: [==========] 19 tests from 1 test suite ran. (5456 ms total) 76: [ PASSED ] 7 tests. 76: [ SKIPPED ] 12 tests, listed below: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu 76/87 Test #76: MdrunMpi2RankPmeTests ..................... Passed 5.48 sec test 77 Start 77: MdrunCoordinationBasicTests1Rank 77: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-coordination-basic-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunCoordinationBasicTests1Rank.xml" 77: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 77: Test timeout computed to be: 1920 77: [==========] Running 1 test from 1 test suite. 77: [----------] Global test environment set-up. 77: [----------] 1 test from BasicPropagators/PeriodicActionsTest 77: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Number of degrees of freedom in T-Coupling group System is 33.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 68.810 K for 77: determining the Verlet buffer size 77: 77: 77: There were 3 NOTEs 77: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 1 OpenMP thread 77: 77: 77: NOTE: Thread affinity was not set. 77: starting mdrun 'Argon' 77: 16 steps, 0.0 ps. 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.032 0.032 99.9 77: (ns/day) (hour/ns) 77: Performance: 45.235 0.531 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Number of degrees of freedom in T-Coupling group System is 33.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 68.810 K for 77: determining the Verlet buffer size 77: 77: 77: There were 3 NOTEs 77: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 1 OpenMP thread 77: 77: 77: NOTE: Thread affinity was not set. 77: starting mdrun 'Argon' 77: 16 steps, 0.0 ps. 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.022 0.022 99.8 77: (ns/day) (hour/ns) 77: Performance: 67.052 0.358 77: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Number of degrees of freedom in T-Coupling group System is 33.00 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 68.810 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: COM removal frequency is set to (1). 77: Other settings require a global communication frequency of 4. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 4. 77: 77: 77: There were 5 NOTEs 77: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 1 OpenMP thread 77: 77: 77: NOTE: Thread affinity was not set. 77: starting mdrun 'Argon' 77: 16 steps, 0.0 ps. 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.027 0.027 99.9 77: (ns/day) (hour/ns) 77: Performance: 54.364 0.441 77: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Number of degrees of freedom in T-Coupling group System is 33.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 68.810 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: COM removal frequency is set to (1). 77: Other settings require a global communication frequency of 100. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 100. 77: 77: 77: There were 4 NOTEs 77: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 1 OpenMP thread 77: 77: 77: NOTE: Thread affinity was not set. 77: starting mdrun 'Argon' 77: 16 steps, 0.0 ps. 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.041 0.041 99.8 77: (ns/day) (hour/ns) 77: Performance: 36.052 0.666 77: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Number of degrees of freedom in T-Coupling group System is 33.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 68.810 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: COM removal frequency is set to (1). 77: Other settings require a global communication frequency of 100. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 100. 77: 77: 77: There were 4 NOTEs 77: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 1 OpenMP thread 77: 77: 77: NOTE: Thread affinity was not set. 77: starting mdrun 'Argon' 77: 16 steps, 0.0 ps. 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.029 0.029 99.8 77: (ns/day) (hour/ns) 77: Performance: 50.756 0.473 77: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Number of degrees of freedom in T-Coupling group System is 33.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 68.810 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: COM removal frequency is set to (1). 77: Other settings require a global communication frequency of 100. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 100. 77: 77: 77: There were 4 NOTEs 77: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 1 OpenMP thread 77: 77: 77: NOTE: Thread affinity was not set. 77: starting mdrun 'Argon' 77: 16 steps, 0.0 ps. 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.033 0.033 99.8 77: (ns/day) (hour/ns) 77: Performance: 44.893 0.535 77: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 77: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (298 ms) 77: [----------] 1 test from BasicPropagators/PeriodicActionsTest (298 ms total) 77: 77: [----------] Global test environment tear-down 77: [==========] 1 test from 1 test suite ran. (332 ms total) 77: [ PASSED ] 1 test. 77/87 Test #77: MdrunCoordinationBasicTests1Rank .......... Passed 0.36 sec test 78 Start 78: MdrunCoordinationBasicTests2Ranks 78: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-coordination-basic-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunCoordinationBasicTests2Ranks.xml" 78: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 78: Test timeout computed to be: 1920 78: [==========] Running 1 test from 1 test suite. 78: [----------] Global test environment set-up. 78: [----------] 1 test from BasicPropagators/PeriodicActionsTest 78: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 78: that with the Verlet scheme, nstlist has no effect on the accuracy of 78: your simulation. 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (1) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: There were 3 NOTEs 78: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI threads 78: Using 1 OpenMP thread per tMPI thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: 78: Dynamic load balancing report: 78: DLB was turned on during the run due to measured imbalance. 78: Average load imbalance: 39.2%. 78: The balanceable part of the MD step is 19%, load imbalance is computed from this. 78: Part of the total run time spent waiting due to load imbalance: 7.6%. 78: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 78: 78: NOTE: 7.6 % of the available CPU time was lost due to load imbalance 78: in the domain decomposition. 78: You can consider manually changing the decomposition (option -dd); 78: e.g. by using fewer domains along the box dimension in which there is 78: considerable inhomogeneity in the simulated system. 78: 78: NOTE: 43 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.047 0.023 199.6 78: (ns/day) (hour/ns) 78: Performance: 62.856 0.382 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 78: that with the Verlet scheme, nstlist has no effect on the accuracy of 78: your simulation. 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (1) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: There were 3 NOTEs 78: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI threads 78: Using 1 OpenMP thread per tMPI thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: 78: Dynamic load balancing report: 78: DLB was off during the run due to low measured imbalance. 78: Average load imbalance: 0.3%. 78: The balanceable part of the MD step is 47%, load imbalance is computed from this. 78: Part of the total run time spent waiting due to load imbalance: 0.2%. 78: 78: 78: NOTE: 49 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.048 0.024 199.5 78: (ns/day) (hour/ns) 78: Performance: 61.150 0.392 78: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 78: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 78: that with the Verlet scheme, nstlist has no effect on the accuracy of 78: your simulation. 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 78: setting nstcomm equal to nstcalcenergy for less overhead 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: COM removal frequency is set to (1). 78: Other settings require a global communication frequency of 4. 78: Note that this will require additional global communication steps, 78: which will reduce performance when using multiple ranks. 78: Consider setting nstcomm to a multiple of 4. 78: 78: 78: There were 5 NOTEs 78: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI threads 78: Using 1 OpenMP thread per tMPI thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: 78: Dynamic load balancing report: 78: DLB was turned on during the run due to measured imbalance. 78: Average load imbalance: 5.6%. 78: The balanceable part of the MD step is 41%, load imbalance is computed from this. 78: Part of the total run time spent waiting due to load imbalance: 2.3%. 78: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 78: 78: 78: NOTE: 49 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.099 0.049 199.7 78: (ns/day) (hour/ns) 78: Performance: 29.722 0.807 78: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 78: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 78: that with the Verlet scheme, nstlist has no effect on the accuracy of 78: your simulation. 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 78: setting nstcomm equal to nstcalcenergy for less overhead 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: COM removal frequency is set to (1). 78: Other settings require a global communication frequency of 100. 78: Note that this will require additional global communication steps, 78: which will reduce performance when using multiple ranks. 78: Consider setting nstcomm to a multiple of 100. 78: 78: 78: There were 4 NOTEs 78: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI threads 78: Using 1 OpenMP thread per tMPI thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: 78: Dynamic load balancing report: 78: DLB was off during the run due to low measured imbalance. 78: Average load imbalance: 5.3%. 78: The balanceable part of the MD step is 24%, load imbalance is computed from this. 78: Part of the total run time spent waiting due to load imbalance: 1.2%. 78: 78: 78: NOTE: 50 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.327 0.163 199.9 78: (ns/day) (hour/ns) 78: Performance: 8.985 2.671 78: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 78: that with the Verlet scheme, nstlist has no effect on the accuracy of 78: your simulation. 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 78: setting nstcomm equal to nstcalcenergy for less overhead 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: COM removal frequency is set to (1). 78: Other settings require a global communication frequency of 100. 78: Note that this will require additional global communication steps, 78: which will reduce performance when using multiple ranks. 78: Consider setting nstcomm to a multiple of 100. 78: 78: 78: There were 4 NOTEs 78: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI threads 78: Using 1 OpenMP thread per tMPI thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: 78: Dynamic load balancing report: 78: DLB was off during the run due to low measured imbalance. 78: Average load imbalance: 4.3%. 78: The balanceable part of the MD step is 41%, load imbalance is computed from this. 78: Part of the total run time spent waiting due to load imbalance: 1.8%. 78: 78: 78: NOTE: 69 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.043 0.023 183.0 78: (ns/day) (hour/ns) 78: Performance: 62.720 0.383 78: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 78: that with the Verlet scheme, nstlist has no effect on the accuracy of 78: your simulation. 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 78: setting nstcomm equal to nstcalcenergy for less overhead 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: COM removal frequency is set to (1). 78: Other settings require a global communication frequency of 100. 78: Note that this will require additional global communication steps, 78: which will reduce performance when using multiple ranks. 78: Consider setting nstcomm to a multiple of 100. 78: 78: 78: There were 4 NOTEs 78: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI threads 78: Using 1 OpenMP thread per tMPI thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: 78: Dynamic load balancing report: 78: DLB was off during the run due to low measured imbalance. 78: Average load imbalance: 3.7%. 78: The balanceable part of the MD step is 42%, load imbalance is computed from this. 78: Part of the total run time spent waiting due to load imbalance: 1.6%. 78: 78: 78: NOTE: 71 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.043 0.037 114.7 78: (ns/day) (hour/ns) 78: Performance: 39.515 0.607 78: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 78: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1441 ms) 78: [----------] 1 test from BasicPropagators/PeriodicActionsTest (1441 ms total) 78: 78: [----------] Global test environment tear-down 78: [==========] 1 test from 1 test suite ran. (1470 ms total) 78: [ PASSED ] 1 test. 78/87 Test #78: MdrunCoordinationBasicTests2Ranks ......... Passed 1.49 sec test 79 Start 79: MdrunCoordinationCouplingTests1Rank 79: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-coordination-coupling-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunCoordinationCouplingTests1Rank.xml" 79: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 79: Test timeout computed to be: 1920 79: [==========] Running 25 tests from 1 test suite. 79: [----------] Global test environment set-up. 79: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.017 99.7 79: (ns/day) (hour/ns) 79: Performance: 85.525 0.281 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.012 0.012 99.6 79: (ns/day) (hour/ns) 79: Performance: 125.958 0.191 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 4. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 4. 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.031 0.032 99.9 79: (ns/day) (hour/ns) 79: Performance: 46.614 0.515 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.038 0.038 99.9 79: (ns/day) (hour/ns) 79: Performance: 38.810 0.618 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.033 0.033 99.9 79: (ns/day) (hour/ns) 79: Performance: 45.097 0.532 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.038 0.038 99.9 79: (ns/day) (hour/ns) 79: Performance: 38.823 0.618 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (287 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.021 99.6 79: (ns/day) (hour/ns) 79: Performance: 69.140 0.347 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.028 0.028 99.5 79: (ns/day) (hour/ns) 79: Performance: 52.674 0.456 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.030 0.030 99.9 79: (ns/day) (hour/ns) 79: Performance: 48.946 0.490 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.038 0.038 99.9 79: (ns/day) (hour/ns) 79: Performance: 38.682 0.620 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.034 0.034 99.9 79: (ns/day) (hour/ns) 79: Performance: 42.799 0.561 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.038 0.038 99.9 79: (ns/day) (hour/ns) 79: Performance: 38.378 0.625 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (286 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.024 0.024 99.8 79: (ns/day) (hour/ns) 79: Performance: 60.119 0.399 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.028 0.028 99.9 79: (ns/day) (hour/ns) 79: Performance: 51.546 0.466 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.026 0.026 99.8 79: (ns/day) (hour/ns) 79: Performance: 56.373 0.426 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.036 0.036 99.9 79: (ns/day) (hour/ns) 79: Performance: 41.261 0.582 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.038 0.038 99.9 79: (ns/day) (hour/ns) 79: Performance: 38.900 0.617 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.039 0.039 99.8 79: (ns/day) (hour/ns) 79: Performance: 37.212 0.645 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (278 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.031 0.031 99.9 79: (ns/day) (hour/ns) 79: Performance: 47.602 0.504 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.029 0.029 99.9 79: (ns/day) (hour/ns) 79: Performance: 50.381 0.476 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.025 0.025 99.8 79: (ns/day) (hour/ns) 79: Performance: 58.007 0.414 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.033 0.033 99.9 79: (ns/day) (hour/ns) 79: Performance: 44.374 0.541 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.038 0.038 99.9 79: (ns/day) (hour/ns) 79: Performance: 38.745 0.619 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.038 0.038 99.9 79: (ns/day) (hour/ns) 79: Performance: 39.023 0.615 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (269 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.020 0.020 99.8 79: (ns/day) (hour/ns) 79: Performance: 74.764 0.321 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.017 99.8 79: (ns/day) (hour/ns) 79: Performance: 88.640 0.271 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.015 99.8 79: (ns/day) (hour/ns) 79: Performance: 95.187 0.252 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.039 0.039 99.9 79: (ns/day) (hour/ns) 79: Performance: 37.565 0.639 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.034 0.034 99.9 79: (ns/day) (hour/ns) 79: Performance: 42.823 0.560 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.040 0.040 99.9 79: (ns/day) (hour/ns) 79: Performance: 37.054 0.648 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (227 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.026 0.026 99.8 79: (ns/day) (hour/ns) 79: Performance: 56.309 0.426 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.019 0.019 99.8 79: (ns/day) (hour/ns) 79: Performance: 75.389 0.318 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.023 0.023 99.8 79: (ns/day) (hour/ns) 79: Performance: 65.171 0.368 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.033 0.033 99.8 79: (ns/day) (hour/ns) 79: Performance: 44.848 0.535 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.029 0.029 99.9 79: (ns/day) (hour/ns) 79: Performance: 50.207 0.478 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.035 0.035 99.9 79: (ns/day) (hour/ns) 79: Performance: 41.425 0.579 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (262 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.026 0.026 99.8 79: (ns/day) (hour/ns) 79: Performance: 55.496 0.432 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.025 0.025 99.8 79: (ns/day) (hour/ns) 79: Performance: 58.653 0.409 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.014 99.7 79: (ns/day) (hour/ns) 79: Performance: 101.865 0.236 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.034 0.034 99.8 79: (ns/day) (hour/ns) 79: Performance: 43.660 0.550 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.036 0.036 99.9 79: (ns/day) (hour/ns) 79: Performance: 41.105 0.584 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.036 0.036 99.9 79: (ns/day) (hour/ns) 79: Performance: 40.537 0.592 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (242 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.026 0.026 99.9 79: (ns/day) (hour/ns) 79: Performance: 55.906 0.429 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.019 0.019 99.9 79: (ns/day) (hour/ns) 79: Performance: 76.965 0.312 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.032 0.032 99.9 79: (ns/day) (hour/ns) 79: Performance: 45.418 0.528 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.025 0.026 99.9 79: (ns/day) (hour/ns) 79: Performance: 57.520 0.417 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.040 0.040 99.8 79: (ns/day) (hour/ns) 79: Performance: 36.439 0.659 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.041 0.041 99.9 79: (ns/day) (hour/ns) 79: Performance: 35.500 0.676 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (282 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.031 0.031 99.8 79: (ns/day) (hour/ns) 79: Performance: 48.044 0.500 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.014 99.8 79: (ns/day) (hour/ns) 79: Performance: 104.949 0.229 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.022 0.022 99.9 79: (ns/day) (hour/ns) 79: Performance: 65.709 0.365 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.159 0.159 100.0 79: (ns/day) (hour/ns) 79: Performance: 9.212 2.605 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.036 0.036 99.9 79: (ns/day) (hour/ns) 79: Performance: 40.859 0.587 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.035 0.035 99.9 79: (ns/day) (hour/ns) 79: Performance: 41.635 0.576 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (373 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.033 0.033 99.9 79: (ns/day) (hour/ns) 79: Performance: 44.877 0.535 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.008 0.008 99.7 79: (ns/day) (hour/ns) 79: Performance: 188.104 0.128 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.022 0.022 99.8 79: (ns/day) (hour/ns) 79: Performance: 68.045 0.353 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.036 0.036 99.9 79: (ns/day) (hour/ns) 79: Performance: 40.302 0.596 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.017 99.8 79: (ns/day) (hour/ns) 79: Performance: 86.098 0.279 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.262 0.262 100.0 79: (ns/day) (hour/ns) 79: Performance: 5.604 4.283 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (451 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.015 99.7 79: (ns/day) (hour/ns) 79: Performance: 97.019 0.247 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.020 0.020 99.8 79: (ns/day) (hour/ns) 79: Performance: 73.928 0.325 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.024 0.024 99.8 79: (ns/day) (hour/ns) 79: Performance: 60.315 0.398 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.043 0.043 99.9 79: (ns/day) (hour/ns) 79: Performance: 33.948 0.707 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.032 0.032 99.9 79: (ns/day) (hour/ns) 79: Performance: 46.074 0.521 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.029 0.029 99.9 79: (ns/day) (hour/ns) 79: Performance: 50.179 0.478 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (246 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.030 0.030 99.8 79: (ns/day) (hour/ns) 79: Performance: 48.763 0.492 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.014 99.8 79: (ns/day) (hour/ns) 79: Performance: 105.974 0.226 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.024 0.024 99.8 79: (ns/day) (hour/ns) 79: Performance: 61.948 0.387 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.026 0.026 99.8 79: (ns/day) (hour/ns) 79: Performance: 55.632 0.431 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.037 0.037 99.9 79: (ns/day) (hour/ns) 79: Performance: 39.328 0.610 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.031 0.032 99.9 79: (ns/day) (hour/ns) 79: Performance: 46.577 0.515 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (260 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.030 0.030 99.9 79: (ns/day) (hour/ns) 79: Performance: 49.270 0.487 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.013 0.013 99.8 79: (ns/day) (hour/ns) 79: Performance: 110.081 0.218 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 4. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 4. 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.032 0.032 99.9 79: (ns/day) (hour/ns) 79: Performance: 45.727 0.525 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.033 0.033 99.9 79: (ns/day) (hour/ns) 79: Performance: 44.350 0.541 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.044 0.044 99.9 79: (ns/day) (hour/ns) 79: Performance: 33.194 0.723 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.020 0.020 99.8 79: (ns/day) (hour/ns) 79: Performance: 72.033 0.333 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (235 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.019 0.019 99.8 79: (ns/day) (hour/ns) 79: Performance: 77.077 0.311 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.009 0.009 99.7 79: (ns/day) (hour/ns) 79: Performance: 162.181 0.148 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.019 0.019 99.8 79: (ns/day) (hour/ns) 79: Performance: 77.785 0.309 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.021 99.8 79: (ns/day) (hour/ns) 79: Performance: 69.923 0.343 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.022 0.022 99.8 79: (ns/day) (hour/ns) 79: Performance: 67.983 0.353 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.020 0.020 99.8 79: (ns/day) (hour/ns) 79: Performance: 73.983 0.324 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (182 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.023 0.023 99.8 79: (ns/day) (hour/ns) 79: Performance: 64.321 0.373 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.014 99.7 79: (ns/day) (hour/ns) 79: Performance: 107.253 0.224 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.015 99.8 79: (ns/day) (hour/ns) 79: Performance: 96.153 0.250 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.024 0.024 99.8 79: (ns/day) (hour/ns) 79: Performance: 60.670 0.396 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.027 0.027 99.9 79: (ns/day) (hour/ns) 79: Performance: 54.895 0.437 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.038 0.038 99.9 79: (ns/day) (hour/ns) 79: Performance: 38.583 0.622 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (196 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.017 99.7 79: (ns/day) (hour/ns) 79: Performance: 85.246 0.282 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.018 0.019 99.7 79: (ns/day) (hour/ns) 79: Performance: 79.360 0.302 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.038 0.038 99.8 79: (ns/day) (hour/ns) 79: Performance: 38.254 0.627 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.033 0.033 99.8 79: (ns/day) (hour/ns) 79: Performance: 44.204 0.543 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.040 0.040 99.9 79: (ns/day) (hour/ns) 79: Performance: 36.556 0.657 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.026 0.026 99.8 79: (ns/day) (hour/ns) 79: Performance: 57.040 0.421 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (282 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.016 99.8 79: (ns/day) (hour/ns) 79: Performance: 94.415 0.254 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.007 0.007 99.7 79: (ns/day) (hour/ns) 79: Performance: 204.223 0.118 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 4. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 4. 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.017 99.8 79: (ns/day) (hour/ns) 79: Performance: 85.791 0.280 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.030 0.030 99.9 79: (ns/day) (hour/ns) 79: Performance: 49.369 0.486 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.197 0.197 100.0 79: (ns/day) (hour/ns) 79: Performance: 7.468 3.214 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.050 0.050 99.9 79: (ns/day) (hour/ns) 79: Performance: 29.630 0.810 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (382 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.034 0.034 99.9 79: (ns/day) (hour/ns) 79: Performance: 43.241 0.555 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.036 0.036 99.9 79: (ns/day) (hour/ns) 79: Performance: 41.179 0.583 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.031 0.031 99.8 79: (ns/day) (hour/ns) 79: Performance: 47.771 0.502 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.040 0.040 99.9 79: (ns/day) (hour/ns) 79: Performance: 36.861 0.651 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.039 0.039 99.9 79: (ns/day) (hour/ns) 79: Performance: 37.274 0.644 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.044 0.044 99.9 79: (ns/day) (hour/ns) 79: Performance: 33.550 0.715 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (307 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.035 0.035 99.9 79: (ns/day) (hour/ns) 79: Performance: 42.377 0.566 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.017 99.9 79: (ns/day) (hour/ns) 79: Performance: 89.004 0.270 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.022 0.022 99.9 79: (ns/day) (hour/ns) 79: Performance: 66.787 0.359 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.029 0.029 99.9 79: (ns/day) (hour/ns) 79: Performance: 49.833 0.482 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.031 0.031 99.9 79: (ns/day) (hour/ns) 79: Performance: 47.591 0.504 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.029 0.029 99.9 79: (ns/day) (hour/ns) 79: Performance: 50.355 0.477 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (211 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.023 0.023 99.8 79: (ns/day) (hour/ns) 79: Performance: 63.392 0.379 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.013 0.013 99.8 79: (ns/day) (hour/ns) 79: Performance: 111.140 0.216 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.018 0.018 99.8 79: (ns/day) (hour/ns) 79: Performance: 82.108 0.292 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.027 0.027 99.8 79: (ns/day) (hour/ns) 79: Performance: 54.051 0.444 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.030 0.030 99.8 79: (ns/day) (hour/ns) 79: Performance: 49.401 0.486 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.030 0.030 99.8 79: (ns/day) (hour/ns) 79: Performance: 48.988 0.490 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (197 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.021 99.7 79: (ns/day) (hour/ns) 79: Performance: 70.337 0.341 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.012 0.012 99.8 79: (ns/day) (hour/ns) 79: Performance: 123.301 0.195 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.021 99.8 79: (ns/day) (hour/ns) 79: Performance: 69.461 0.346 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.026 0.026 99.8 79: (ns/day) (hour/ns) 79: Performance: 56.962 0.421 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.030 0.030 99.8 79: (ns/day) (hour/ns) 79: Performance: 49.212 0.488 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.025 0.025 99.8 79: (ns/day) (hour/ns) 79: Performance: 58.847 0.408 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (205 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.022 0.022 99.8 79: (ns/day) (hour/ns) 79: Performance: 67.574 0.355 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.021 99.8 79: (ns/day) (hour/ns) 79: Performance: 70.728 0.339 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.025 0.025 99.8 79: (ns/day) (hour/ns) 79: Performance: 58.973 0.407 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.027 0.027 99.8 79: (ns/day) (hour/ns) 79: Performance: 53.537 0.448 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.029 0.029 99.8 79: (ns/day) (hour/ns) 79: Performance: 49.915 0.481 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.024 0.024 99.8 79: (ns/day) (hour/ns) 79: Performance: 62.330 0.385 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (206 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.022 0.022 99.8 79: (ns/day) (hour/ns) 79: Performance: 67.289 0.357 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.020 0.020 99.7 79: (ns/day) (hour/ns) 79: Performance: 73.092 0.328 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.021 99.8 79: (ns/day) (hour/ns) 79: Performance: 68.863 0.349 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.029 0.030 99.8 79: (ns/day) (hour/ns) 79: Performance: 49.771 0.482 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.025 0.025 99.8 79: (ns/day) (hour/ns) 79: Performance: 57.799 0.415 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.025 0.025 99.8 79: (ns/day) (hour/ns) 79: Performance: 59.347 0.404 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (210 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: for current Trotter decomposition methods with vv, nsttcouple and 79: nstpcouple must be equal. Both have been reset to 79: min(nsttcouple,nstpcouple) = 2 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.020 0.020 99.7 79: (ns/day) (hour/ns) 79: Performance: 72.733 0.330 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: for current Trotter decomposition methods with vv, nsttcouple and 79: nstpcouple must be equal. Both have been reset to 79: min(nsttcouple,nstpcouple) = 2 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.019 0.019 99.7 79: (ns/day) (hour/ns) 79: Performance: 77.800 0.308 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: for current Trotter decomposition methods with vv, nsttcouple and 79: nstpcouple must be equal. Both have been reset to 79: min(nsttcouple,nstpcouple) = 2 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.020 0.020 99.8 79: (ns/day) (hour/ns) 79: Performance: 72.885 0.329 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: for current Trotter decomposition methods with vv, nsttcouple and 79: nstpcouple must be equal. Both have been reset to 79: min(nsttcouple,nstpcouple) = 2 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.034 0.034 99.8 79: (ns/day) (hour/ns) 79: Performance: 43.659 0.550 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: for current Trotter decomposition methods with vv, nsttcouple and 79: nstpcouple must be equal. Both have been reset to 79: min(nsttcouple,nstpcouple) = 2 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.028 0.028 99.8 79: (ns/day) (hour/ns) 79: Performance: 52.862 0.454 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: for current Trotter decomposition methods with vv, nsttcouple and 79: nstpcouple must be equal. Both have been reset to 79: min(nsttcouple,nstpcouple) = 2 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.032 0.032 99.8 79: (ns/day) (hour/ns) 79: Performance: 45.272 0.530 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (189 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.021 99.8 79: (ns/day) (hour/ns) 79: Performance: 69.660 0.345 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.021 99.8 79: (ns/day) (hour/ns) 79: Performance: 70.796 0.339 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.024 0.024 99.8 79: (ns/day) (hour/ns) 79: Performance: 61.451 0.391 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.030 0.030 99.8 79: (ns/day) (hour/ns) 79: Performance: 48.748 0.492 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.026 0.026 99.8 79: (ns/day) (hour/ns) 79: Performance: 57.152 0.420 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.025 0.025 99.8 79: (ns/day) (hour/ns) 79: Performance: 57.881 0.415 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (206 ms) 79: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (6483 ms total) 79: 79: [----------] Global test environment tear-down 79: [==========] 25 tests from 1 test suite ran. (6511 ms total) 79: [ PASSED ] 25 tests. 79/87 Test #79: MdrunCoordinationCouplingTests1Rank ....... Passed 6.53 sec test 80 Start 80: MdrunCoordinationCouplingTests2Ranks 80: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-coordination-coupling-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunCoordinationCouplingTests2Ranks.xml" 80: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 80: Test timeout computed to be: 1920 80: [==========] Running 25 tests from 1 test suite. 80: [----------] Global test environment set-up. 80: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 2.2%. 80: The balanceable part of the MD step is 51%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.1%. 80: 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.026 0.013 199.3 80: (ns/day) (hour/ns) 80: Performance: 111.482 0.215 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.8%. 80: The balanceable part of the MD step is 43%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.8%. 80: 80: 80: NOTE: 47 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.016 0.008 199.1 80: (ns/day) (hour/ns) 80: Performance: 180.153 0.133 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 4. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 4. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 5.6%. 80: The balanceable part of the MD step is 36%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 2.1%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.019 0.009 198.5 80: (ns/day) (hour/ns) 80: Performance: 155.026 0.155 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 7.3%. 80: The balanceable part of the MD step is 35%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 2.5%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.034 0.017 199.3 80: (ns/day) (hour/ns) 80: Performance: 86.433 0.278 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 5.6%. 80: The balanceable part of the MD step is 27%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.5%. 80: 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.056 0.028 199.7 80: (ns/day) (hour/ns) 80: Performance: 52.526 0.457 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 6.7%. 80: The balanceable part of the MD step is 36%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 2.4%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: 80: NOTE: 55 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.030 0.015 199.1 80: (ns/day) (hour/ns) 80: Performance: 96.049 0.250 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (546 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 0.8%. 80: The balanceable part of the MD step is 49%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.4%. 80: 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.036 0.018 199.6 80: (ns/day) (hour/ns) 80: Performance: 82.521 0.291 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 4.9%. 80: The balanceable part of the MD step is 41%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 2.0%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.035 0.017 199.4 80: (ns/day) (hour/ns) 80: Performance: 84.317 0.285 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.1%. 80: The balanceable part of the MD step is 39%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.4%. 80: 80: 80: NOTE: 51 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.038 0.019 199.3 80: (ns/day) (hour/ns) 80: Performance: 76.437 0.314 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 9.8%. 80: The balanceable part of the MD step is 39%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 3.9%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.042 0.021 199.4 80: (ns/day) (hour/ns) 80: Performance: 70.245 0.342 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 8.7%. 80: The balanceable part of the MD step is 39%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 3.4%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: 80: NOTE: 53 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.044 0.022 199.1 80: (ns/day) (hour/ns) 80: Performance: 65.735 0.365 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 4.5%. 80: The balanceable part of the MD step is 41%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.8%. 80: 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.033 0.016 199.2 80: (ns/day) (hour/ns) 80: Performance: 89.811 0.267 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (230 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.0%. 80: The balanceable part of the MD step is 52%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.5%. 80: 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.034 0.017 199.5 80: (ns/day) (hour/ns) 80: Performance: 86.874 0.276 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 4.1%. 80: The balanceable part of the MD step is 45%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.8%. 80: 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.030 0.015 199.2 80: (ns/day) (hour/ns) 80: Performance: 98.868 0.243 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 3.3%. 80: The balanceable part of the MD step is 41%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.3%. 80: 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.024 0.012 199.3 80: (ns/day) (hour/ns) 80: Performance: 120.138 0.200 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 2.5%. 80: The balanceable part of the MD step is 42%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.0%. 80: 80: 80: NOTE: 70 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.044 0.024 179.2 80: (ns/day) (hour/ns) 80: Performance: 60.351 0.398 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 2.5%. 80: The balanceable part of the MD step is 41%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.0%. 80: 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.050 0.025 199.5 80: (ns/day) (hour/ns) 80: Performance: 58.171 0.413 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 4.5%. 80: The balanceable part of the MD step is 41%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.8%. 80: 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.036 0.018 199.4 80: (ns/day) (hour/ns) 80: Performance: 82.332 0.292 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (405 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 5.5%. 80: The balanceable part of the MD step is 45%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 2.5%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: 80: NOTE: 50 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.356 0.178 199.9 80: (ns/day) (hour/ns) 80: Performance: 8.240 2.913 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 19.9%. 80: The balanceable part of the MD step is 53%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 10.5%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: NOTE: 10.5 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: You can consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 17 % of the run time was spent in domain decomposition, 80: 0 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 53 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.322 0.161 199.9 80: (ns/day) (hour/ns) 80: Performance: 9.113 2.633 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 19.9%. 80: The balanceable part of the MD step is 55%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 10.9%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: NOTE: 10.9 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: You can consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 17 % of the run time was spent in domain decomposition, 80: 0 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 50 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.104 0.568 194.4 80: (ns/day) (hour/ns) 80: Performance: 2.587 9.279 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 9.3%. 80: The balanceable part of the MD step is 37%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 3.5%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.051 0.026 199.6 80: (ns/day) (hour/ns) 80: Performance: 57.570 0.417 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 2.0%. 80: The balanceable part of the MD step is 31%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.6%. 80: 80: 80: NOTE: 50 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.050 0.025 199.6 80: (ns/day) (hour/ns) 80: Performance: 58.632 0.409 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 2.9%. 80: The balanceable part of the MD step is 12%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.4%. 80: 80: 80: NOTE: 45 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.033 0.017 199.4 80: (ns/day) (hour/ns) 80: Performance: 88.679 0.271 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (2477 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 50 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.047 0.023 199.6 80: (ns/day) (hour/ns) 80: Performance: 62.627 0.383 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 50 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.027 0.013 199.2 80: (ns/day) (hour/ns) 80: Performance: 109.228 0.220 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.020 0.010 198.6 80: (ns/day) (hour/ns) 80: Performance: 142.740 0.168 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 56 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.050 0.025 199.0 80: (ns/day) (hour/ns) 80: Performance: 58.923 0.407 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.038 0.019 199.3 80: (ns/day) (hour/ns) 80: Performance: 77.732 0.309 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 64 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.069 0.051 137.0 80: (ns/day) (hour/ns) 80: Performance: 28.957 0.829 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (478 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.036 0.018 199.3 80: (ns/day) (hour/ns) 80: Performance: 82.100 0.292 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.033 0.017 199.5 80: (ns/day) (hour/ns) 80: Performance: 88.464 0.271 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.028 0.014 199.4 80: (ns/day) (hour/ns) 80: Performance: 106.162 0.226 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 11 % of the run time was spent in domain decomposition, 80: 0 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 50 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.504 0.268 188.1 80: (ns/day) (hour/ns) 80: Performance: 5.481 4.379 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.035 0.018 199.2 80: (ns/day) (hour/ns) 80: Performance: 83.146 0.289 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 66 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.042 0.037 113.1 80: (ns/day) (hour/ns) 80: Performance: 39.959 0.601 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (1550 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 51 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.065 0.033 199.6 80: (ns/day) (hour/ns) 80: Performance: 44.939 0.534 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.035 0.017 199.4 80: (ns/day) (hour/ns) 80: Performance: 84.881 0.283 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 13 % of the run time was spent in domain decomposition, 80: 0 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 56 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.418 0.209 199.9 80: (ns/day) (hour/ns) 80: Performance: 7.029 3.414 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 69 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.066 0.049 134.9 80: (ns/day) (hour/ns) 80: Performance: 29.959 0.801 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.035 0.018 199.5 80: (ns/day) (hour/ns) 80: Performance: 83.700 0.287 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.028 0.014 198.8 80: (ns/day) (hour/ns) 80: Performance: 102.848 0.233 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (1432 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 66 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.065 0.049 134.4 80: (ns/day) (hour/ns) 80: Performance: 30.152 0.796 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.030 0.015 199.3 80: (ns/day) (hour/ns) 80: Performance: 96.686 0.248 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.030 0.015 199.5 80: (ns/day) (hour/ns) 80: Performance: 97.953 0.245 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.038 0.019 199.2 80: (ns/day) (hour/ns) 80: Performance: 76.719 0.313 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 53 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.028 0.033 85.7 80: (ns/day) (hour/ns) 80: Performance: 44.187 0.543 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.036 0.018 199.2 80: (ns/day) (hour/ns) 80: Performance: 81.510 0.294 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (1212 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 69 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.056 0.050 111.8 80: (ns/day) (hour/ns) 80: Performance: 29.482 0.814 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.020 0.010 199.2 80: (ns/day) (hour/ns) 80: Performance: 148.082 0.162 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.020 0.010 198.8 80: (ns/day) (hour/ns) 80: Performance: 147.878 0.162 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.036 0.018 199.4 80: (ns/day) (hour/ns) 80: Performance: 81.760 0.294 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.030 0.015 199.4 80: (ns/day) (hour/ns) 80: Performance: 98.953 0.243 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.023 0.011 199.5 80: (ns/day) (hour/ns) 80: Performance: 128.192 0.187 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (1112 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 47 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.140 0.570 200.0 80: (ns/day) (hour/ns) 80: Performance: 2.577 9.314 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 54 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.030 0.015 199.3 80: (ns/day) (hour/ns) 80: Performance: 96.547 0.249 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.021 0.011 199.3 80: (ns/day) (hour/ns) 80: Performance: 136.462 0.176 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.032 0.016 199.4 80: (ns/day) (hour/ns) 80: Performance: 90.378 0.266 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.022 0.011 198.7 80: (ns/day) (hour/ns) 80: Performance: 130.186 0.184 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.042 0.021 199.6 80: (ns/day) (hour/ns) 80: Performance: 69.490 0.345 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (1600 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 53 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.027 0.014 199.3 80: (ns/day) (hour/ns) 80: Performance: 108.433 0.221 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 50 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.033 0.016 199.5 80: (ns/day) (hour/ns) 80: Performance: 89.606 0.268 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 50 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.021 0.010 199.0 80: (ns/day) (hour/ns) 80: Performance: 142.555 0.168 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.034 0.017 199.4 80: (ns/day) (hour/ns) 80: Performance: 86.940 0.276 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.029 0.015 199.3 80: (ns/day) (hour/ns) 80: Performance: 100.228 0.239 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.036 0.018 199.2 80: (ns/day) (hour/ns) 80: Performance: 81.631 0.294 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (513 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.035 0.017 199.4 80: (ns/day) (hour/ns) 80: Performance: 84.761 0.283 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.021 0.011 199.1 80: (ns/day) (hour/ns) 80: Performance: 136.724 0.176 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.017 0.009 199.1 80: (ns/day) (hour/ns) 80: Performance: 169.875 0.141 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 69 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.042 0.023 182.4 80: (ns/day) (hour/ns) 80: Performance: 64.354 0.373 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 73 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.042 0.037 113.6 80: (ns/day) (hour/ns) 80: Performance: 39.667 0.605 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 50 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.612 0.306 200.0 80: (ns/day) (hour/ns) 80: Performance: 4.803 4.997 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (751 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.033 0.017 199.7 80: (ns/day) (hour/ns) 80: Performance: 88.769 0.270 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 60 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.030 0.015 199.6 80: (ns/day) (hour/ns) 80: Performance: 99.285 0.242 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 4. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 4. 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 37 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.628 0.314 200.0 80: (ns/day) (hour/ns) 80: Performance: 4.674 5.134 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 24 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.605 0.303 200.0 80: (ns/day) (hour/ns) 80: Performance: 4.853 4.946 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.044 0.022 199.5 80: (ns/day) (hour/ns) 80: Performance: 66.802 0.359 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 63 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.054 0.027 199.6 80: (ns/day) (hour/ns) 80: Performance: 54.122 0.443 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (1996 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.035 0.018 199.3 80: (ns/day) (hour/ns) 80: Performance: 83.209 0.288 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.016 0.008 198.6 80: (ns/day) (hour/ns) 80: Performance: 187.998 0.128 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.017 0.009 199.4 80: (ns/day) (hour/ns) 80: Performance: 169.543 0.142 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 72 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.042 0.037 113.3 80: (ns/day) (hour/ns) 80: Performance: 39.856 0.602 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 71 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.042 0.037 113.5 80: (ns/day) (hour/ns) 80: Performance: 39.776 0.603 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 53 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.038 0.019 199.2 80: (ns/day) (hour/ns) 80: Performance: 77.974 0.308 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (407 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.027 0.013 199.1 80: (ns/day) (hour/ns) 80: Performance: 109.090 0.220 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.024 0.012 199.5 80: (ns/day) (hour/ns) 80: Performance: 120.642 0.199 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.021 0.010 199.4 80: (ns/day) (hour/ns) 80: Performance: 141.789 0.169 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.038 0.019 199.3 80: (ns/day) (hour/ns) 80: Performance: 76.927 0.312 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 24 % of the run time was spent in domain decomposition, 80: 0 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 37 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.028 0.014 199.5 80: (ns/day) (hour/ns) 80: Performance: 105.683 0.227 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 64 % of the run time was spent in domain decomposition, 80: 0 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 16 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.088 0.044 199.7 80: (ns/day) (hour/ns) 80: Performance: 33.486 0.717 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (970 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.038 0.019 199.4 80: (ns/day) (hour/ns) 80: Performance: 76.624 0.313 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 50 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.622 0.311 200.0 80: (ns/day) (hour/ns) 80: Performance: 4.722 5.082 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.029 0.015 199.4 80: (ns/day) (hour/ns) 80: Performance: 100.308 0.239 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 66 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.066 0.049 134.7 80: (ns/day) (hour/ns) 80: Performance: 30.037 0.799 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.031 0.015 199.3 80: (ns/day) (hour/ns) 80: Performance: 95.011 0.253 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 71 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.056 0.044 127.5 80: (ns/day) (hour/ns) 80: Performance: 33.314 0.720 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (1767 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.5%. 80: The balanceable part of the MD step is 57%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.8%. 80: 80: 80: NOTE: 11 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.563 0.297 189.3 80: (ns/day) (hour/ns) 80: Performance: 4.940 4.858 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 3.2%. 80: The balanceable part of the MD step is 54%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.7%. 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.020 0.010 197.9 80: (ns/day) (hour/ns) 80: Performance: 148.679 0.161 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 4. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 4. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 2.7%. 80: The balanceable part of the MD step is 43%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.2%. 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.018 0.009 196.8 80: (ns/day) (hour/ns) 80: Performance: 163.454 0.147 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 39.9%. 80: The balanceable part of the MD step is 39%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 15.6%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: NOTE: 15.6 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: You can consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 13 % of the run time was spent in domain decomposition, 80: 0 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 19 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.372 0.686 200.0 80: (ns/day) (hour/ns) 80: Performance: 2.140 11.215 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 4.4%. 80: The balanceable part of the MD step is 41%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.8%. 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.048 0.024 199.3 80: (ns/day) (hour/ns) 80: Performance: 61.115 0.393 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 6.2%. 80: The balanceable part of the MD step is 41%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 2.5%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.046 0.023 199.3 80: (ns/day) (hour/ns) 80: Performance: 63.231 0.380 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (1749 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 9.9%. 80: The balanceable part of the MD step is 64%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 6.3%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: NOTE: 6.3 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: You can consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 46 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.246 1.123 200.0 80: (ns/day) (hour/ns) 80: Performance: 1.308 18.355 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 3.7%. 80: The balanceable part of the MD step is 55%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 2.1%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: 80: NOTE: 9 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.047 0.024 199.0 80: (ns/day) (hour/ns) 80: Performance: 62.380 0.385 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 2.0%. 80: The balanceable part of the MD step is 48%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.0%. 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.038 0.023 164.2 80: (ns/day) (hour/ns) 80: Performance: 63.343 0.379 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 3.3%. 80: The balanceable part of the MD step is 48%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.6%. 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.053 0.026 199.0 80: (ns/day) (hour/ns) 80: Performance: 55.609 0.432 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 3.9%. 80: The balanceable part of the MD step is 49%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.9%. 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.060 0.030 199.3 80: (ns/day) (hour/ns) 80: Performance: 48.805 0.492 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 3.3%. 80: The balanceable part of the MD step is 47%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.5%. 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.365 0.183 199.9 80: (ns/day) (hour/ns) 80: Performance: 8.044 2.984 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (2546 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 3.3%. 80: The balanceable part of the MD step is 57%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.9%. 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.036 0.018 199.2 80: (ns/day) (hour/ns) 80: Performance: 81.744 0.294 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 3.6%. 80: The balanceable part of the MD step is 57%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 2.0%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.033 0.016 198.7 80: (ns/day) (hour/ns) 80: Performance: 89.326 0.269 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 4.9%. 80: The balanceable part of the MD step is 55%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 2.7%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.035 0.018 198.4 80: (ns/day) (hour/ns) 80: Performance: 83.137 0.289 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 5.5%. 80: The balanceable part of the MD step is 50%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 2.7%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.039 0.020 198.8 80: (ns/day) (hour/ns) 80: Performance: 75.152 0.319 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 3.4%. 80: The balanceable part of the MD step is 50%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.7%. 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.039 0.020 199.0 80: (ns/day) (hour/ns) 80: Performance: 74.602 0.322 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 2.8%. 80: The balanceable part of the MD step is 45%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.3%. 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.213 0.107 199.8 80: (ns/day) (hour/ns) 80: Performance: 13.764 1.744 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (1014 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.091 0.545 200.0 80: (ns/day) (hour/ns) 80: Performance: 2.693 8.913 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 56 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.944 0.988 196.8 80: (ns/day) (hour/ns) 80: Performance: 1.487 16.142 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.016 0.008 198.0 80: (ns/day) (hour/ns) 80: Performance: 180.003 0.133 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.032 0.016 198.5 80: (ns/day) (hour/ns) 80: Performance: 92.030 0.261 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.031 0.015 198.5 80: (ns/day) (hour/ns) 80: Performance: 95.292 0.252 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 26 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.079 0.039 199.3 80: (ns/day) (hour/ns) 80: Performance: 37.212 0.645 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (2367 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 36 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.324 0.662 200.0 80: (ns/day) (hour/ns) 80: Performance: 2.218 10.821 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 46 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.226 0.137 165.1 80: (ns/day) (hour/ns) 80: Performance: 10.730 2.237 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.090 0.069 130.8 80: (ns/day) (hour/ns) 80: Performance: 21.291 1.127 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.052 0.026 199.2 80: (ns/day) (hour/ns) 80: Performance: 56.146 0.427 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.048 0.024 197.5 80: (ns/day) (hour/ns) 80: Performance: 60.635 0.396 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.048 0.024 199.1 80: (ns/day) (hour/ns) 80: Performance: 61.088 0.393 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (1636 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.048 0.024 199.0 80: (ns/day) (hour/ns) 80: Performance: 61.349 0.391 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.047 0.024 199.0 80: (ns/day) (hour/ns) 80: Performance: 62.196 0.386 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.044 0.022 199.1 80: (ns/day) (hour/ns) 80: Performance: 66.254 0.362 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.035 0.017 199.1 80: (ns/day) (hour/ns) 80: Performance: 84.240 0.285 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.041 0.020 199.2 80: (ns/day) (hour/ns) 80: Performance: 71.924 0.334 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.046 0.023 199.1 80: (ns/day) (hour/ns) 80: Performance: 62.926 0.381 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (282 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.056 0.028 199.3 80: (ns/day) (hour/ns) 80: Performance: 52.686 0.456 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 11 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.074 0.037 199.3 80: (ns/day) (hour/ns) 80: Performance: 39.457 0.608 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 38 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.095 0.048 199.1 80: (ns/day) (hour/ns) 80: Performance: 30.812 0.779 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.051 0.049 103.9 80: (ns/day) (hour/ns) 80: Performance: 29.943 0.802 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.050 0.025 198.5 80: (ns/day) (hour/ns) 80: Performance: 57.793 0.415 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 55 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.036 1.019 199.9 80: (ns/day) (hour/ns) 80: Performance: 1.442 16.643 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (2126 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: for current Trotter decomposition methods with vv, nsttcouple and 80: nstpcouple must be equal. Both have been reset to 80: min(nsttcouple,nstpcouple) = 2 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 36 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.096 0.050 190.2 80: (ns/day) (hour/ns) 80: Performance: 29.204 0.822 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: for current Trotter decomposition methods with vv, nsttcouple and 80: nstpcouple must be equal. Both have been reset to 80: min(nsttcouple,nstpcouple) = 2 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.034 0.018 196.3 80: (ns/day) (hour/ns) 80: Performance: 83.924 0.286 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: for current Trotter decomposition methods with vv, nsttcouple and 80: nstpcouple must be equal. Both have been reset to 80: min(nsttcouple,nstpcouple) = 2 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.043 0.022 198.8 80: (ns/day) (hour/ns) 80: Performance: 68.215 0.352 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: for current Trotter decomposition methods with vv, nsttcouple and 80: nstpcouple must be equal. Both have been reset to 80: min(nsttcouple,nstpcouple) = 2 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 9 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.046 0.023 198.8 80: (ns/day) (hour/ns) 80: Performance: 62.904 0.382 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: for current Trotter decomposition methods with vv, nsttcouple and 80: nstpcouple must be equal. Both have been reset to 80: min(nsttcouple,nstpcouple) = 2 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.033 0.017 198.9 80: (ns/day) (hour/ns) 80: Performance: 88.714 0.271 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: for current Trotter decomposition methods with vv, nsttcouple and 80: nstpcouple must be equal. Both have been reset to 80: min(nsttcouple,nstpcouple) = 2 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.031 0.015 198.7 80: (ns/day) (hour/ns) 80: Performance: 94.904 0.253 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (368 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 22 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.055 0.027 199.0 80: (ns/day) (hour/ns) 80: Performance: 53.460 0.449 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.034 0.017 198.8 80: (ns/day) (hour/ns) 80: Performance: 85.908 0.279 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.029 0.015 197.7 80: (ns/day) (hour/ns) 80: Performance: 98.860 0.243 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 38 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.169 0.100 168.5 80: (ns/day) (hour/ns) 80: Performance: 14.645 1.639 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 39 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.163 0.097 167.4 80: (ns/day) (hour/ns) 80: Performance: 15.106 1.589 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.034 0.017 198.7 80: (ns/day) (hour/ns) 80: Performance: 86.585 0.277 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (558 ms) 80: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (30112 ms total) 80: 80: [----------] Global test environment tear-down 80: [==========] 25 tests from 1 test suite ran. (30138 ms total) 80: [ PASSED ] 25 tests. 80/87 Test #80: MdrunCoordinationCouplingTests2Ranks ...... Passed 30.16 sec test 81 Start 81: MdrunCoordinationConstraintsTests1Rank 81: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-coordination-constraints-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunCoordinationConstraintsTests1Rank.xml" 81: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 81: Test timeout computed to be: 1920 81: [==========] Running 13 tests from 1 test suite. 81: [----------] Global test environment set-up. 81: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.019 0.019 99.8 81: (ns/day) (hour/ns) 81: Performance: 76.358 0.314 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.013 0.013 99.8 81: (ns/day) (hour/ns) 81: Performance: 111.303 0.216 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 4. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 4. 81: 81: 81: There were 5 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.012 0.012 99.8 81: (ns/day) (hour/ns) 81: Performance: 125.621 0.191 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 5 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.016 0.016 99.8 81: (ns/day) (hour/ns) 81: Performance: 89.271 0.269 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 5 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.017 0.017 99.8 81: (ns/day) (hour/ns) 81: Performance: 87.444 0.274 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 5 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.370 0.370 100.0 81: (ns/day) (hour/ns) 81: Performance: 3.968 6.049 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (2412 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.019 0.019 99.8 81: (ns/day) (hour/ns) 81: Performance: 76.422 0.314 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.014 0.014 99.8 81: (ns/day) (hour/ns) 81: Performance: 103.079 0.233 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.012 0.012 99.8 81: (ns/day) (hour/ns) 81: Performance: 124.774 0.192 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.016 0.016 99.8 81: (ns/day) (hour/ns) 81: Performance: 89.891 0.267 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.016 0.016 99.7 81: (ns/day) (hour/ns) 81: Performance: 89.047 0.270 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.263 0.263 100.0 81: (ns/day) (hour/ns) 81: Performance: 5.590 4.293 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (1678 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.014 0.014 99.7 81: (ns/day) (hour/ns) 81: Performance: 106.071 0.226 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.013 0.013 99.7 81: (ns/day) (hour/ns) 81: Performance: 109.234 0.220 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.012 0.012 99.7 81: (ns/day) (hour/ns) 81: Performance: 124.698 0.192 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.016 0.016 99.7 81: (ns/day) (hour/ns) 81: Performance: 91.242 0.263 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.014 0.014 99.8 81: (ns/day) (hour/ns) 81: Performance: 103.726 0.231 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.017 0.017 99.8 81: (ns/day) (hour/ns) 81: Performance: 88.280 0.272 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (1810 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.016 0.016 99.8 81: (ns/day) (hour/ns) 81: Performance: 94.140 0.255 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.012 0.012 99.7 81: (ns/day) (hour/ns) 81: Performance: 121.386 0.198 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.012 0.012 99.7 81: (ns/day) (hour/ns) 81: Performance: 125.557 0.191 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.018 0.018 99.7 81: (ns/day) (hour/ns) 81: Performance: 83.616 0.287 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.015 0.015 99.8 81: (ns/day) (hour/ns) 81: Performance: 98.873 0.243 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.016 0.016 99.8 81: (ns/day) (hour/ns) 81: Performance: 90.140 0.266 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (1618 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.013 0.013 99.8 81: (ns/day) (hour/ns) 81: Performance: 109.374 0.219 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.014 0.014 99.8 81: (ns/day) (hour/ns) 81: Performance: 105.709 0.227 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.017 0.017 99.8 81: (ns/day) (hour/ns) 81: Performance: 86.212 0.278 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.025 0.025 99.8 81: (ns/day) (hour/ns) 81: Performance: 58.580 0.410 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.014 0.014 99.5 81: (ns/day) (hour/ns) 81: Performance: 107.436 0.223 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.015 0.015 99.7 81: (ns/day) (hour/ns) 81: Performance: 94.773 0.253 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (1842 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.021 0.021 99.8 81: (ns/day) (hour/ns) 81: Performance: 69.546 0.345 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.013 0.013 99.6 81: (ns/day) (hour/ns) 81: Performance: 116.389 0.206 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.016 0.016 99.8 81: (ns/day) (hour/ns) 81: Performance: 89.063 0.269 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.044 0.044 99.9 81: (ns/day) (hour/ns) 81: Performance: 33.678 0.713 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.025 0.025 99.7 81: (ns/day) (hour/ns) 81: Performance: 58.458 0.411 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.148 0.148 100.0 81: (ns/day) (hour/ns) 81: Performance: 9.908 2.422 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (2438 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.017 0.017 99.7 81: (ns/day) (hour/ns) 81: Performance: 88.405 0.271 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.016 0.016 99.8 81: (ns/day) (hour/ns) 81: Performance: 90.907 0.264 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 4. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 4. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.013 0.013 99.8 81: (ns/day) (hour/ns) 81: Performance: 113.582 0.211 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.019 0.019 99.8 81: (ns/day) (hour/ns) 81: Performance: 77.936 0.308 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.048 0.048 99.9 81: (ns/day) (hour/ns) 81: Performance: 30.878 0.777 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.020 0.020 99.8 81: (ns/day) (hour/ns) 81: Performance: 72.070 0.333 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (1771 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.017 0.017 99.8 81: (ns/day) (hour/ns) 81: Performance: 84.528 0.284 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.010 0.010 99.8 81: (ns/day) (hour/ns) 81: Performance: 153.424 0.156 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.013 0.013 99.7 81: (ns/day) (hour/ns) 81: Performance: 113.171 0.212 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.016 0.016 99.8 81: (ns/day) (hour/ns) 81: Performance: 91.650 0.262 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.245 0.245 100.0 81: (ns/day) (hour/ns) 81: Performance: 5.990 4.007 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.027 0.027 99.9 81: (ns/day) (hour/ns) 81: Performance: 55.115 0.435 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (2545 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.032 0.032 99.8 81: (ns/day) (hour/ns) 81: Performance: 46.238 0.519 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.023 0.023 99.9 81: (ns/day) (hour/ns) 81: Performance: 63.062 0.381 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.021 0.022 99.9 81: (ns/day) (hour/ns) 81: Performance: 68.263 0.352 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.026 0.026 99.8 81: (ns/day) (hour/ns) 81: Performance: 57.213 0.419 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.017 0.017 99.8 81: (ns/day) (hour/ns) 81: Performance: 88.680 0.271 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.019 0.019 99.8 81: (ns/day) (hour/ns) 81: Performance: 76.813 0.312 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (1752 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.023 0.023 99.7 81: (ns/day) (hour/ns) 81: Performance: 65.084 0.369 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.017 0.017 99.8 81: (ns/day) (hour/ns) 81: Performance: 87.760 0.273 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 4. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 4. 81: 81: 81: There were 5 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.028 0.029 99.8 81: (ns/day) (hour/ns) 81: Performance: 51.445 0.467 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 5 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.299 0.299 100.0 81: (ns/day) (hour/ns) 81: Performance: 4.918 4.880 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 5 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.208 0.208 100.0 81: (ns/day) (hour/ns) 81: Performance: 7.057 3.401 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 5 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.030 0.030 99.9 81: (ns/day) (hour/ns) 81: Performance: 49.501 0.485 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (3446 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.022 0.022 99.7 81: (ns/day) (hour/ns) 81: Performance: 67.377 0.356 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.020 0.020 99.4 81: (ns/day) (hour/ns) 81: Performance: 74.830 0.321 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.022 0.022 99.7 81: (ns/day) (hour/ns) 81: Performance: 65.630 0.366 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.018 0.018 99.5 81: (ns/day) (hour/ns) 81: Performance: 79.969 0.300 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.021 0.021 99.8 81: (ns/day) (hour/ns) 81: Performance: 70.092 0.342 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.025 0.025 99.8 81: (ns/day) (hour/ns) 81: Performance: 58.821 0.408 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (1979 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.021 0.021 99.9 81: (ns/day) (hour/ns) 81: Performance: 71.108 0.338 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.015 0.015 99.8 81: (ns/day) (hour/ns) 81: Performance: 99.696 0.241 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.019 0.019 99.7 81: (ns/day) (hour/ns) 81: Performance: 78.854 0.304 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.019 0.019 99.9 81: (ns/day) (hour/ns) 81: Performance: 77.567 0.309 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.027 0.027 99.8 81: (ns/day) (hour/ns) 81: Performance: 55.164 0.435 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.021 0.021 99.8 81: (ns/day) (hour/ns) 81: Performance: 70.736 0.339 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (1886 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.026 0.026 99.9 81: (ns/day) (hour/ns) 81: Performance: 56.846 0.422 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.365 0.365 100.0 81: (ns/day) (hour/ns) 81: Performance: 4.026 5.961 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.075 0.075 99.9 81: (ns/day) (hour/ns) 81: Performance: 19.517 1.230 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.020 0.020 99.7 81: (ns/day) (hour/ns) 81: Performance: 72.889 0.329 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.026 0.026 99.8 81: (ns/day) (hour/ns) 81: Performance: 56.082 0.428 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.024 0.024 99.9 81: (ns/day) (hour/ns) 81: Performance: 61.995 0.387 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (2466 ms) 81: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (27652 ms total) 81: 81: [----------] Global test environment tear-down 81: [==========] 13 tests from 1 test suite ran. (27691 ms total) 81: [ PASSED ] 13 tests. 81/87 Test #81: MdrunCoordinationConstraintsTests1Rank .... Passed 27.74 sec test 82 Start 82: MdrunCoordinationConstraintsTests2Ranks 82: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-coordination-constraints-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunCoordinationConstraintsTests2Ranks.xml" 82: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 82: Test timeout computed to be: 1920 82: [==========] Running 13 tests from 1 test suite. 82: [----------] Global test environment set-up. 82: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.5%. 82: The balanceable part of the MD step is 50%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.7%. 82: 82: 82: NOTE: 52 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.038 0.019 199.2 82: (ns/day) (hour/ns) 82: Performance: 77.887 0.308 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.3%. 82: The balanceable part of the MD step is 45%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.1%. 82: 82: 82: NOTE: 51 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.030 0.015 199.4 82: (ns/day) (hour/ns) 82: Performance: 97.145 0.247 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 4. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 4. 82: 82: 82: There were 5 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.7%. 82: The balanceable part of the MD step is 39%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.7%. 82: 82: 82: NOTE: 51 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.016 0.008 198.3 82: (ns/day) (hour/ns) 82: Performance: 180.697 0.133 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 5 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB got disabled because it was unsuitable to use. 82: Average load imbalance: 7.2%. 82: The balanceable part of the MD step is 33%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 2.4%. 82: 82: 82: NOTE: 50 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.512 0.256 200.0 82: (ns/day) (hour/ns) 82: Performance: 5.732 4.187 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 5 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 4.1%. 82: The balanceable part of the MD step is 34%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.4%. 82: 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.037 0.018 199.2 82: (ns/day) (hour/ns) 82: Performance: 80.094 0.300 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 5 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 14.9%. 82: The balanceable part of the MD step is 3%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.5%. 82: 82: 82: NOTE: 69 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.047 0.024 199.6 82: (ns/day) (hour/ns) 82: Performance: 61.948 0.387 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (2180 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.7%. 82: The balanceable part of the MD step is 49%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.3%. 82: 82: 82: NOTE: 50 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 1.278 0.639 200.0 82: (ns/day) (hour/ns) 82: Performance: 2.298 10.443 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.5%. 82: The balanceable part of the MD step is 45%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.2%. 82: 82: 82: NOTE: 51 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.029 0.014 199.5 82: (ns/day) (hour/ns) 82: Performance: 102.079 0.235 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.0%. 82: The balanceable part of the MD step is 40%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.4%. 82: 82: 82: NOTE: 50 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.428 0.214 200.0 82: (ns/day) (hour/ns) 82: Performance: 6.866 3.496 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.8%. 82: The balanceable part of the MD step is 39%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.3%. 82: 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.034 0.017 199.5 82: (ns/day) (hour/ns) 82: Performance: 85.898 0.279 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.3%. 82: The balanceable part of the MD step is 24%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.3%. 82: 82: 82: NOTE: 50 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.305 0.153 199.9 82: (ns/day) (hour/ns) 82: Performance: 9.616 2.496 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.1%. 82: The balanceable part of the MD step is 41%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.5%. 82: 82: 82: NOTE: 50 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.276 0.138 199.9 82: (ns/day) (hour/ns) 82: Performance: 10.629 2.258 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (3716 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.2%. 82: The balanceable part of the MD step is 47%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.1%. 82: 82: 82: NOTE: 48 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.036 0.018 199.3 82: (ns/day) (hour/ns) 82: Performance: 80.689 0.297 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.2%. 82: The balanceable part of the MD step is 31%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.4%. 82: 82: 82: NOTE: 47 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.021 0.011 198.8 82: (ns/day) (hour/ns) 82: Performance: 136.129 0.176 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 2.4%. 82: The balanceable part of the MD step is 41%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.0%. 82: 82: 82: NOTE: 55 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.030 0.015 199.1 82: (ns/day) (hour/ns) 82: Performance: 98.940 0.243 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB got disabled because it was unsuitable to use. 82: Average load imbalance: 5.4%. 82: The balanceable part of the MD step is 41%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 2.2%. 82: 82: 82: NOTE: 56 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.065 0.033 199.5 82: (ns/day) (hour/ns) 82: Performance: 44.753 0.536 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.8%. 82: The balanceable part of the MD step is 41%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.7%. 82: 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.069 0.035 199.7 82: (ns/day) (hour/ns) 82: Performance: 42.374 0.566 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.3%. 82: The balanceable part of the MD step is 41%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.5%. 82: 82: 82: NOTE: 50 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 1.201 0.601 200.0 82: (ns/day) (hour/ns) 82: Performance: 2.446 9.814 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (3314 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.849 0.424 200.0 82: (ns/day) (hour/ns) 82: Performance: 3.461 6.934 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 2.124 1.062 200.0 82: (ns/day) (hour/ns) 82: Performance: 1.383 17.353 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.211 0.105 199.9 82: (ns/day) (hour/ns) 82: Performance: 13.937 1.722 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.039 0.019 199.3 82: (ns/day) (hour/ns) 82: Performance: 75.386 0.318 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.035 0.018 199.1 82: (ns/day) (hour/ns) 82: Performance: 82.635 0.290 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.328 0.164 199.9 82: (ns/day) (hour/ns) 82: Performance: 8.965 2.677 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (4621 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.030 0.015 199.0 82: (ns/day) (hour/ns) 82: Performance: 96.034 0.250 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.318 0.159 199.9 82: (ns/day) (hour/ns) 82: Performance: 9.230 2.600 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.150 0.075 199.8 82: (ns/day) (hour/ns) 82: Performance: 19.601 1.224 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.057 0.029 199.5 82: (ns/day) (hour/ns) 82: Performance: 51.112 0.470 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: NOTE: 32 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.102 0.053 192.3 82: (ns/day) (hour/ns) 82: Performance: 27.559 0.871 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.147 0.074 199.8 82: (ns/day) (hour/ns) 82: Performance: 19.922 1.205 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (2107 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.110 0.055 199.8 82: (ns/day) (hour/ns) 82: Performance: 26.701 0.899 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.079 0.040 199.6 82: (ns/day) (hour/ns) 82: Performance: 36.900 0.650 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.044 0.029 149.9 82: (ns/day) (hour/ns) 82: Performance: 49.963 0.480 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.025 0.012 199.0 82: (ns/day) (hour/ns) 82: Performance: 118.185 0.203 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.490 0.245 199.9 82: (ns/day) (hour/ns) 82: Performance: 5.992 4.006 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.026 0.013 199.2 82: (ns/day) (hour/ns) 82: Performance: 113.294 0.212 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (2853 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.045 0.024 188.1 82: (ns/day) (hour/ns) 82: Performance: 61.096 0.393 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.122 0.061 199.8 82: (ns/day) (hour/ns) 82: Performance: 24.087 0.996 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 4. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 4. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.092 0.050 184.4 82: (ns/day) (hour/ns) 82: Performance: 29.327 0.818 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.030 0.015 199.3 82: (ns/day) (hour/ns) 82: Performance: 97.823 0.245 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.031 0.016 199.3 82: (ns/day) (hour/ns) 82: Performance: 93.486 0.257 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.684 0.342 200.0 82: (ns/day) (hour/ns) 82: Performance: 4.291 5.593 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (2948 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.542 0.271 200.0 82: (ns/day) (hour/ns) 82: Performance: 5.415 4.432 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.030 0.015 199.4 82: (ns/day) (hour/ns) 82: Performance: 96.225 0.249 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.032 0.016 197.0 82: (ns/day) (hour/ns) 82: Performance: 90.972 0.264 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.036 0.018 199.3 82: (ns/day) (hour/ns) 82: Performance: 80.537 0.298 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: NOTE: 14 % of the run time was spent in domain decomposition, 82: 0 % of the run time was spent in pair search, 82: you might want to increase nstlist (this has no effect on accuracy) 82: 82: NOTE: 14 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.945 0.473 200.0 82: (ns/day) (hour/ns) 82: Performance: 3.108 7.723 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.051 0.025 199.5 82: (ns/day) (hour/ns) 82: Performance: 58.010 0.414 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (3452 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: NOTE: 6 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.069 0.035 199.2 82: (ns/day) (hour/ns) 82: Performance: 42.256 0.568 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.023 0.011 199.3 82: (ns/day) (hour/ns) 82: Performance: 128.232 0.187 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.052 0.026 199.2 82: (ns/day) (hour/ns) 82: Performance: 56.031 0.428 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.036 0.018 199.1 82: (ns/day) (hour/ns) 82: Performance: 81.340 0.295 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.737 0.369 200.0 82: (ns/day) (hour/ns) 82: Performance: 3.982 6.027 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.495 0.248 199.4 82: (ns/day) (hour/ns) 82: Performance: 5.917 4.056 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (3201 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.3%. 82: The balanceable part of the MD step is 55%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.7%. 82: 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.394 0.197 199.9 82: (ns/day) (hour/ns) 82: Performance: 7.445 3.224 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.1%. 82: The balanceable part of the MD step is 54%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.6%. 82: 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.458 0.229 199.9 82: (ns/day) (hour/ns) 82: Performance: 6.418 3.740 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 4. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 4. 82: 82: 82: There were 5 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 2.7%. 82: The balanceable part of the MD step is 45%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.2%. 82: 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.113 0.057 199.2 82: (ns/day) (hour/ns) 82: Performance: 25.790 0.931 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 5 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 4.4%. 82: The balanceable part of the MD step is 44%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.9%. 82: 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.143 0.072 199.6 82: (ns/day) (hour/ns) 82: Performance: 20.434 1.175 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 5 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.5%. 82: The balanceable part of the MD step is 46%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.2%. 82: 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.048 0.024 198.0 82: (ns/day) (hour/ns) 82: Performance: 60.005 0.400 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 5 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 3.7%. 82: The balanceable part of the MD step is 48%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.8%. 82: 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.308 0.154 199.7 82: (ns/day) (hour/ns) 82: Performance: 9.525 2.520 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (2989 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.1%. 82: The balanceable part of the MD step is 50%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.1%. 82: 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.311 0.156 199.8 82: (ns/day) (hour/ns) 82: Performance: 9.444 2.541 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.4%. 82: The balanceable part of the MD step is 53%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.7%. 82: 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.080 0.040 199.5 82: (ns/day) (hour/ns) 82: Performance: 36.514 0.657 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB got disabled because it was unsuitable to use. 82: Average load imbalance: 4.6%. 82: The balanceable part of the MD step is 51%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 2.3%. 82: 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.271 0.159 169.8 82: (ns/day) (hour/ns) 82: Performance: 9.220 2.603 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.9%. 82: The balanceable part of the MD step is 51%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.0%. 82: 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.223 0.112 199.9 82: (ns/day) (hour/ns) 82: Performance: 13.164 1.823 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 3.6%. 82: The balanceable part of the MD step is 51%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.9%. 82: 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.035 0.018 197.4 82: (ns/day) (hour/ns) 82: Performance: 82.272 0.292 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.1%. 82: The balanceable part of the MD step is 51%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.1%. 82: 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.047 0.024 198.8 82: (ns/day) (hour/ns) 82: Performance: 62.102 0.386 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (3278 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.518 0.259 199.9 82: (ns/day) (hour/ns) 82: Performance: 5.668 4.234 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.394 0.197 199.9 82: (ns/day) (hour/ns) 82: Performance: 7.455 3.219 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.282 0.141 199.8 82: (ns/day) (hour/ns) 82: Performance: 10.397 2.308 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.362 0.181 199.9 82: (ns/day) (hour/ns) 82: Performance: 8.120 2.955 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.094 0.048 195.6 82: (ns/day) (hour/ns) 82: Performance: 30.625 0.784 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.047 0.023 198.9 82: (ns/day) (hour/ns) 82: Performance: 62.615 0.383 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (2680 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.053 0.027 199.2 82: (ns/day) (hour/ns) 82: Performance: 55.363 0.434 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: NOTE: 11 % of the run time was spent in domain decomposition, 82: 0 % of the run time was spent in pair search, 82: you might want to increase nstlist (this has no effect on accuracy) 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.641 0.321 199.9 82: (ns/day) (hour/ns) 82: Performance: 4.579 5.242 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.032 0.028 115.5 82: (ns/day) (hour/ns) 82: Performance: 52.221 0.460 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.046 0.023 197.0 82: (ns/day) (hour/ns) 82: Performance: 62.632 0.383 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.054 0.027 198.0 82: (ns/day) (hour/ns) 82: Performance: 53.895 0.445 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.052 0.026 198.4 82: (ns/day) (hour/ns) 82: Performance: 55.527 0.432 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (2810 ms) 82: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (40165 ms total) 82: 82: [----------] Global test environment tear-down 82: [==========] 13 tests from 1 test suite ran. (40203 ms total) 82: [ PASSED ] 13 tests. 82/87 Test #82: MdrunCoordinationConstraintsTests2Ranks ... Passed 40.25 sec test 83 Start 83: MdrunFEPTests 83: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-fep-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunFEPTests.xml" 83: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 83: Test timeout computed to be: 600 83: [==========] Running 12 tests from 1 test suite. 83: [----------] Global test environment set-up. 83: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp, line 149]: 83: For proper sampling of the (nearly) decoupled state, stochastic dynamics 83: should be used 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 355.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 10 to 100, rlist from 1 to 1 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: Setting the LD random seed to -268568260 83: 83: Generated 153 of the 153 non-bonded parameter combinations 83: 83: Generated 153 of the 153 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: 83: Coupling 1 copies of molecule type 'ASN' 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 0.94 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.847 0.424 200.0 83: (ns/day) (hour/ns) 83: Performance: 4.284 5.602 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_energy.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 trr version: GMX_trn_file (single precision) 83: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s (902 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp, line 148]: 83: For proper sampling of the (nearly) decoupled state, stochastic dynamics 83: should be used 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 355.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 10 to 100, rlist from 1 to 1 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: Setting the LD random seed to -1073897569 83: 83: Generated 153 of the 153 non-bonded parameter combinations 83: 83: Generated 153 of the 153 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: 83: Coupling 1 copies of molecule type 'ASN' 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 0.94 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.864 0.432 200.0 83: (ns/day) (hour/ns) 83: Performance: 4.201 5.713 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_energy.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s (602 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp, line 147]: 83: For proper sampling of the (nearly) decoupled state, stochastic dynamics 83: should be used 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 83: With PME there is a minor soft core effect present at the cut-off, 83: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 83: energy conservation, but usually other effects dominate. With a common 83: sigma value of 0.34 nm the fraction of the particle-particle potential at 83: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 355.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 4 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 10 to 100, rlist from 1 to 1 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: Setting the LD random seed to -4882443 83: 83: Generated 153 of the 153 non-bonded parameter combinations 83: 83: Generated 153 of the 153 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: 83: Coupling 1 copies of molecule type 'ASN' 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 0.94 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.263 0.132 199.8 83: (ns/day) (hour/ns) 83: Performance: 13.775 1.742 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_energy.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s (368 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_s 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp, line 147]: 83: For proper sampling of the (nearly) decoupled state, stochastic dynamics 83: should be used 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 83: With PME there is a minor soft core effect present at the cut-off, 83: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 83: energy conservation, but usually other effects dominate. With a common 83: sigma value of 0.34 nm the fraction of the particle-particle potential at 83: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: 83: NOTE 3 [file topol.top, line 155]: 83: System has non-zero total charge: 1.000000 83: Total charge should normally be an integer. See 83: https://manual.gromacs.org/current/user-guide/floating-point.html 83: for discussion on how close it should be to an integer. 83: 83: 83: 83: 83: WARNING 2 [file topol.top, line 155]: 83: You are using Ewald electrostatics in a system with net charge. This can 83: lead to severe artifacts, such as ions moving into regions with low 83: dielectric, due to the uniform background charge. We suggest to 83: neutralize your system with counter ions, possibly in combination with a 83: physiological salt concentration. 83: 83: Setting the LD random seed to -620808645 83: 83: Generated 171 of the 171 non-bonded parameter combinations 83: 83: Generated 171 of the 171 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: 83: Excluding 1 bonded neighbours molecule type 'NA' 83: 83: turning H bonds into constraints... 83: 83: Coupling 1 copies of molecule type 'ASN' 83: 83: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 83: J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof 83: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 83: Charge 83: J. Chem. Theory Comput. 10 (2014) pp. 381-393 83: -------- -------- --- Thank You --- -------- -------- 83: 83: Number of degrees of freedom in T-Coupling group System is 358.00 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 5 NOTEs 83: 83: There were 2 WARNINGs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 10 to 50, rlist from 1.004 to 1.101 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: There are: 1 Ion residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 83: 83: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 83: 83: Estimate for the relative computational load of the PME mesh part: 0.96 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.108 0.054 199.7 83: (ns/day) (hour/ns) 83: Performance: 33.579 0.715 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_s_energy.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_s (353 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_s 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp, line 147]: 83: For proper sampling of the (nearly) decoupled state, stochastic dynamics 83: should be used 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 83: With PME there is a minor soft core effect present at the cut-off, 83: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 83: energy conservation, but usually other effects dominate. With a common 83: sigma value of 0.34 nm the fraction of the particle-particle potential at 83: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: 83: NOTE 3 [file topol.top, line 165]: 83: System has non-zero total charge: 1.000000 83: Total charge should normally be an integer. See 83: https://manual.gromacs.org/current/user-guide/floating-point.html 83: for discussion on how close it should be to an integer. 83: 83: 83: 83: 83: WARNING 2 [file topol.top, line 165]: 83: You are using Ewald electrostatics in a system with net charge. This can 83: lead to severe artifacts, such as ions moving into regions with low 83: dielectric, due to the uniform background charge. We suggest to 83: neutralize your system with counter ions, possibly in combination with a 83: physiological salt concentration. 83: 83: Setting the LD random seed to 2045377503 83: 83: Generated 190 of the 190 non-bonded parameter combinations 83: 83: Generated 190 of the 190 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: 83: Excluding 1 bonded neighbours molecule type 'NA' 83: 83: turning H bonds into constraints... 83: 83: Excluding 1 bonded neighbours molecule type 'CL' 83: 83: turning H bonds into constraints... 83: 83: Coupling 1 copies of molecule type 'CL' 83: 83: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 83: J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof 83: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 83: Charge 83: J. Chem. Theory Comput. 10 (2014) pp. 381-393 83: -------- -------- --- Thank You --- -------- -------- 83: 83: Number of degrees of freedom in T-Coupling group System is 361.00 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 5 NOTEs 83: 83: There were 2 WARNINGs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 10 to 50, rlist from 1.004 to 1.102 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: There are: 2 Ion residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 83: 83: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 83: 83: Estimate for the relative computational load of the PME mesh part: 0.96 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.106 0.053 199.8 83: (ns/day) (hour/ns) 83: Performance: 34.155 0.703 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_s_energy.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_s (215 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp, line 171]: 83: For proper sampling of the (nearly) decoupled state, stochastic dynamics 83: should be used 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 83: Replacing vdwtype=Shift by the equivalent combination of vdwtype=Cut-off 83: and vdw_modifier=Force-switch 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 355.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 4 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 10 to 100, rlist from 1 to 1 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 100 steps, 0.1 ps. 83: Setting the LD random seed to -276861013 83: 83: Generated 153 of the 153 non-bonded parameter combinations 83: 83: Generated 153 of the 153 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: 83: Coupling 1 copies of molecule type 'ASN' 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 0.94 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.674 0.337 200.0 83: (ns/day) (hour/ns) 83: Performance: 25.886 0.927 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_energy.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Reading energy frame 30 time 0.030 Reading energy frame 40 time 0.040 Reading energy frame 50 time 0.050 Reading energy frame 60 time 0.060 Reading energy frame 70 time 0.070 Reading energy frame 80 time 0.080 Reading energy frame 90 time 0.090 Reading energy frame 100 time 0.100 Last energy frame read 100 time 0.100 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s (427 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: 83: WARNING 2 [file topol.top, line 72]: 83: No default Bond types for perturbed atoms, using normal values 83: 83: 83: WARNING 3 [file topol.top, line 73]: 83: No default Bond types for perturbed atoms, using normal values 83: 83: 83: WARNING 4 [file topol.top, line 98]: 83: No default Angle types for perturbed atoms, using normal values 83: 83: 83: WARNING 5 [file topol.top, line 99]: 83: No default Angle types for perturbed atoms, using normal values 83: 83: 83: WARNING 6 [file topol.top, line 100]: 83: No default Angle types for perturbed atoms, using normal values 83: 83: 83: WARNING 7 [file topol.top, line 101]: 83: No default Angle types for perturbed atoms, using normal values 83: 83: 83: WARNING 8 [file topol.top, line 111]: 83: No default Ryckaert-Bell. types for perturbed atoms, using normal values 83: 83: 83: WARNING 9 [file topol.top, line 112]: 83: No default Ryckaert-Bell. types for perturbed atoms, using normal values 83: 83: 83: WARNING 10 [file topol.top, line 113]: 83: No default Ryckaert-Bell. types for perturbed atoms, using normal values 83: 83: 83: WARNING 11 [file topol.top, line 114]: 83: No default Ryckaert-Bell. types for perturbed atoms, using normal values 83: 83: Number of degrees of freedom in T-Coupling group System is 355.00 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 2 NOTEs 83: 83: There were 11 WARNINGs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 10 to 100, rlist from 1 to 1 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: Setting the LD random seed to -609427466 83: 83: Generated 136 of the 136 non-bonded parameter combinations 83: 83: Generated 136 of the 136 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 0.94 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.160 0.080 199.8 83: (ns/day) (hour/ns) 83: Performance: 22.673 1.059 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_energy.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s (416 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: 83: WARNING 2 [file topol.top, line 72]: 83: No default Bond types for perturbed atoms, using normal values 83: 83: 83: WARNING 3 [file topol.top, line 73]: 83: No default Bond types for perturbed atoms, using normal values 83: 83: 83: WARNING 4 [file topol.top, line 98]: 83: No default Angle types for perturbed atoms, using normal values 83: 83: 83: WARNING 5 [file topol.top, line 99]: 83: No default Angle types for perturbed atoms, using normal values 83: 83: 83: WARNING 6 [file topol.top, line 100]: 83: No default Angle types for perturbed atoms, using normal values 83: 83: 83: WARNING 7 [file topol.top, line 101]: 83: No default Angle types for perturbed atoms, using normal values 83: 83: 83: WARNING 8 [file topol.top, line 111]: 83: No default Ryckaert-Bell. types for perturbed atoms, using normal values 83: 83: 83: WARNING 9 [file topol.top, line 112]: 83: No default Ryckaert-Bell. types for perturbed atoms, using normal values 83: 83: 83: WARNING 10 [file topol.top, line 113]: 83: No default Ryckaert-Bell. types for perturbed atoms, using normal values 83: 83: 83: WARNING 11 [file topol.top, line 114]: 83: No default Ryckaert-Bell. types for perturbed atoms, using normal values 83: 83: Number of degrees of freedom in T-Coupling group System is 355.00 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 83: Removing center of mass motion in the presence of position restraints 83: might cause artifacts. When you are using position restraints to 83: equilibrate a macro-molecule, the artifacts are usually negligible. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 3 NOTEs 83: 83: There were 11 WARNINGs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 10 to 100, rlist from 1 to 1 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: Setting the LD random seed to -77595169 83: 83: Generated 136 of the 136 non-bonded parameter combinations 83: 83: Generated 136 of the 136 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 0.94 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.157 0.079 199.7 83: (ns/day) (hour/ns) 83: Performance: 23.093 1.039 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_energy.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s (238 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 355.00 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 10 to 100, rlist from 1 to 1 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: Setting the LD random seed to -174588041 83: 83: Generated 136 of the 136 non-bonded parameter combinations 83: 83: Generated 136 of the 136 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 0.88 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.180 0.090 199.8 83: (ns/day) (hour/ns) 83: Performance: 20.153 1.191 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_energy.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s (195 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 355.00 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: There was 1 NOTE 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 10 to 100, rlist from 1 to 1 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: NOTE: 11 % of the run time was spent in domain decomposition, 83: 2 % of the run time was spent in pair search, 83: you might want to increase nstlist (this has no effect on accuracy) 83: 83: Core t (s) Wall t (s) (%) 83: Time: 1.448 0.724 200.0 83: (ns/day) (hour/ns) 83: Performance: 2.506 9.575 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_energy.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Setting the LD random seed to -469779522 83: 83: Generated 136 of the 136 non-bonded parameter combinations 83: 83: Generated 136 of the 136 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: Analysing Protein... 83: 83: The largest distance between excluded atoms is 0.331 nm between atom 1 and 9 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 0.88 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s (1050 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 83: With PME there is a minor soft core effect present at the cut-off, 83: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 83: energy conservation, but usually other effects dominate. With a common 83: sigma value of 0.34 nm the fraction of the particle-particle potential at 83: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 355.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 10 to 100, rlist from 1 to 1 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: Setting the LD random seed to -100675649 83: 83: Generated 136 of the 136 non-bonded parameter combinations 83: 83: Generated 136 of the 136 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 0.94 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 1.897 0.949 200.0 83: (ns/day) (hour/ns) 83: Performance: 1.912 12.550 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_energy.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s (1188 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 83: With PME there is a minor soft core effect present at the cut-off, 83: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 83: energy conservation, but usually other effects dominate. With a common 83: sigma value of 0.34 nm the fraction of the particle-particle potential at 83: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 355.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 10 to 100, rlist from 1 to 1 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: Setting the LD random seed to -8453 83: 83: Generated 136 of the 136 non-bonded parameter combinations 83: 83: Generated 136 of the 136 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.172 nm between atom 8 and 9 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 0.88 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.082 0.041 199.6 83: (ns/day) (hour/ns) 83: Performance: 44.281 0.542 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_energy.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s (143 ms) 83: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest (6108 ms total) 83: 83: [----------] Global test environment tear-down 83: [==========] 12 tests from 1 test suite ran. (6149 ms total) 83: [ PASSED ] 12 tests. 83/87 Test #83: MdrunFEPTests ............................. Passed 6.18 sec test 84 Start 84: MdrunPullTests 84: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-pull-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunPullTests.xml" 84: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 84: Test timeout computed to be: 600 84: [==========] Running 4 tests from 1 test suite. 84: [----------] Global test environment set-up. 84: [----------] 4 tests from PullTest/PullIntegrationTest 84: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/0 84: Generating 1-4 interactions: fudge = 0.5 84: Pull group 1 'r_1' has 3 atoms 84: Pull group 2 'r_2' has 3 atoms 84: Number of degrees of freedom in T-Coupling group System is 1293.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 303.122 K for 84: determining the Verlet buffer size 84: 84: Pull group natoms pbc atom distance at start reference at t=0 84: 1 3 2 84: 2 3 5 0.575 nm 0.600 nm 84: 84: There was 1 NOTE 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 20 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.191 0.096 199.9 84: (ns/day) (hour/ns) 84: Performance: 18.957 1.266 84: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/0 (611 ms) 84: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/1 84: Generating 1-4 interactions: fudge = 0.5 84: Pull group 1 'r_1' has 3 atoms 84: Pull group 2 'r_2' has 3 atoms 84: Number of degrees of freedom in T-Coupling group System is 1293.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 303.122 K for 84: determining the Verlet buffer size 84: 84: Pull group natoms pbc atom distance at start reference at t=0 84: 1 3 2 84: 2 3 5 0.301 nm 0.400 nm 84: 84: There was 1 NOTE 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 20 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: NOTE: 22 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.084 0.042 199.8 84: (ns/day) (hour/ns) 84: Performance: 43.338 0.554 84: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/1 (364 ms) 84: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/2 84: Generating 1-4 interactions: fudge = 0.5 84: Pull group 1 'r_1' has 3 atoms 84: Pull group 2 'r_2' has 3 atoms 84: Pull group 3 'r_3' has 3 atoms 84: Number of degrees of freedom in T-Coupling group System is 1292.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 303.357 K for 84: determining the Verlet buffer size 84: 84: Pull group natoms pbc atom distance at start reference at t=0 84: 1 3 2 84: 2 3 5 0.575 nm 0.500 nm 84: 1 3 2 84: 3 3 8 0.331 nm 0.400 nm 84: 84: There was 1 NOTE 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 20 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.357 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.335 0.168 199.9 84: (ns/day) (hour/ns) 84: Performance: 10.812 2.220 84: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/2 (550 ms) 84: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/3 84: Generating 1-4 interactions: fudge = 0.5 84: Pull group 1 'r_1' has 3 atoms 84: Pull group 2 'r_2' has 3 atoms 84: Number of degrees of freedom in T-Coupling group System is 1293.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 303.122 K for 84: determining the Verlet buffer size 84: 84: Pull group natoms pbc atom distance at start reference at t=0 84: 1 3 2 84: 2 3 5 0.575 nm 0.000 nm 84: 1 3 2 84: 2 3 5 0.050 nm 0.000 nm 84: 84: There was 1 NOTE 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 20 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.106 0.053 199.8 84: (ns/day) (hour/ns) 84: Performance: 34.346 0.699 84: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/3 (486 ms) 84: [----------] 4 tests from PullTest/PullIntegrationTest (2013 ms total) 84: 84: [----------] Global test environment tear-down 84: [==========] 4 tests from 1 test suite ran. (2042 ms total) 84: [ PASSED ] 4 tests. 84/87 Test #84: MdrunPullTests ............................ Passed 2.08 sec test 85 Start 85: MdrunRotationTests 85: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-rotation-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunRotationTests.xml" 85: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 85: Test timeout computed to be: 600 85: [==========] Running 12 tests from 1 test suite. 85: [----------] Global test environment set-up. 85: [----------] 12 tests from RotationWorks/RotationTest 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 85: Enforced rotation: Group 0 (iso) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: trr version: GMX_trn_file (single precision) 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to -1080313745 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.039 0.020 199.7 85: (ns/day) (hour/ns) 85: Performance: 228.875 0.105 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 (33 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 85: Enforced rotation: Group 0 (iso-pf) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to -53315714 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.039 0.020 199.7 85: (ns/day) (hour/ns) 85: Performance: 230.169 0.104 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 (27 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 85: Enforced rotation: Group 0 (pm) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to -1426063521 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 26 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.244 0.122 199.9 85: (ns/day) (hour/ns) 85: Performance: 36.769 0.653 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 (184 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 85: Enforced rotation: Group 0 (pm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to -1879506977 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.033 0.017 199.5 85: (ns/day) (hour/ns) 85: Performance: 271.780 0.088 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 (30 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 85: Enforced rotation: Group 0 (rm) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to -1091745793 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.030 0.015 199.4 85: (ns/day) (hour/ns) 85: Performance: 301.724 0.080 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 (32 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 85: Enforced rotation: Group 0 (rm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to 183483999 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.083 0.042 199.7 85: (ns/day) (hour/ns) 85: Performance: 107.555 0.223 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 (97 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 85: Enforced rotation: Group 0 (rm2) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to 637467575 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.084 0.042 199.7 85: (ns/day) (hour/ns) 85: Performance: 106.467 0.225 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 (50 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 85: Enforced rotation: Group 0 (rm2-pf) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to -1310724393 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.030 0.015 199.4 85: (ns/day) (hour/ns) 85: Performance: 296.455 0.081 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 (43 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 85: Enforced rotation: Group 0 (flex) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to -68788747 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.032 0.016 199.6 85: (ns/day) (hour/ns) 85: Performance: 278.896 0.086 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 (27 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 85: Enforced rotation: Group 0 (flex-t) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to -110624777 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 17 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.368 0.184 199.9 85: (ns/day) (hour/ns) 85: Performance: 24.399 0.984 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 (249 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 85: Enforced rotation: Group 0 (flex2) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to 1828714493 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.040 0.020 199.4 85: (ns/day) (hour/ns) 85: Performance: 222.626 0.108 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 (28 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 85: Enforced rotation: Group 0 (flex2-t) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to -672585995 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 35 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.184 0.092 199.8 85: (ns/day) (hour/ns) 85: Performance: 48.720 0.493 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 (152 ms) 85: [----------] 12 tests from RotationWorks/RotationTest (959 ms total) 85: 85: [----------] Global test environment tear-down 85: [==========] 12 tests from 1 test suite ran. (986 ms total) 85: [ PASSED ] 12 tests. 85/87 Test #85: MdrunRotationTests ........................ Passed 1.01 sec test 86 Start 86: MdrunSimulatorComparison 86: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-simulator-comparison-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunSimulatorComparison.xml" 86: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 86: Test timeout computed to be: 600 86: [==========] Running 0 tests from 0 test suites. 86: [==========] 0 tests from 0 test suites ran. (0 ms total) 86: [ PASSED ] 0 tests. 86: 86: YOU HAVE 82 DISABLED TESTS 86: 86/87 Test #86: MdrunSimulatorComparison .................. Passed 0.03 sec test 87 Start 87: MdrunVirtualSiteTests 87: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-vsites-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunVirtualSiteTests.xml" 87: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 87: Test timeout computed to be: 600 87: [==========] Running 37 tests from 2 test suites. 87: [----------] Global test environment set-up. 87: [----------] 1 test from VirtualSiteVelocityTest 87: [ RUN ] VirtualSiteVelocityTest.ReferenceIsCorrect 87: [ OK ] VirtualSiteVelocityTest.ReferenceIsCorrect (0 ms) 87: [----------] 1 test from VirtualSiteVelocityTest (0 ms total) 87: 87: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.0%. 87: The balanceable part of the MD step is 39%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.4%. 87: 87: 87: NOTE: 49 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.035 0.017 199.2 87: (ns/day) (hour/ns) 87: Performance: 44.546 0.539 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: trr version: GMX_trn_file (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 (31 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.5%. 87: The balanceable part of the MD step is 35%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.2%. 87: 87: 87: NOTE: 73 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.042 0.037 113.3 87: (ns/day) (hour/ns) 87: Performance: 21.086 1.138 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 (149 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 2.0%. 87: The balanceable part of the MD step is 36%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.7%. 87: 87: 87: NOTE: 49 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.037 0.018 199.0 87: (ns/day) (hour/ns) 87: Performance: 42.150 0.569 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 (31 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 71 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.043 0.038 115.2 87: (ns/day) (hour/ns) 87: Performance: 20.665 1.161 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 (168 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 49 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.036 0.018 199.5 87: (ns/day) (hour/ns) 87: Performance: 42.894 0.560 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 (75 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 52 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.060 0.030 199.3 87: (ns/day) (hour/ns) 87: Performance: 25.740 0.932 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 (233 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 87: 1 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 5 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 54 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.047 0.023 199.6 87: (ns/day) (hour/ns) 87: Performance: 33.098 0.725 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 (95 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 87: 1 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 5 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 50 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.230 0.115 199.9 87: (ns/day) (hour/ns) 87: Performance: 6.751 3.555 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 (160 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 87: 1 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 5 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 49 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.036 0.018 199.0 87: (ns/day) (hour/ns) 87: Performance: 42.721 0.562 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 (136 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.0%. 87: The balanceable part of the MD step is 36%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.4%. 87: 87: 87: NOTE: 49 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.033 0.017 199.1 87: (ns/day) (hour/ns) 87: Performance: 46.546 0.516 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 (29 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.4%. 87: The balanceable part of the MD step is 38%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.5%. 87: 87: 87: NOTE: 48 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.026 0.013 198.9 87: (ns/day) (hour/ns) 87: Performance: 59.702 0.402 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 (87 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 53 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.045 0.023 199.7 87: (ns/day) (hour/ns) 87: Performance: 34.462 0.696 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 (42 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 48 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.024 0.012 199.1 87: (ns/day) (hour/ns) 87: Performance: 64.969 0.369 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 (98 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 52 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.037 0.018 199.5 87: (ns/day) (hour/ns) 87: Performance: 42.049 0.571 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 (37 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 54 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.029 0.015 199.0 87: (ns/day) (hour/ns) 87: Performance: 53.591 0.448 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 (39 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 49 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.029 0.015 199.5 87: (ns/day) (hour/ns) 87: Performance: 53.475 0.449 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 (36 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 15 % of the run time was spent in domain decomposition, 87: 0 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 12 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.864 0.448 192.9 87: (ns/day) (hour/ns) 87: Performance: 1.736 13.824 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 (1175 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 50 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.034 0.017 199.1 87: (ns/day) (hour/ns) 87: Performance: 45.235 0.531 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 (299 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 50 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.036 0.018 199.6 87: (ns/day) (hour/ns) 87: Performance: 43.671 0.550 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 (295 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 48 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.027 0.013 199.0 87: (ns/day) (hour/ns) 87: Performance: 58.096 0.413 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 (68 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 50 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.825 0.413 199.9 87: (ns/day) (hour/ns) 87: Performance: 1.884 12.737 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 (439 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 (0 ms) 87: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest (3737 ms total) 87: 87: [----------] Global test environment tear-down 87: [==========] 37 tests from 2 test suites ran. (3769 ms total) 87: [ PASSED ] 37 tests. 87/87 Test #87: MdrunVirtualSiteTests ..................... Passed 3.79 sec 100% tests passed, 0 tests failed out of 87 Label Time Summary: GTest = 450.44 sec*proc (85 tests) IntegrationTest = 242.40 sec*proc (28 tests) MpiTest = 337.09 sec*proc (21 tests) QuickGpuTest = 79.07 sec*proc (20 tests) SlowGpuTest = 343.60 sec*proc (14 tests) SlowTest = 197.48 sec*proc (13 tests) UnitTest = 10.55 sec*proc (44 tests) Total Test time (real) = 224.08 sec /usr/bin/make -j12 -C build/basic-dp tests make[1]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2024.4 -B/build/reproducible-path/gromacs-2024.4/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 tests make[2]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2024.4 -B/build/reproducible-path/gromacs-2024.4/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E 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'/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/external/googletest/googletest/CMakeFiles/gtest.dir/build.make src/external/googletest/googletest/CMakeFiles/gtest.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/external/googletest/googletest && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_CREATE_SHARED_LIBRARY=1 -DGTEST_LANG_CXX11 -Dgtest_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -I/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -Wall -Wshadow -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -MD -MT src/external/googletest/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o -MF CMakeFiles/gtest.dir/src/gtest-all.cc.o.d -o CMakeFiles/gtest.dir/src/gtest-all.cc.o -c /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/src/gtest-all.cc make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2024.4-Debian_2024.4_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2024.4 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2024.4/build/basic-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2024.4/build/basic-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2024.4-1 -P /build/reproducible-path/gromacs-2024.4/cmake/gmxGenerateVersionInfoWithoutGit.cmake /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 0%] Built target lmfit_objlib make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 0%] Built target release-version-info make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[4]: Leaving directory 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'/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/options/CMakeFiles/options.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling /build/reproducible-path/gromacs-2024.4/build/basic-dp 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'/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 9%] Built target colvars_objlib make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 9%] Built target taskassignment make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 10%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/basic-dp 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/build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/gmxapi /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[4]: Nothing to be done for 'api/gmxapi/CMakeFiles/gmxapi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build [ 64%] Built target gmxapi make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 65%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[4]: Nothing to be done for 'api/nblib/samples/CMakeFiles/methane-water-integration.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[4]: Nothing to be done for 'api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 66%] Built target methane-water-integration [ 66%] Built target argon-forces-integration cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/external/googletest/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file,CMakeFiles/gtest.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgtest.so.1.13.0 -o ../../../../lib/libgtest.so.1.13.0 "CMakeFiles/gtest.dir/src/gtest-all.cc.o" cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/external/googletest/googletest && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgtest.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 66%] Built target gtest /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/external/googletest/googlemock /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/external/googletest/googlemock/CMakeFiles/gmock.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/external/googletest/googlemock && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -D_GNU_SOURCE=1 -Dgmock_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -I/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem 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/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file,CMakeFiles/gmock.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmock.so.1.13.0 -o ../../../../lib/libgmock.so.1.13.0 "CMakeFiles/gmock.dir/src/gmock-all.cc.o" ../../../../lib/libgtest.so.1.13.0 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/external/googletest/googlemock && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgmock.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 66%] Built target gmock /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' 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make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 68%] Built target testutils /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/depend /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/build.make api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/depend /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 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'/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxlib/nonbonded/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp 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make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build.make src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/energycomparison.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -MF CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o.d -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/qmmm/tests/qmmmtopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -MF CMakeFiles/testutils-test.dir/refdata_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/tests/refdata_tests.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/tests/colvarsoptions.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/calcvir.cpp.o -MF CMakeFiles/mdlib-test.dir/calcvir.cpp.o.d -o CMakeFiles/mdlib-test.dir/calcvir.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/calcvir.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/utility-mpi-test.dir/link.d "CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o" "CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 68%] Built target utility-mpi-test /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -MF CMakeFiles/applied_forces-test.dir/electricfield.cpp.o.d -o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/tests/electricfield.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/densityfitting/tests/densityfittingamplitudelookup.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/testutils-mpi-test.dir/link.d "CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o" "CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o" -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libtestutils.a ../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 68%] Built target testutils-mpi-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -MF CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/tests/testasserts_tests.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constr.cpp.o -MF CMakeFiles/mdlib-test.dir/constr.cpp.o.d -o CMakeFiles/mdlib-test.dir/constr.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/constr.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/moduletest.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias.cpp.o -MF CMakeFiles/awh-test.dir/bias.cpp.o.d -o CMakeFiles/awh-test.dir/bias.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/bias.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests && 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem 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src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/densityfitting/tests/densityfittingforceprovider.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulatorcomparison.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -MF CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/tests/xvgtest_tests.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/applied_forces-test.dir/link.d 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-DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biasgrid.cpp.o -MF CMakeFiles/awh-test.dir/biasgrid.cpp.o.d -o CMakeFiles/awh-test.dir/biasgrid.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/biasgrid.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxlib/nonbonded/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxlib/nonbonded/tests\" 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests && /usr/bin/cmake -P CMakeFiles/nblib_test_infrastructure.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib_test_infrastructure.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../lib/libnblib_test_infrastructure.a CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o /usr/bin/ranlib ../../../lib/libnblib_test_infrastructure.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 68%] Built target nblib_test_infrastructure cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/terminationhelper.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/densityfitting/tests/densityfittingoptions.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include 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src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/tests/colvarspreprocessor.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -DGMX_CP2K=0 -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/qmmm/tests/qmmmforceprovider.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -MF CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o.d -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxlib/nonbonded/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nonbonded-fep-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/nonbonded-fep-test.dir/link.d "CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o" "CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/nonbonded-fep-test ../../../../../lib/libtestutils.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.9.0.0 -lm ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 68%] Built target nonbonded-fep-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biassharing.cpp.o -MF CMakeFiles/awh-test.dir/biassharing.cpp.o.d -o CMakeFiles/awh-test.dir/biassharing.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/biassharing.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/trajectorycomparison.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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-I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask32.cpp.o -MF CMakeFiles/utility-test.dir/bitmask32.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/bitmask32.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 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../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 68%] Built target testutils-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/qmmm/tests/qmmm.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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-DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem 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Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -isystem 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CMakeFiles/listed_forces-test.dir/bonded.cpp.o.d -o CMakeFiles/listed_forces-test.dir/bonded.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/tests/bonded.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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-fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/pairs.cpp.o -MF CMakeFiles/listed_forces-test.dir/pairs.cpp.o.d -o CMakeFiles/listed_forces-test.dir/pairs.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/tests/pairs.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -MF CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o.d -o CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external 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/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/constrtestrunners.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/ebin.cpp.o -MF CMakeFiles/mdlib-test.dir/ebin.cpp.o.d -o CMakeFiles/mdlib-test.dir/ebin.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/ebin.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/density_fitting_applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/density_fitting_applied_forces-test.dir/link.d "CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/density_fitting_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.9.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 68%] Built target density_fitting_applied_forces-test /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/exclusions.cpp.o -MF CMakeFiles/nbnxm-test.dir/exclusions.cpp.o.d -o CMakeFiles/nbnxm-test.dir/exclusions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/exclusions.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/colvars_applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 68%] Built target colvars_applied_forces-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o -MF CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o.d -o CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/energydrifttracker.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/qmmm_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o -MF CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o.d -o CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/qmmm_applied_forces-test.dir/link.d "CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/qmmm_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.9.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 68%] Built target qmmm_applied_forces-test /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -MF CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o.d -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/tests/mock_helptopic.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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/usr/bin/ranlib ../../../../lib/libmdrun_test_infrastructure.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 68%] Built target mdrun_test_infrastructure cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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-fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask128.cpp.o -MF CMakeFiles/utility-test.dir/bitmask128.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/bitmask128.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src 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/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/tests/position_restraints.cpp /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem 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src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/expanded.cpp.o -MF CMakeFiles/mdlib-test.dir/expanded.cpp.o.d -o CMakeFiles/mdlib-test.dir/expanded.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/expanded.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem 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cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -MF CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o.d -o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/defaultinitializationallocator.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -MF CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o.d -o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/enumerationhelpers.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/awh-test.dir/link.d "CMakeFiles/awh-test.dir/awh_setup.cpp.o" 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -MF CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o.d -o CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/freeenergyparameters.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include 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-DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrog.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/leapfrog.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nbnxm-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/nbnxm-test.dir/link.d "CMakeFiles/nbnxm-test.dir/exclusions.cpp.o" "CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o" "CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o" "CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nbnxm-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 69%] Built target nbnxm-test /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -MF CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmebsplinetest.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -MF CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o.d -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/keyvaluetreeserializer.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -MF CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o.d -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/keyvaluetreetransform.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/listoflists.cpp.o -MF CMakeFiles/utility-test.dir/listoflists.cpp.o.d -o CMakeFiles/utility-test.dir/listoflists.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/listoflists.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/logger.cpp.o -MF CMakeFiles/utility-test.dir/logger.cpp.o.d -o CMakeFiles/utility-test.dir/logger.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/logger.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/listed_forces-test.dir/link.d "CMakeFiles/listed_forces-test.dir/bonded.cpp.o" "CMakeFiles/listed_forces-test.dir/pairs.cpp.o" "CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o" "CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/listed_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 69%] Built target listed_forces-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/leapfrogtestdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/domdec-test.dir/link.d "CMakeFiles/domdec-test.dir/hashedmap.cpp.o" "CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o" "CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 69%] Built target domdec-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmegathertest.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external 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/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/parrinellorahman.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settle.cpp.o -MF CMakeFiles/mdlib-test.dir/settle.cpp.o.d -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/settle.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-mpi-test.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fft/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fft/tests/CMakeFiles/fft-test.dir/fft.cpp.o -MF CMakeFiles/fft-test.dir/fft.cpp.o.d -o CMakeFiles/fft-test.dir/fft.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests/fft.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/domdec-mpi-test.dir/link.d "CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o" "CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 70%] Built target domdec-mpi-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem 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src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -MF CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o.d -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/simulationsignal.cpp /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -MF CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o.d -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/tests/hardwaretopology.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd 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CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/tests/mockhardwaretopology.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem 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src/gromacs/utility/tests/CMakeFiles/utility-test.dir/range.cpp.o -MF CMakeFiles/utility-test.dir/range.cpp.o.d -o CMakeFiles/utility-test.dir/range.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/range.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/tests/device_stream_manager.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -MF CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmesplinespreadtest.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -MF CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o.d -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmetestcommon.cpp /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -MF CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o.d -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/fft-test.dir/link.d "CMakeFiles/fft-test.dir/fft.cpp.o" "CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 72%] Built target fft-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/strconvert.cpp.o -MF CMakeFiles/utility-test.dir/strconvert.cpp.o.d -o CMakeFiles/utility-test.dir/strconvert.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/strconvert.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/constrtestrunners_gpu.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/leapfrogtestrunners_gpu.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem 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-I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/stringutil.cpp.o -MF CMakeFiles/utility-test.dir/stringutil.cpp.o.d -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/stringutil.cpp /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 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/usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build.make src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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/build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/template_mp.cpp.o -MF CMakeFiles/utility-test.dir/template_mp.cpp.o.d -o CMakeFiles/utility-test.dir/template_mp.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/template_mp.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o -MF CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o.d -o CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/wholemoleculetransform.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/ewald-test.dir/link.d "CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o" "CMakeFiles/ewald-test.dir/pmegathertest.cpp.o" "CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o" "CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o" "CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o" "CMakeFiles/ewald-test.dir/pme.cpp.o" "CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 72%] Built target ewald-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/textreader.cpp.o -MF CMakeFiles/utility-test.dir/textreader.cpp.o.d -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/textreader.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libmdrunutility-test-shared.a "CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o" "CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libmdrunutility-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 72%] Built target mdrunutility-test-shared /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem 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-DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/tests/helpmanager.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/hardware-test.dir/link.d "CMakeFiles/hardware-test.dir/cpuinfo.cpp.o" "CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/device_management.cpp.o" "CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 72%] Built target hardware-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/tests/helpwritercontext.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" 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/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/observablesreducer.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -MF 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-I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/functions.cpp.o -MF CMakeFiles/math-test.dir/functions.cpp.o.d -o CMakeFiles/math-test.dir/functions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/functions.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/tests/gpueventsynchronizer.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/extensions.cpp.o -MF CMakeFiles/mdspan-test.dir/extensions.cpp.o.d -o CMakeFiles/mdspan-test.dir/extensions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/tests/extensions.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/gausstransform.cpp.o -MF CMakeFiles/math-test.dir/gausstransform.cpp.o.d -o CMakeFiles/math-test.dir/gausstransform.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/gausstransform.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdlib-test.dir/link.d "CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o" "CMakeFiles/mdlib-test.dir/calcvir.cpp.o" "CMakeFiles/mdlib-test.dir/constr.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/ebin.cpp.o" "CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o" "CMakeFiles/mdlib-test.dir/energyoutput.cpp.o" "CMakeFiles/mdlib-test.dir/expanded.cpp.o" "CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrog.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o" "CMakeFiles/mdlib-test.dir/settle.cpp.o" "CMakeFiles/mdlib-test.dir/settletestdata.cpp.o" 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mdlib-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/invertmatrix.cpp.o -MF CMakeFiles/math-test.dir/invertmatrix.cpp.o.d -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/invertmatrix.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include 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-DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem 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-DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoption.cpp.o -MF CMakeFiles/options-test.dir/filenameoption.cpp.o.d -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/tests/filenameoption.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/gpu_utils-test.dir/link.d "CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o" "CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o" "CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o" "CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o" "CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o" "CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o" "CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 74%] Built target gpu_utils-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/optimization.cpp.o -MF CMakeFiles/math-test.dir/optimization.cpp.o.d -o CMakeFiles/math-test.dir/optimization.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/optimization.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -MF CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o.d -o CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -MF CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o.d -o CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/forcebuffers.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF 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'/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/manager.cpp.o -MF CMakeFiles/restraintpotential-test.dir/manager.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/tests/manager.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/gammadistribution.cpp.o -MF CMakeFiles/random-test.dir/gammadistribution.cpp.o.d -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/random/tests/gammadistribution.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o -MF CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o.d -o CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/multipletimestepping.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/mshift.cpp.o -MF CMakeFiles/pbcutil-test.dir/mshift.cpp.o.d -o CMakeFiles/pbcutil-test.dir/mshift.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/tests/mshift.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/paddedvector.cpp.o -MF CMakeFiles/math-test.dir/paddedvector.cpp.o.d -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/paddedvector.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdspan-test.dir/link.d "CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o" "CMakeFiles/mdspan-test.dir/extents.cpp.o" "CMakeFiles/mdspan-test.dir/extensions.cpp.o" "CMakeFiles/mdspan-test.dir/layouts.cpp.o" "CMakeFiles/mdspan-test.dir/mdspan.cpp.o" "CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/vectypes.cpp.o -MF CMakeFiles/math-test.dir/vectypes.cpp.o.d -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/vectypes.cpp [ 74%] Built target mdspan-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbc.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbc.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/tests/pbc.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/utility-test.dir/link.d "CMakeFiles/utility-test.dir/alignedallocator.cpp.o" "CMakeFiles/utility-test.dir/arrayref.cpp.o" "CMakeFiles/utility-test.dir/booltype.cpp.o" "CMakeFiles/utility-test.dir/bitmask32.cpp.o" "CMakeFiles/utility-test.dir/bitmask64.cpp.o" "CMakeFiles/utility-test.dir/bitmask128.cpp.o" "CMakeFiles/utility-test.dir/cstringutil.cpp.o" "CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o" "CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o" "CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o" "CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o" "CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o" "CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o" "CMakeFiles/utility-test.dir/listoflists.cpp.o" "CMakeFiles/utility-test.dir/logger.cpp.o" "CMakeFiles/utility-test.dir/message_string_collector.cpp.o" "CMakeFiles/utility-test.dir/path.cpp.o" "CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o" "CMakeFiles/utility-test.dir/range.cpp.o" "CMakeFiles/utility-test.dir/strconvert.cpp.o" "CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o" "CMakeFiles/utility-test.dir/stringutil.cpp.o" "CMakeFiles/utility-test.dir/template_mp.cpp.o" "CMakeFiles/utility-test.dir/textreader.cpp.o" "CMakeFiles/utility-test.dir/textwriter.cpp.o" "CMakeFiles/utility-test.dir/typetraits.cpp.o" "CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 76%] Built target utility-test /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/tables/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tables/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY 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/build/reproducible-path/gromacs-2024.4/src/gromacs/random/tests/normaldistribution.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 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/usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 76%] Built target restraintpotential-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tables/tests/CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/tests/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/option.cpp.o -MF CMakeFiles/options-test.dir/option.cpp.o.d -o CMakeFiles/options-test.dir/option.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/tests/option.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/optionsassigner.cpp.o -MF CMakeFiles/options-test.dir/optionsassigner.cpp.o.d -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/tests/optionsassigner.cpp /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd 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/build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -MF CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o.d -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/tests/usergpuids.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem 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CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/random/tests/tabulatednormaldistribution.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/repeatingsection.cpp.o -MF CMakeFiles/options-test.dir/repeatingsection.cpp.o.d -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/tests/repeatingsection.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/pbcutil-test.dir/link.d "CMakeFiles/pbcutil-test.dir/com.cpp.o" "CMakeFiles/pbcutil-test.dir/mshift.cpp.o" "CMakeFiles/pbcutil-test.dir/pbc.cpp.o" "CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o" "CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 76%] Built target pbcutil-test /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/timing/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/timing/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/timing/tests/CMakeFiles/timing-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/timing/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/timing/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/timing/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/timing/tests/CMakeFiles/timing-test.dir/timing.cpp.o -MF CMakeFiles/timing-test.dir/timing.cpp.o.d -o CMakeFiles/timing-test.dir/timing.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/timing/tests/timing.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/threefry.cpp.o -MF CMakeFiles/random-test.dir/threefry.cpp.o.d -o CMakeFiles/random-test.dir/threefry.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/random/tests/threefry.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/base.cpp.o -MF CMakeFiles/simd-test.dir/base.cpp.o.d -o CMakeFiles/simd-test.dir/base.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/base.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdtypes-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdtypes-test.dir/link.d "CMakeFiles/mdtypes-test.dir/enerdata.cpp.o" "CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o" "CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o" "CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o" "CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o" "CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdtypes-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 76%] Built target mdtypes-test /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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&& /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pulling/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/taskassignment-test.dir/link.d "CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o" "CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o ../CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o ../CMakeFiles/taskassignment.dir/findallgputasks.cpp.o ../CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o ../CMakeFiles/taskassignment.dir/resourcedivision.cpp.o ../CMakeFiles/taskassignment.dir/taskassignment.cpp.o ../CMakeFiles/taskassignment.dir/usergpuids.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 77%] Built target taskassignment-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -MF CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o.d -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/bootstrap_loadstore.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar.cpp.o -MF CMakeFiles/simd-test.dir/scalar.cpp.o.d -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/scalar.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/table-test.dir/link.d "CMakeFiles/table-test.dir/splinetable.cpp.o" "CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 77%] Built target table-test /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/entropy.cpp.o -MF CMakeFiles/gmxana-test.dir/entropy.cpp.o.d -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/tests/entropy.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/random-test.dir/link.d "CMakeFiles/random-test.dir/exponentialdistribution.cpp.o" "CMakeFiles/random-test.dir/gammadistribution.cpp.o" "CMakeFiles/random-test.dir/normaldistribution.cpp.o" "CMakeFiles/random-test.dir/seed.cpp.o" "CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o" "CMakeFiles/random-test.dir/threefry.cpp.o" "CMakeFiles/random-test.dir/uniformintdistribution.cpp.o" "CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o" "CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 78%] Built target random-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/tests/gmx_chi.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/compat-test.dir/link.d "CMakeFiles/compat-test.dir/mp11.cpp.o" "CMakeFiles/compat-test.dir/pointers.cpp.o" "CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend make[4]: Entering directory 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-fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/tests/gmx_mindist.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/pull-test.dir/link.d "CMakeFiles/pull-test.dir/pull.cpp.o" "CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/pulling.dir/output.cpp.o ../CMakeFiles/pulling.dir/pull.cpp.o ../CMakeFiles/pulling.dir/pull_rotation.cpp.o ../CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o ../CMakeFiles/pulling.dir/pullutil.cpp.o ../CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lmuparser -lm ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 78%] Built target pull-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd.cpp.o -MF CMakeFiles/simd-test.dir/simd.cpp.o.d -o CMakeFiles/simd-test.dir/simd.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/simd.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem 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-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -MF CMakeFiles/topology-test.dir/exclusionblocks.cpp.o.d -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/exclusionblocks.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/options-test.dir/link.d "CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o" "CMakeFiles/options-test.dir/filenameoption.cpp.o" "CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o" "CMakeFiles/options-test.dir/option.cpp.o" "CMakeFiles/options-test.dir/optionsassigner.cpp.o" "CMakeFiles/options-test.dir/repeatingsection.cpp.o" "CMakeFiles/options-test.dir/timeunitmanager.cpp.o" "CMakeFiles/options-test.dir/treesupport.cpp.o" "CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 80%] Built target options-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem 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-fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/mtop.cpp.o -MF CMakeFiles/topology-test.dir/mtop.cpp.o.d -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/mtop.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/gmxana-test.dir/link.d "CMakeFiles/gmxana-test.dir/entropy.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o" "CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 80%] Built target gmxana-test /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/autocorr.cpp.o -MF CMakeFiles/correlations-test.dir/autocorr.cpp.o.d -o CMakeFiles/correlations-test.dir/autocorr.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/tests/autocorr.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/pdb2gmx2-test.dir/link.d "CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx2-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 80%] Built target pdb2gmx2-test /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/tests/datatest.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/pdb2gmx1-test.dir/link.d "CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx1-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 80%] Built target pdb2gmx1-test cd 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/tests/mock_datamodule.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_math.cpp.o -MF CMakeFiles/simd-test.dir/simd_math.cpp.o.d -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/simd_math.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/symtab.cpp.o -MF CMakeFiles/topology-test.dir/symtab.cpp.o.d -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/symtab.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_memory.cpp.o -MF CMakeFiles/simd-test.dir/simd_memory.cpp.o.d -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/simd_memory.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -MF CMakeFiles/correlations-test.dir/correlationdataset.cpp.o.d -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/tests/correlationdataset.cpp /usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/coordinateio/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/builder.cpp.o -MF CMakeFiles/coordinateio-test.dir/builder.cpp.o.d -o CMakeFiles/coordinateio-test.dir/builder.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/tests/builder.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/math-test.dir/link.d "CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o" "CMakeFiles/math-test.dir/boxmatrix.cpp.o" "CMakeFiles/math-test.dir/coordinatetransformation.cpp.o" "CMakeFiles/math-test.dir/densityfit.cpp.o" "CMakeFiles/math-test.dir/dofit.cpp.o" "CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o" "CMakeFiles/math-test.dir/functions.cpp.o" "CMakeFiles/math-test.dir/gausstransform.cpp.o" "CMakeFiles/math-test.dir/densityfittingforce.cpp.o" "CMakeFiles/math-test.dir/invertmatrix.cpp.o" "CMakeFiles/math-test.dir/matrix.cpp.o" "CMakeFiles/math-test.dir/multidimarray.cpp.o" "CMakeFiles/math-test.dir/neldermead.cpp.o" "CMakeFiles/math-test.dir/optimization.cpp.o" "CMakeFiles/math-test.dir/paddedvector.cpp.o" "CMakeFiles/math-test.dir/vectypes.cpp.o" "CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 81%] Built target math-test /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/energyterm.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast 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Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/tools/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/pdb2gmx3-test.dir/link.d "CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx3-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 81%] Built target pdb2gmx3-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -MF CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o.d -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -MF 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-I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -MF CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o.d -o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/tests/outputadaptercontainer.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" 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directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/selection/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/energyanalysis-test.dir/link.d "CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o" "CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o" "CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 81%] Built target energyanalysis-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem 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src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/register.cpp.o -MF CMakeFiles/coordinateio-test.dir/register.cpp.o.d -o CMakeFiles/coordinateio-test.dir/register.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/tests/register.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/report_methods.cpp.o -MF CMakeFiles/tool-test.dir/report_methods.cpp.o.d -o CMakeFiles/tool-test.dir/report_methods.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/tools/tests/report_methods.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/confio.cpp.o -MF CMakeFiles/fileio-test.dir/confio.cpp.o.d -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/confio.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/massrepartitioning.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/correlations-test.dir/link.d "CMakeFiles/correlations-test.dir/autocorr.cpp.o" "CMakeFiles/correlations-test.dir/correlationdataset.cpp.o" "CMakeFiles/correlations-test.dir/expfit.cpp.o" "CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o" "CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 82%] Built target correlations-test 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/simd4_floatingpoint.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/filemd5.cpp.o -MF CMakeFiles/fileio-test.dir/filemd5.cpp.o.d -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/filemd5.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/topology/tests && 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/build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. 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-I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/requirements.cpp.o -MF CMakeFiles/coordinateio-test.dir/requirements.cpp.o.d -o CMakeFiles/coordinateio-test.dir/requirements.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/tests/requirements.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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/usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem 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/usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 84%] Built target topology-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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-I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -P CMakeFiles/analysisdata-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test-shared.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 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Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -MF CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/compressed_x_output.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem 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/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/tests/setatoms.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/convert-tpr.cpp.o -MF CMakeFiles/tool-test.dir/convert-tpr.cpp.o.d -o CMakeFiles/tool-test.dir/convert-tpr.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/tools/tests/convert-tpr.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/simd-test.dir/link.d "CMakeFiles/simd-test.dir/base.cpp.o" "CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o" "CMakeFiles/simd-test.dir/scalar.cpp.o" "CMakeFiles/simd-test.dir/scalar_util.cpp.o" "CMakeFiles/simd-test.dir/scalar_math.cpp.o" "CMakeFiles/simd-test.dir/simd.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o" "CMakeFiles/simd-test.dir/simd_integer.cpp.o" "CMakeFiles/simd-test.dir/simd_math.cpp.o" "CMakeFiles/simd-test.dir/simd_memory.cpp.o" "CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/simd4.cpp.o" "CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd4_math.cpp.o" "CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 85%] Built target simd-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -MF CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/tests/setbothtime.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/gmxpreprocess-test.dir/link.d "CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 86%] Built target gmxpreprocess-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/poscalc.cpp.o -MF CMakeFiles/selection-test.dir/poscalc.cpp.o.d -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/poscalc.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/timecontrol.cpp.o -MF CMakeFiles/fileio-test.dir/timecontrol.cpp.o.d -o CMakeFiles/fileio-test.dir/timecontrol.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/timecontrol.cpp cd 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/build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/helpwriting.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/tests/settimestep.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make 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'/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -MF CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/checkpoint.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem 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/build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/outputfiles.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o -MF CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o.d -o CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/multiple_time_stepping.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -MF CMakeFiles/coordinateio-test.dir/testmodule.cpp.o.d -o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/tests/testmodule.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectioncollection.cpp.o -MF CMakeFiles/selection-test.dir/selectioncollection.cpp.o.d -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/selectioncollection.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 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src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make 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../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -MF CMakeFiles/mdrun-test.dir/swapcoords.cpp.o.d -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/swapcoords.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/mimic.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1 /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/minimize.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/coordinateio-test.dir/link.d "CMakeFiles/coordinateio-test.dir/builder.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o" "CMakeFiles/coordinateio-test.dir/register.cpp.o" "CMakeFiles/coordinateio-test.dir/requirements.cpp.o" "CMakeFiles/coordinateio-test.dir/setatoms.cpp.o" "CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o" "CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o" "CMakeFiles/coordinateio-test.dir/settimestep.cpp.o" "CMakeFiles/coordinateio-test.dir/testmodule.cpp.o" "CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 86%] Built target coordinateio-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && 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src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem 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src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-output-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-modules-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-output-test.dir/link.d "CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o" "CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o" "CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o" "CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o" "CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-output-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 86%] Built target mdrun-output-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem 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CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/normalmodes.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.d "CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-single-rank-algorithms-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-modules-test.dir/link.d "CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o" "CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o" "CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o" "CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-modules-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 86%] Built target mdrun-modules-test [ 86%] Built target mdrun-single-rank-algorithms-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" 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-DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/rerun.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 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../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 86%] Built target mdrun-tpi-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 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-I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/multisimtest.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -MF CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/initialconstraints.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/fileio-test.dir/link.d "CMakeFiles/fileio-test.dir/checkpoint.cpp.o" "CMakeFiles/fileio-test.dir/confio.cpp.o" "CMakeFiles/fileio-test.dir/filemd5.cpp.o" "CMakeFiles/fileio-test.dir/filetypes.cpp.o" "CMakeFiles/fileio-test.dir/mrcserializer.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o" "CMakeFiles/fileio-test.dir/readinp.cpp.o" "CMakeFiles/fileio-test.dir/timecontrol.cpp.o" "CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o" "CMakeFiles/fileio-test.dir/tngio.cpp.o" "CMakeFiles/fileio-test.dir/xvgio.cpp.o" "CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/minimize-test.dir/link.txt --verbose=1 [ 86%] Built target fileio-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/termination.cpp.o -MF CMakeFiles/mdrun-io-test.dir/termination.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/termination.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/termination.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/minimize-test.dir/link.d "CMakeFiles/minimize-test.dir/minimize.cpp.o" "CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/minimize-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 86%] Built target minimize-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/toputils.cpp.o -MF CMakeFiles/selection-test.dir/toputils.cpp.o.d -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/toputils.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/replicaexchange.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/multisimtest.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o -MF CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o.d -o CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/constantacceleration.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 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'/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/periodicactions.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/periodicactions.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include 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-I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/periodicactions_coupling.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-non-integrator-test.dir/link.d "CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 88%] Built target mdrun-non-integrator-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-multisim-replex-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 89%] Built target mdrun-multisim-replex-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem 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--verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-test.dir/link.d "CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o" "CMakeFiles/mdrun-test.dir/swapcoords.cpp.o" "CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o" "CMakeFiles/mdrun-test.dir/freezegroups.cpp.o" "CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o" "CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o" "CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 90%] Built target mdrun-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -MF CMakeFiles/mdrun-pull-test.dir/pull.cpp.o.d -o CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/pull.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/selection-test.dir/link.d "CMakeFiles/selection-test.dir/indexutil.cpp.o" "CMakeFiles/selection-test.dir/nbsearch.cpp.o" "CMakeFiles/selection-test.dir/poscalc.cpp.o" "CMakeFiles/selection-test.dir/selectioncollection.cpp.o" "CMakeFiles/selection-test.dir/selectionoption.cpp.o" "CMakeFiles/selection-test.dir/toputils.cpp.o" "CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 90%] Built target selection-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/testutils/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o -MF CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o.d -o CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/pull_rotation.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-pme-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/c++ -g 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/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -MF 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-I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/periodicactions_basic.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-coupling-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-coordination-coupling-test.dir/link.d "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-coupling-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 90%] Built target mdrun-coordination-coupling-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/depend /usr/bin/make -f api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem 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-f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o -MF CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o.d -o CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/virtualsites.cpp /usr/bin/make -f api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/workflow/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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-DTEST_DATA_PATH=\"api/gmxapi/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/workflow/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2024.4/api/nblib/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o -MF CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o.d -o CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/integrator.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-coordination-constraints-test.dir/link.d "CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o" "CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-constraints-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 90%] Built target mdrun-coordination-constraints-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-rotation-test.dir/link.d "CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o" "CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-rotation-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 90%] Built target mdrun-rotation-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-setup-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-setup-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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cmake_link_script CMakeFiles/mdrun-simulator-comparison-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-simulator-comparison-test.dir/link.d "CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o" "CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-simulator-comparison-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 90%] Built target mdrun-simulator-comparison-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 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/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests/runner.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src 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api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-fep-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-fep-test.dir/link.d "CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o" "CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-fep-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 90%] Built target mdrun-fep-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/tests 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-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/tests/bondtypes.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/workflow-details-test.dir/link.d "CMakeFiles/workflow-details-test.dir/workflow.cpp.o" "CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o 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"--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src 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../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-basic-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-tpr-test.dir/link.txt --verbose=1 [ 92%] Built target mdrun-coordination-basic-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -MF CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/pbcholder.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/nblib-tpr-test.dir/link.d "CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o" "CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-tpr-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 92%] Built target nblib-tpr-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/tests/gmxcalculator.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-pull-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-equivalence-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 92%] Built target mdrun-multisim-replex-equivalence-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/tests/helpers.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-pull-test.dir/link.d "CMakeFiles/mdrun-pull-test.dir/pull.cpp.o" "CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-pull-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 93%] Built target mdrun-pull-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -MF CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/nbkernelsystem.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -MF CMakeFiles/nblib-integration-test.dir/simstate.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/simstate.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/traits.cpp.o -MF CMakeFiles/nblib-util-test.dir/traits.cpp.o.d -o CMakeFiles/nblib-util-test.dir/traits.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/util/tests/traits.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o -MF CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/nbnxmsetup.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/status.cpp.o -MF CMakeFiles/gmxapi-test.dir/status.cpp.o.d -o CMakeFiles/gmxapi-test.dir/status.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests/status.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-vsites-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/tests/listedtesthelpers.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-vsites-test.dir/link.d "CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o" "CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-vsites-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 93%] Built target mdrun-vsites-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integrator-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/nblib-integrator-test.dir/link.d "CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o" "CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integrator-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 93%] Built target nblib-integrator-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/topology.cpp.o -MF CMakeFiles/nblib-setup-test.dir/topology.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/topology.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/topology.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/tests/cmdlineparser.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/system.cpp.o -MF CMakeFiles/gmxapi-test.dir/system.cpp.o.d -o CMakeFiles/gmxapi-test.dir/system.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests/system.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integration-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/util/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-util-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/nblib-integration-test.dir/link.d "CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o" "CMakeFiles/nblib-integration-test.dir/simstate.cpp.o" "CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integration-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 93%] Built target nblib-integration-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o -MF CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/tests/mdmodulesnotifier.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/nblib-util-test.dir/link.d "CMakeFiles/nblib-util-test.dir/setup.cpp.o" "CMakeFiles/nblib-util-test.dir/traits.cpp.o" "CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-util-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 93%] Built target nblib-util-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -MF CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/tests/threadaffinity.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/tests/kernels.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem 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-Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/virials.cpp.o -MF CMakeFiles/nblib-setup-test.dir/virials.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/virials.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/tests/shiftforces.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-test.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/gmxapi-test.dir/link.d "CMakeFiles/gmxapi-test.dir/restraint.cpp.o" "CMakeFiles/gmxapi-test.dir/runner.cpp.o" "CMakeFiles/gmxapi-test.dir/status.cpp.o" "CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o" "CMakeFiles/gmxapi-test.dir/system.cpp.o" "CMakeFiles/gmxapi-test.dir/version.cpp.o" "CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi_d.so.0.4.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 93%] Built target gmxapi-test /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem 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-I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -MF CMakeFiles/analysisdata-test.dir/arraydata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/tests/arraydata.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrunutility-test.dir/link.d "CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o" "CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o" "CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 94%] Built target mdrunutility-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/tests/transformations.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/average.cpp.o -MF 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Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src 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-I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/histogram.cpp.o -MF CMakeFiles/analysisdata-test.dir/histogram.cpp.o.d -o CMakeFiles/analysisdata-test.dir/histogram.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/tests/histogram.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/commandline-test.dir/link.d "CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o" "CMakeFiles/commandline-test.dir/filenm.cpp.o" "CMakeFiles/commandline-test.dir/pargs.cpp.o" "CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 96%] Built target commandline-test cd 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/msd.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-setup-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/pairdist.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 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-I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/sasa.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/nblib-setup-test.dir/link.d "CMakeFiles/nblib-setup-test.dir/box.cpp.o" "CMakeFiles/nblib-setup-test.dir/interactions.cpp.o" "CMakeFiles/nblib-setup-test.dir/particletype.cpp.o" "CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o" "CMakeFiles/nblib-setup-test.dir/molecules.cpp.o" "CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o" "CMakeFiles/nblib-setup-test.dir/topology.cpp.o" "CMakeFiles/nblib-setup-test.dir/virials.cpp.o" "CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-setup-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 97%] Built target nblib-setup-test /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/CMakeFiles/nblib-tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib-tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 97%] Built target nblib-tests cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/select.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/scattering.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/topologyinformation.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trajectory.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/unionfind.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/analysisdata-test.dir/link.d "CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o" "CMakeFiles/analysisdata-test.dir/arraydata.cpp.o" "CMakeFiles/analysisdata-test.dir/average.cpp.o" "CMakeFiles/analysisdata-test.dir/histogram.cpp.o" "CMakeFiles/analysisdata-test.dir/lifetime.cpp.o" "CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 97%] Built target analysisdata-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-listed-forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/nblib-listed-forces-test.dir/link.d "CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 98%] Built target nblib-listed-forces-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/trajectoryanalysis-test.dir/link.d "CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [100%] Built target trajectoryanalysis-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/CMakeFiles/tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [100%] Built target tests make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2024.4/build/basic-dp/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[1]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' (cd build/basic-dp; LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2024.4/build/basic-dp/lib ctest -V) UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2024.4/build/basic-dp/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2024.4/build/basic-dp/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2024.4/build/basic-dp/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2024.4/build/basic-dp/DartConfiguration.tcl Test project /build/reproducible-path/gromacs-2024.4/build/basic-dp Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: GmxapiExternalInterfaceTests 1: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/gmxapi-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/GmxapiExternalInterfaceTests.xml" 1: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests 1: Test timeout computed to be: 600 1: [==========] Running 9 tests from 1 test suite. 1: [----------] Global test environment set-up. 1: [----------] 9 tests from GmxApiTest 1: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -353722369 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.545 0.273 200.0 1: (ns/day) (hour/ns) 1: Performance: 1.858 12.921 1: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (1035 ms) 1: [ RUN ] GmxApiTest.RunnerBasicMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -1757578305 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.839 0.419 200.0 1: (ns/day) (hour/ns) 1: Performance: 1.207 19.884 1: [ OK ] GmxApiTest.RunnerBasicMD (877 ms) 1: [ RUN ] GmxApiTest.RunnerReinitialize 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: 1: Received the remote INT/TERM signal, stopping within 200 steps 1: 1: Setting the LD random seed to -1158177413 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.456 0.228 199.9 1: (ns/day) (hour/ns) 1: Performance: 15.533 1.545 1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.660 0.330 200.0 1: (ns/day) (hour/ns) 1: Performance: 10.732 2.236 1: [ OK ] GmxApiTest.RunnerReinitialize (1338 ms) 1: [ RUN ] GmxApiTest.RunnerChainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -8585857 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.622 0.311 200.0 1: (ns/day) (hour/ns) 1: Performance: 1.629 14.736 1: trr version: GMX_trn_file (double precision) 1: 1: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 1: Setting nsteps to 4 1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 1: Input file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 2 1: Runtime for the run 0.00390625 ps 1: Run end step 2 1: Run end time 0.00390625 ps 1: 1: 1: Output file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 4 1: Runtime for the run 0.0078125 ps 1: Run end step 4 1: Run end time 0.0078125 ps 1: 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.598 0.299 200.0 1: (ns/day) (hour/ns) 1: Performance: 1.694 14.170 1: 1: [ OK ] GmxApiTest.RunnerChainedMD (1095 ms) 1: [ RUN ] GmxApiTest.Status 1: [ OK ] GmxApiTest.Status (0 ms) 1: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 1: Changing nstlist from 10 to 1, rlist from 1.062 to 1 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: Setting the LD random seed to 1944059709 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.247 0.124 199.9 1: (ns/day) (hour/ns) 1: Performance: 6.822 3.518 1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 1: Overriding nsteps with value passed on the command line: 4 steps, 0.00781 ps 1: Changing nstlist from 10 to 1, rlist from 1.062 to 1 1: 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.107 0.054 199.7 1: (ns/day) (hour/ns) 1: Performance: 6.292 3.815 1: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (884 ms) 1: [ RUN ] GmxApiTest.SystemConstruction 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Setting the LD random seed to -1175068865 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: [ OK ] GmxApiTest.SystemConstruction (476 ms) 1: [ RUN ] GmxApiTest.SaneVersionComparisons 1: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms) 1: [ RUN ] GmxApiTest.VersionNamed0_1_Features 1: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) 1: [----------] 9 tests from GmxApiTest (5711 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 9 tests from 1 test suite ran. (5819 ms total) 1: [ PASSED ] 9 tests. 1/87 Test #1: GmxapiExternalInterfaceTests .............. Passed 6.07 sec test 2 Start 2: GmxapiInternalInterfaceTests 2: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/workflow-details-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/GmxapiInternalInterfaceTests.xml" 2: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/workflow/tests 2: Test timeout computed to be: 600 2: [==========] Running 2 tests from 1 test suite. 2: [----------] Global test environment set-up. 2: [----------] 2 tests from GmxApiTest 2: [ RUN ] GmxApiTest.BuildApiWorkflowImpl 2: Generating 1-4 interactions: fudge = 0.5 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Setting the LD random seed to -204505611 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: [ OK ] GmxApiTest.BuildApiWorkflowImpl (613 ms) 2: [ RUN ] GmxApiTest.CreateApiWorkflow 2: Generating 1-4 interactions: fudge = 0.5 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Setting the LD random seed to -8651929 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: [ OK ] GmxApiTest.CreateApiWorkflow (637 ms) 2: [----------] 2 tests from GmxApiTest (1250 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 2 tests from 1 test suite ran. (1283 ms total) 2: [ PASSED ] 2 tests. 2/87 Test #2: GmxapiInternalInterfaceTests .............. Passed 1.33 sec test 3 Start 3: NbLibListedForcesTests 3: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/nblib-listed-forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/NbLibListedForcesTests.xml" 3: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/listed_forces/tests 3: Test timeout computed to be: 600 3: [==========] Running 44 tests from 22 test suites. 3: [----------] Global test environment set-up. 3: [----------] 8 tests from NBlibTest 3: [ RUN ] NBlibTest.BondTypesOperatorEqualWorks 3: [ OK ] NBlibTest.BondTypesOperatorEqualWorks (0 ms) 3: [ RUN ] NBlibTest.BondTypesLessThanWorks 3: [ OK ] NBlibTest.BondTypesLessThanWorks (0 ms) 3: [ RUN ] NBlibTest.CanSplitListedWork 3: [ OK ] NBlibTest.CanSplitListedWork (0 ms) 3: [ RUN ] NBlibTest.ListedForceBuffer 3: [ OK ] NBlibTest.ListedForceBuffer (0 ms) 3: [ RUN ] NBlibTest.ListedForceCalculatorCanConstruct 3: [ OK ] NBlibTest.ListedForceCalculatorCanConstruct (1 ms) 3: [ RUN ] NBlibTest.GmxToNblibConversionAllTypes 3: [ OK ] NBlibTest.GmxToNblibConversionAllTypes (11 ms) 3: [ RUN ] NBlibTest.EndToEndListedComparison 3: [ OK ] NBlibTest.EndToEndListedComparison (0 ms) 3: [ RUN ] NBlibTest.shiftForcesAreCorrect 3: [ OK ] NBlibTest.shiftForcesAreCorrect (36 ms) 3: [----------] 8 tests from NBlibTest (49 ms total) 3: 3: [----------] 1 test from Kernels 3: [ RUN ] Kernels.HarmonicScalarKernelCanCompute 3: [ OK ] Kernels.HarmonicScalarKernelCanCompute (0 ms) 3: [----------] 1 test from Kernels (0 ms total) 3: 3: [----------] 1 test from FourCenter 3: [ RUN ] FourCenter.ListedForcesProperDihedralTest 3: [ OK ] FourCenter.ListedForcesProperDihedralTest (0 ms) 3: [----------] 1 test from FourCenter (0 ms total) 3: 3: [----------] 7 tests from ThreeCenter 3: [ RUN ] ThreeCenter.ListedForcesG96AngleTest 3: [ OK ] ThreeCenter.ListedForcesG96AngleTest (1 ms) 3: [ RUN ] ThreeCenter.ListedForcesHarmonicAngleTest 3: [ OK ] ThreeCenter.ListedForcesHarmonicAngleTest (2 ms) 3: [ RUN ] ThreeCenter.ListedForcesLinearAngleTest 3: [ OK ] ThreeCenter.ListedForcesLinearAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesCrossBondBondTest 3: [ OK ] ThreeCenter.ListedForcesCrossBondBondTest (1 ms) 3: [ RUN ] ThreeCenter.ListedForcesCrossBondAngleTest 3: [ OK ] ThreeCenter.ListedForcesCrossBondAngleTest (1 ms) 3: [ RUN ] ThreeCenter.ListedForcesQuarticAngleTest 3: [ OK ] ThreeCenter.ListedForcesQuarticAngleTest (2 ms) 3: [ RUN ] ThreeCenter.ListedForcesRestrictedAngleTest 3: [ OK ] ThreeCenter.ListedForcesRestrictedAngleTest (0 ms) 3: [----------] 7 tests from ThreeCenter (10 ms total) 3: 3: [----------] 5 tests from TwoCenter 3: [ RUN ] TwoCenter.ListedForcesHarmonicBondTest 3: [ OK ] TwoCenter.ListedForcesHarmonicBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesG96BondTest 3: [ OK ] TwoCenter.ListedForcesG96BondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesCubicBondTest 3: [ OK ] TwoCenter.ListedForcesCubicBondTest (2 ms) 3: [ RUN ] TwoCenter.ListedForcesMorseBondTest 3: [ OK ] TwoCenter.ListedForcesMorseBondTest (4 ms) 3: [ RUN ] TwoCenter.ListedForcesFeneBondTest 3: [ OK ] TwoCenter.ListedForcesFeneBondTest (4 ms) 3: [----------] 5 tests from TwoCenter (13 ms total) 3: 3: [----------] 5 tests from ListedExampleData 3: [ RUN ] ListedExampleData.ComputeHarmonicBondForces 3: [ OK ] ListedExampleData.ComputeHarmonicBondForces (0 ms) 3: [ RUN ] ListedExampleData.ComputeHarmonicBondEnergies 3: [ OK ] ListedExampleData.ComputeHarmonicBondEnergies (0 ms) 3: [ RUN ] ListedExampleData.ComputeHarmonicAngleForces 3: [ OK ] ListedExampleData.ComputeHarmonicAngleForces (0 ms) 3: [ RUN ] ListedExampleData.CanReduceForces 3: [ OK ] ListedExampleData.CanReduceForces (0 ms) 3: [ RUN ] ListedExampleData.CanReduceEnergies 3: [ OK ] ListedExampleData.CanReduceEnergies (0 ms) 3: [----------] 5 tests from ListedExampleData (2 ms total) 3: 3: [----------] 1 test from LinearChainDataFixture 3: [ RUN ] LinearChainDataFixture.Multithreading 3: [ OK ] LinearChainDataFixture.Multithreading (47 ms) 3: [----------] 1 test from LinearChainDataFixture (47 ms total) 3: 3: [----------] 2 tests from ListedShims 3: [ RUN ] ListedShims.ParameterConversion 3: [ OK ] ListedShims.ParameterConversion (0 ms) 3: [ RUN ] ListedShims.GmxToNblibConversion 3: [ OK ] ListedShims.GmxToNblibConversion (0 ms) 3: [----------] 2 tests from ListedShims (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1, where TypeParam = nblib::G96BondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2, where TypeParam = nblib::CubicBondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3, where TypeParam = nblib::MorseBondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5, where TypeParam = nblib::AngleInteractionType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6, where TypeParam = nblib::CosineParamAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7, where TypeParam = nblib::CosineParamAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9, where TypeParam = nblib::QuarticAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth (4 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9 (4 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10, where TypeParam = nblib::CrossBondBond 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11, where TypeParam = nblib::CrossBondAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12, where TypeParam = nblib::ProperDihedral 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12 (0 ms total) 3: 3: [----------] 1 test from ListedTransformations 3: [ RUN ] ListedTransformations.SortInteractionIndices 3: [ OK ] ListedTransformations.SortInteractionIndices (0 ms) 3: [----------] 1 test from ListedTransformations (0 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 44 tests from 22 test suites ran. (132 ms total) 3: [ PASSED ] 44 tests. 3/87 Test #3: NbLibListedForcesTests .................... Passed 0.20 sec test 4 Start 4: NbLibSamplesTestArgon 4: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/argon-forces-integration 4: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/samples 4: Test timeout computed to be: 1500 4: initial forces on particle 0: x 0.000000 y 0.000000 z 0.000000 4: final forces on particle 0: x -0.412988 y -1.098243 z -0.113189 4: initial position of particle 0: x 0.794000 y 1.439000 z 0.610000 4: final position of particle 0: x 0.789162 y 1.271508 z 0.819867 4/87 Test #4: NbLibSamplesTestArgon ..................... Passed 0.03 sec test 5 Start 5: NbLibSamplesTestMethaneWater 5: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/methane-water-integration 5: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/samples 5: Test timeout computed to be: 1500 5: initial position of particle 0: x 0.005000 y 0.600000 z 0.244000 5: final position of particle 9: x 77.358372 y 5.325207 z -80.600064 5/87 Test #5: NbLibSamplesTestMethaneWater .............. Passed 0.09 sec test 6 Start 6: NbLibUtilTests 6: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/nblib-util-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/NbLibUtilTests.xml" 6: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/util/tests 6: Test timeout computed to be: 30 6: [==========] Running 16 tests from 2 test suites. 6: [----------] Global test environment set-up. 6: [----------] 6 tests from NBlibTest 6: [ RUN ] NBlibTest.isRealValued 6: [ OK ] NBlibTest.isRealValued (0 ms) 6: [ RUN ] NBlibTest.checkNumericValuesHasNan 6: [ OK ] NBlibTest.checkNumericValuesHasNan (0 ms) 6: [ RUN ] NBlibTest.checkNumericValuesHasInf 6: [ OK ] NBlibTest.checkNumericValuesHasInf (0 ms) 6: [ RUN ] NBlibTest.GeneratedVelocitiesAreCorrect 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.GeneratedVelocitiesAreCorrect (0 ms) 6: [ RUN ] NBlibTest.generateVelocitySize 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.generateVelocitySize (0 ms) 6: [ RUN ] NBlibTest.generateVelocityCheckNumbers 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.generateVelocityCheckNumbers (0 ms) 6: [----------] 6 tests from NBlibTest (0 ms total) 6: 6: [----------] 10 tests from NblibTraitsUtils 6: [ RUN ] NblibTraitsUtils.FuseTwo 6: [ OK ] NblibTraitsUtils.FuseTwo (0 ms) 6: [ RUN ] NblibTraitsUtils.Fuse 6: [ OK ] NblibTraitsUtils.Fuse (0 ms) 6: [ RUN ] NblibTraitsUtils.Repeat 6: [ OK ] NblibTraitsUtils.Repeat (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTuple1 6: [ OK ] NblibTraitsUtils.FindIndexTuple1 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTuple2 6: [ OK ] NblibTraitsUtils.FindIndexTuple2 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeList1 6: [ OK ] NblibTraitsUtils.FindIndexTypeList1 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeList2 6: [ OK ] NblibTraitsUtils.FindIndexTypeList2 (0 ms) 6: [ RUN ] NblibTraitsUtils.Contains 6: [ OK ] NblibTraitsUtils.Contains (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTupleRepeated 6: [ OK ] NblibTraitsUtils.FindIndexTupleRepeated (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeListRepeated 6: [ OK ] NblibTraitsUtils.FindIndexTypeListRepeated (0 ms) 6: [----------] 10 tests from NblibTraitsUtils (0 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 16 tests from 2 test suites ran. (0 ms total) 6: [ PASSED ] 16 tests. 6/87 Test #6: NbLibUtilTests ............................ Passed 0.02 sec test 7 Start 7: NbLibSetupTests 7: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/nblib-setup-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/NbLibSetupTests.xml" 7: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests 7: Test timeout computed to be: 600 7: [==========] Running 57 tests from 3 test suites. 7: [----------] Global test environment set-up. 7: [----------] 41 tests from NBlibTest 7: [ RUN ] NBlibTest.CubicBoxCannotHaveNaN 7: [ OK ] NBlibTest.CubicBoxCannotHaveNaN (0 ms) 7: [ RUN ] NBlibTest.CubicBoxCannotHaveInf 7: [ OK ] NBlibTest.CubicBoxCannotHaveInf (0 ms) 7: [ RUN ] NBlibTest.RectangularBoxCannotHaveNaN 7: [ OK ] NBlibTest.RectangularBoxCannotHaveNaN (0 ms) 7: [ RUN ] NBlibTest.RectangularBoxCannotHaveInf 7: [ OK ] NBlibTest.RectangularBoxCannotHaveInf (0 ms) 7: [ RUN ] NBlibTest.CubicBoxWorks 7: [ OK ] NBlibTest.CubicBoxWorks (0 ms) 7: [ RUN ] NBlibTest.BoxEqual 7: [ OK ] NBlibTest.BoxEqual (0 ms) 7: [ RUN ] NBlibTest.NonBondedForceParamsCorrect 7: [ OK ] NBlibTest.NonBondedForceParamsCorrect (0 ms) 7: [ RUN ] NBlibTest.CanMergeInteractions 7: [ OK ] NBlibTest.CanMergeInteractions (0 ms) 7: [ RUN ] NBlibTest.ParticleTypeNameCanBeConstructed 7: [ OK ] NBlibTest.ParticleTypeNameCanBeConstructed (0 ms) 7: [ RUN ] NBlibTest.ParticleTypeMassCanBeConstructed 7: [ OK ] NBlibTest.ParticleTypeMassCanBeConstructed (0 ms) 7: [ RUN ] NBlibTest.PbcHolderWorks 7: [ OK ] NBlibTest.PbcHolderWorks (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName (0 ms) 7: [ RUN ] NBlibTest.CanGetNumParticlesInMolecule 7: [ OK ] NBlibTest.CanGetNumParticlesInMolecule (0 ms) 7: [ RUN ] NBlibTest.CanConstructExclusionListFromNames 7: [ OK ] NBlibTest.CanConstructExclusionListFromNames (0 ms) 7: [ RUN ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed 7: [ OK ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed (0 ms) 7: [ RUN ] NBlibTest.AtWorks 7: [ OK ] NBlibTest.AtWorks (0 ms) 7: [ RUN ] NBlibTest.AtThrows 7: [ OK ] NBlibTest.AtThrows (1 ms) 7: [ RUN ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass 7: [ OK ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass (0 ms) 7: [ RUN ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass 7: [ OK ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass (0 ms) 7: [ RUN ] NBlibTest.MoleculeNoThrowsSameParticleTypeName 7: [ OK ] NBlibTest.MoleculeNoThrowsSameParticleTypeName (0 ms) 7: [ RUN ] NBlibTest.CanAddInteractions 7: [ OK ] NBlibTest.CanAddInteractions (0 ms) 7: [ RUN ] NBlibTest.CanAddUreyBradley 7: [ OK ] NBlibTest.CanAddUreyBradley (0 ms) 7: [ RUN ] NBlibTest.TopologyHasNumParticles 7: [ OK ] NBlibTest.TopologyHasNumParticles (0 ms) 7: [ RUN ] NBlibTest.TopologyHasCharges 7: [ OK ] NBlibTest.TopologyHasCharges (0 ms) 7: [ RUN ] NBlibTest.TopologyHasMasses 7: [ OK ] NBlibTest.TopologyHasMasses (0 ms) 7: [ RUN ] NBlibTest.TopologyHasParticleTypes 7: [ OK ] NBlibTest.TopologyHasParticleTypes (0 ms) 7: [ RUN ] NBlibTest.TopologyHasParticleTypeIds 7: [ OK ] NBlibTest.TopologyHasParticleTypeIds (0 ms) 7: [ RUN ] NBlibTest.TopologyThrowsIdenticalParticleType 7: [ OK ] NBlibTest.TopologyThrowsIdenticalParticleType (0 ms) 7: [ RUN ] NBlibTest.TopologyHasExclusions 7: [ OK ] NBlibTest.TopologyHasExclusions (0 ms) 7: [ RUN ] NBlibTest.TopologyHasSequencing 7: [ OK ] NBlibTest.TopologyHasSequencing (0 ms) 7: [ RUN ] NBlibTest.TopologyCanAggregateBonds 7: [ OK ] NBlibTest.TopologyCanAggregateBonds (0 ms) 7: [ RUN ] NBlibTest.TopologyCanSequencePairIDs 7: [ OK ] NBlibTest.TopologyCanSequencePairIDs (0 ms) 7: [ RUN ] NBlibTest.TopologySequenceIdThrows 7: No particle O-Atom in residue SOL in molecule SOL found 7: [ OK ] NBlibTest.TopologySequenceIdThrows (0 ms) 7: [ RUN ] NBlibTest.TopologyCanEliminateDuplicateBonds 7: [ OK ] NBlibTest.TopologyCanEliminateDuplicateBonds (0 ms) 7: [ RUN ] NBlibTest.TopologyListedInteractions 7: [ OK ] NBlibTest.TopologyListedInteractions (0 ms) 7: [ RUN ] NBlibTest.TopologyListedInteractionsMultipleTypes 7: [ OK ] NBlibTest.TopologyListedInteractionsMultipleTypes (0 ms) 7: [ RUN ] NBlibTest.TopologyInvalidParticleInInteractionThrows 7: No particle Iron in residue SOL in molecule SOL found 7: [ OK ] NBlibTest.TopologyInvalidParticleInInteractionThrows (0 ms) 7: [ RUN ] NBlibTest.toGmxExclusionBlockWorks 7: [ OK ] NBlibTest.toGmxExclusionBlockWorks (0 ms) 7: [----------] 41 tests from NBlibTest (2 ms total) 7: 7: [----------] 15 tests from NbnxmSetupTest 7: [ RUN ] NbnxmSetupTest.findNumEnergyGroups 7: [ OK ] NbnxmSetupTest.findNumEnergyGroups (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumNo 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumNo (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM (0 ms) 7: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsAuto 7: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsAuto (0 ms) 7: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsCount 7: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsCount (0 ms) 7: [ RUN ] NbnxmSetupTest.canCreateKernelSetupPlain 7: [ OK ] NbnxmSetupTest.canCreateKernelSetupPlain (0 ms) 7: [ RUN ] NbnxmSetupTest.canCreateParticleInfoAllVdv 7: [ OK ] NbnxmSetupTest.canCreateParticleInfoAllVdv (0 ms) 7: [ RUN ] NbnxmSetupTest.ewaldCoeffWorks 7: [ OK ] NbnxmSetupTest.ewaldCoeffWorks (0 ms) 7: [ RUN ] NbnxmSetupTest.updateForcerecWorks 7: [ OK ] NbnxmSetupTest.updateForcerecWorks (0 ms) 7: [ RUN ] NbnxmSetupTest.canCheckKernelSetup 7: [ OK ] NbnxmSetupTest.canCheckKernelSetup (0 ms) 7: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM 7: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM (0 ms) 7: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM 7: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM (0 ms) 7: [ RUN ] NbnxmSetupTest.CanCreateNbnxmCPU 7: [ OK ] NbnxmSetupTest.CanCreateNbnxmCPU (0 ms) 7: [----------] 15 tests from NbnxmSetupTest (0 ms total) 7: 7: [----------] 1 test from VirialsTest 7: [ RUN ] VirialsTest.computeVirialTensorWorks 7: [ OK ] VirialsTest.computeVirialTensorWorks (0 ms) 7: [----------] 1 test from VirialsTest (0 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 57 tests from 3 test suites ran. (2 ms total) 7: [ PASSED ] 57 tests. 7/87 Test #7: NbLibSetupTests ........................... Passed 0.08 sec test 8 Start 8: NbLibTprTests 8: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/nblib-tpr-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/NbLibTprTests.xml" 8: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests 8: Test timeout computed to be: 30 8: [==========] Running 4 tests from 1 test suite. 8: [----------] Global test environment set-up. 8: [----------] 4 tests from TprReaderTest 8: [ RUN ] TprReaderTest.SimDBTprIsCreated 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.SimDBTprIsCreated (43 ms) 8: [ RUN ] TprReaderTest.Spc2Reads 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Generating 1-4 interactions: fudge = 0.5 8: Number of degrees of freedom in T-Coupling group System is 9.00 8: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: NVE simulation: will use the initial temperature of 2573.591 K for 8: determining the Verlet buffer size 8: 8: 8: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: You are using a plain Coulomb cut-off, which might produce artifacts. 8: You might want to consider using PME electrostatics. 8: 8: 8: 8: There were 4 NOTEs 8: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 8: Generated 3 of the 3 non-bonded parameter combinations 8: 8: Generated 3 of the 3 1-4 parameter combinations 8: 8: Excluding 2 bonded neighbours molecule type 'SOL' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.Spc2Reads (29 ms) 8: [ RUN ] TprReaderTest.ArgonImportedDataIsCorrect 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.ArgonImportedDataIsCorrect (61 ms) 8: [ RUN ] TprReaderTest.FCfromTprDataWorks 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.FCfromTprDataWorks (14 ms) 8: [----------] 4 tests from TprReaderTest (148 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 4 tests from 1 test suite ran. (221 ms total) 8: [ PASSED ] 4 tests. 8/87 Test #8: NbLibTprTests ............................. Passed 0.26 sec test 9 Start 9: NbLibIntegrationTests 9: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/nblib-integration-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/NbLibIntegrationTests.xml" 9: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests 9: Test timeout computed to be: 600 9: [==========] Running 20 tests from 1 test suite. 9: [----------] Global test environment set-up. 9: [----------] 20 tests from NBlibTest 9: [ RUN ] NBlibTest.GmxForceCalculatorCanCompute 9: [ OK ] NBlibTest.GmxForceCalculatorCanCompute (0 ms) 9: [ RUN ] NBlibTest.ArgonVirialsAreCorrect 9: [ OK ] NBlibTest.ArgonVirialsAreCorrect (2 ms) 9: [ RUN ] NBlibTest.ArgonEnergiesAreCorrect 9: [ OK ] NBlibTest.ArgonEnergiesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.SpcMethanolEnergiesAreCorrect 9: [ OK ] NBlibTest.SpcMethanolEnergiesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.SpcMethanolForcesAreCorrect 9: [ OK ] NBlibTest.SpcMethanolForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ExpectedNumberOfForces 9: [ OK ] NBlibTest.ExpectedNumberOfForces (0 ms) 9: [ RUN ] NBlibTest.CanIntegrateSystem 9: [ OK ] NBlibTest.CanIntegrateSystem (0 ms) 9: [ RUN ] NBlibTest.UpdateChangesForces 9: [ OK ] NBlibTest.UpdateChangesForces (0 ms) 9: [ RUN ] NBlibTest.ArgonOplsaForcesAreCorrect 9: [ OK ] NBlibTest.ArgonOplsaForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ArgonGromos43A1ForcesAreCorrect 9: [ OK ] NBlibTest.ArgonGromos43A1ForcesAreCorrect (4 ms) 9: [ RUN ] NBlibTest.CanConstructSimulationState 9: [ OK ] NBlibTest.CanConstructSimulationState (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateNAN 9: [ OK ] NBlibTest.SimulationStateThrowsCoordinateNAN (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateINF 9: [ OK ] NBlibTest.SimulationStateThrowsCoordinateINF (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsVelocityNAN 9: [ OK ] NBlibTest.SimulationStateThrowsVelocityNAN (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsVelocityINF 9: [ OK ] NBlibTest.SimulationStateThrowsVelocityINF (0 ms) 9: [ RUN ] NBlibTest.SimulationStateCanMove 9: [ OK ] NBlibTest.SimulationStateCanMove (0 ms) 9: [ RUN ] NBlibTest.SimulationStateCanAssign 9: [ OK ] NBlibTest.SimulationStateCanAssign (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasBox 9: [ OK ] NBlibTest.SimulationStateHasBox (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasCorrectCoordinates 9: [ OK ] NBlibTest.SimulationStateHasCorrectCoordinates (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasCorrectVelocities 9: [ OK ] NBlibTest.SimulationStateHasCorrectVelocities (0 ms) 9: [----------] 20 tests from NBlibTest (12 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 20 tests from 1 test suite ran. (12 ms total) 9: [ PASSED ] 20 tests. 9/87 Test #9: NbLibIntegrationTests ..................... Passed 0.05 sec test 10 Start 10: NbLibIntegratorTests 10: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/nblib-integrator-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/NbLibIntegratorTests.xml" 10: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests 10: Test timeout computed to be: 600 10: [==========] Running 1 test from 1 test suite. 10: [----------] Global test environment set-up. 10: [----------] 1 test from NBlibTest 10: [ RUN ] NBlibTest.IntegratorWorks 10: [ OK ] NBlibTest.IntegratorWorks (0 ms) 10: [----------] 1 test from NBlibTest (0 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 1 test from 1 test suite ran. (0 ms total) 10: [ PASSED ] 1 test. 10/87 Test #10: NbLibIntegratorTests ...................... Passed 0.03 sec test 11 Start 11: TestUtilsUnitTests 11: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/testutils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/TestUtilsUnitTests.xml" 11: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/testutils/tests 11: Test timeout computed to be: 30 11: [==========] Running 59 tests from 5 test suites. 11: [----------] Global test environment set-up. 11: [----------] 10 tests from InteractiveTestHelperTest 11: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 11: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (0 ms) 11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (0 ms) 11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 11: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 11: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 11: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 11: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 11: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 11: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (0 ms) 11: [----------] 10 tests from InteractiveTestHelperTest (2 ms total) 11: 11: [----------] 34 tests from ReferenceDataTest 11: [ RUN ] ReferenceDataTest.HandlesSimpleData 11: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 11: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 11: [ OK ] ReferenceDataTest.HandlesPresenceChecks (4 ms) 11: [ RUN ] ReferenceDataTest.HandlesStringBlockData 11: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesVectorData 11: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSequenceData 11: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 11: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesIncorrectData 11: [ OK ] ReferenceDataTest.HandlesIncorrectData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 11: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMissingData 11: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUncheckedData 11: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 11: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 11: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesAnys 11: [ OK ] ReferenceDataTest.HandlesAnys (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 11: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 11: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 11: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue 11: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType 11: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 11: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 11: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 11: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 11: [ OK ] ReferenceDataTest.HandlesEmptyStrings (10 ms) 11: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 11: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 11: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 11: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 11: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 11: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesReadingValues 11: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (0 ms) 11: [----------] 34 tests from ReferenceDataTest (18 ms total) 11: 11: [----------] 7 tests from FloatingPointDifferenceTest 11: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 11: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 11: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 11: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 11: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 11: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 11: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 11: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 11: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 11: 11: [----------] 4 tests from FloatingPointToleranceTest 11: [ RUN ] FloatingPointToleranceTest.UlpTolerance 11: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 11: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 11: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 11: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 11: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 11: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 11: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 11: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 11: 11: [----------] 4 tests from XvgTests 11: [ RUN ] XvgTests.CreateFile 11: [ OK ] XvgTests.CreateFile (0 ms) 11: [ RUN ] XvgTests.CheckMissing 11: [ OK ] XvgTests.CheckMissing (0 ms) 11: [ RUN ] XvgTests.CheckExtra 11: [ OK ] XvgTests.CheckExtra (0 ms) 11: [ RUN ] XvgTests.ReadIncorrect 11: [ OK ] XvgTests.ReadIncorrect (0 ms) 11: [----------] 4 tests from XvgTests (0 ms total) 11: 11: [----------] Global test environment tear-down 11: [==========] 59 tests from 5 test suites ran. (21 ms total) 11: [ PASSED ] 59 tests. 11/87 Test #11: TestUtilsUnitTests ........................ Passed 0.07 sec test 12 Start 12: TestUtilsMpiUnitTests 12: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/TestUtilsMpiUnitTests.xml" 12: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/testutils/tests 12: Test timeout computed to be: 30 12: [==========] Running 1 test from 1 test suite. 12: [----------] Global test environment set-up. 12: [----------] 1 test from MpiSelfTest 12: [ RUN ] MpiSelfTest.Runs 12: [ OK ] MpiSelfTest.Runs (35 ms) 12: [----------] 1 test from MpiSelfTest (35 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 1 test from 1 test suite ran. (35 ms total) 12: [ PASSED ] 1 test. 12/87 Test #12: TestUtilsMpiUnitTests ..................... Passed 0.08 sec test 13 Start 13: UtilityUnitTests 13: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/utility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/UtilityUnitTests.xml" 13: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests 13: Test timeout computed to be: 30 13: [==========] Running 400 tests from 62 test suites. 13: [----------] Global test environment set-up. 13: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/0.Move 13: [ OK ] AllocatorTest/0.Move (0 ms) 13: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 13: [----------] 5 tests from AllocatorTest/0 (0 ms total) 13: 13: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/1.Move 13: [ OK ] AllocatorTest/1.Move (0 ms) 13: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 13: [----------] 5 tests from AllocatorTest/1 (0 ms total) 13: 13: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/2.Move 13: [ OK ] AllocatorTest/2.Move (0 ms) 13: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 13: [----------] 5 tests from AllocatorTest/2 (0 ms total) 13: 13: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/3.Move 13: [ OK ] AllocatorTest/3.Move (0 ms) 13: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 13: [----------] 5 tests from AllocatorTest/3 (0 ms total) 13: 13: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 13: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/4.Move 13: [ OK ] AllocatorTest/4.Move (0 ms) 13: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 13: [----------] 5 tests from AllocatorTest/4 (0 ms total) 13: 13: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> 13: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/5.Move 13: [ OK ] AllocatorTest/5.Move (0 ms) 13: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 13: [----------] 5 tests from AllocatorTest/5 (0 ms total) 13: 13: [----------] 1 test from AllocatorUntypedTest 13: [ RUN ] AllocatorUntypedTest.Comparison 13: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 13: [----------] 1 test from AllocatorUntypedTest (0 ms total) 13: 13: [----------] 4 tests from EmptyArrayRefTest 13: [ RUN ] EmptyArrayRefTest.IsEmpty 13: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 13: [ RUN ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty 13: [ OK ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty (0 ms) 13: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr 13: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr (0 ms) 13: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull 13: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull (0 ms) 13: [----------] 4 tests from EmptyArrayRefTest (0 ms total) 13: 13: [----------] 1 test from EmptyConstArrayRefTest 13: [ RUN ] EmptyConstArrayRefTest.IsEmpty 13: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 13: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/8 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/14 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 13: 13: [----------] 8 tests from BoolType 13: [ RUN ] BoolType.ImplicitConversion 13: [ OK ] BoolType.ImplicitConversion (0 ms) 13: [ RUN ] BoolType.FalseByDefault 13: [ OK ] BoolType.FalseByDefault (0 ms) 13: [ RUN ] BoolType.Assignment 13: [ OK ] BoolType.Assignment (0 ms) 13: [ RUN ] BoolType.Copy 13: [ OK ] BoolType.Copy (0 ms) 13: [ RUN ] BoolType.ArrayRefCanBeCreated 13: [ OK ] BoolType.ArrayRefCanBeCreated (0 ms) 13: [ RUN ] BoolType.CanBeCastToBool 13: [ OK ] BoolType.CanBeCastToBool (0 ms) 13: [ RUN ] BoolType.HasSizeOfBool 13: [ OK ] BoolType.HasSizeOfBool (0 ms) 13: [ RUN ] BoolType.HasAlignmentOfBool 13: [ OK ] BoolType.HasAlignmentOfBool (0 ms) 13: [----------] 8 tests from BoolType (0 ms total) 13: 13: [----------] 4 tests from ArrayRefFromBoolTypeVector 13: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructEmpty 13: [ OK ] ArrayRefFromBoolTypeVector.CanConstructEmpty (0 ms) 13: [ RUN ] ArrayRefFromBoolTypeVector.Works 13: [ OK ] ArrayRefFromBoolTypeVector.Works (0 ms) 13: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty 13: [ OK ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty (0 ms) 13: [ RUN ] ArrayRefFromBoolTypeVector.ConstWorks 13: [ OK ] ArrayRefFromBoolTypeVector.ConstWorks (0 ms) 13: [----------] 4 tests from ArrayRefFromBoolTypeVector (0 ms total) 13: 13: [----------] 7 tests from CStringUtilityTest 13: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison 13: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms) 13: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength 13: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms) 13: [ RUN ] CStringUtilityTest.strip_comment 13: [ OK ] CStringUtilityTest.strip_comment (0 ms) 13: [ RUN ] CStringUtilityTest.upstring 13: [ OK ] CStringUtilityTest.upstring (0 ms) 13: [ RUN ] CStringUtilityTest.ltrim 13: [ OK ] CStringUtilityTest.ltrim (0 ms) 13: [ RUN ] CStringUtilityTest.rtrim 13: [ OK ] CStringUtilityTest.rtrim (0 ms) 13: [ RUN ] CStringUtilityTest.trim 13: [ OK ] CStringUtilityTest.trim (0 ms) 13: [----------] 7 tests from CStringUtilityTest (0 ms total) 13: 13: [----------] 2 tests from DefaultInitializationAllocator 13: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization 13: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms) 13: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization 13: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms) 13: [----------] 2 tests from DefaultInitializationAllocator (0 ms total) 13: 13: [----------] 4 tests from EnumerationHelpersTest 13: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks 13: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms) 13: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks 13: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms) 13: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe 13: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms) 13: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks 13: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms) 13: [----------] 4 tests from EnumerationHelpersTest (0 ms total) 13: 13: [----------] 9 tests from FixedCapacityVectorTest 13: [ RUN ] FixedCapacityVectorTest.IsEmpty 13: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms) 13: [ RUN ] FixedCapacityVectorTest.PushWorks 13: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.PopWorks 13: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ClearWorks 13: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks 13: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.AtThrows 13: [ OK ] FixedCapacityVectorTest.AtThrows (4 ms) 13: [ RUN ] FixedCapacityVectorTest.IteratorWorks 13: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks 13: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks 13: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms) 13: [----------] 9 tests from FixedCapacityVectorTest (4 ms total) 13: 13: [----------] 5 tests from InMemorySerializerTest 13: [ RUN ] InMemorySerializerTest.Roundtrip 13: [ OK ] InMemorySerializerTest.Roundtrip (0 ms) 13: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap 13: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms) 13: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap 13: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms) 13: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap 13: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms) 13: [ RUN ] InMemorySerializerTest.SizeIsCorrect 13: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms) 13: [----------] 5 tests from InMemorySerializerTest (0 ms total) 13: 13: [----------] 4 tests from KeyValueTreeSerializerTest 13: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 13: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms) 13: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 13: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms) 13: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 13: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms) 13: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 13: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms) 13: [----------] 4 tests from KeyValueTreeSerializerTest (2 ms total) 13: 13: [----------] 7 tests from TreeValueTransformTest 13: [ RUN ] TreeValueTransformTest.SimpleTransforms 13: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms) 13: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 13: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms) 13: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 13: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms) 13: [ RUN ] TreeValueTransformTest.ObjectFromString 13: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms) 13: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 13: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms) 13: [ RUN ] TreeValueTransformTest.ScopedTransformRules 13: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) 13: [ RUN ] TreeValueTransformTest.CanAssignUserMultiValue 13: [ OK ] TreeValueTransformTest.CanAssignUserMultiValue (0 ms) 13: [----------] 7 tests from TreeValueTransformTest (4 ms total) 13: 13: [----------] 1 test from TreeValueTransformErrorTest 13: [ RUN ] TreeValueTransformErrorTest.ConversionError 13: [ OK ] TreeValueTransformErrorTest.ConversionError (1 ms) 13: [----------] 1 test from TreeValueTransformErrorTest (1 ms total) 13: 13: [----------] 9 tests from ListOfLists 13: [ RUN ] ListOfLists.EmptyListOfListsWorks 13: [ OK ] ListOfLists.EmptyListOfListsWorks (0 ms) 13: [ RUN ] ListOfLists.AppendWorks 13: [ OK ] ListOfLists.AppendWorks (0 ms) 13: [ RUN ] ListOfLists.EmptyListWorks 13: [ OK ] ListOfLists.EmptyListWorks (0 ms) 13: [ RUN ] ListOfLists.AppendAccessWorks 13: [ OK ] ListOfLists.AppendAccessWorks (0 ms) 13: [ RUN ] ListOfLists.ClearWorks 13: [ OK ] ListOfLists.ClearWorks (0 ms) 13: [ RUN ] ListOfLists.OutOfRangeAccessThrows 13: [ OK ] ListOfLists.OutOfRangeAccessThrows (0 ms) 13: [ RUN ] ListOfLists.FrontAndBackWork 13: [ OK ] ListOfLists.FrontAndBackWork (0 ms) 13: [ RUN ] ListOfLists.ExtractsAndRestores 13: [ OK ] ListOfLists.ExtractsAndRestores (0 ms) 13: [ RUN ] ListOfLists.AppendsListOfListsWithOffset 13: [ OK ] ListOfLists.AppendsListOfListsWithOffset (0 ms) 13: [----------] 9 tests from ListOfLists (0 ms total) 13: 13: [----------] 7 tests from LoggerTest 13: [ RUN ] LoggerTest.EmptyLoggerWorks 13: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 13: [ RUN ] LoggerTest.LogsToStream 13: [ OK ] LoggerTest.LogsToStream (0 ms) 13: [ RUN ] LoggerTest.LogsToFile 13: [ OK ] LoggerTest.LogsToFile (1 ms) 13: [ RUN ] LoggerTest.LevelFilteringWorks 13: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) 13: [ RUN ] LoggerTest.LogsToMultipleStreams 13: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) 13: [ RUN ] LoggerTest.LogsToMultipleFiles 13: [ OK ] LoggerTest.LogsToMultipleFiles (0 ms) 13: [ RUN ] LoggerTest.LogsToStreamAndFile 13: [ OK ] LoggerTest.LogsToStreamAndFile (0 ms) 13: [----------] 7 tests from LoggerTest (5 ms total) 13: 13: [----------] 7 tests from MessageStringCollectorTest 13: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext 13: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext 13: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddStringMessages 13: [ OK ] MessageStringCollectorTest.CanAddStringMessages (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddCharMessagesConditionally 13: [ OK ] MessageStringCollectorTest.CanAddCharMessagesConditionally (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddStringMessagesConditionally 13: [ OK ] MessageStringCollectorTest.CanAddStringMessagesConditionally (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanMoveConstruct 13: [ OK ] MessageStringCollectorTest.CanMoveConstruct (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanMoveAssign 13: [ OK ] MessageStringCollectorTest.CanMoveAssign (0 ms) 13: [----------] 7 tests from MessageStringCollectorTest (0 ms total) 13: 13: [----------] 1 test from PathTest 13: [ RUN ] PathTest.StripSourcePrefixWorks 13: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 13: [----------] 1 test from PathTest (0 ms total) 13: 13: [----------] 2 tests from PhysicalNodeCommunicatorTest 13: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 13: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 13: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 13: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 13: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 13: 13: [----------] 5 tests from Range 13: [ RUN ] Range.EmptyRangeWorks 13: [ OK ] Range.EmptyRangeWorks (0 ms) 13: [ RUN ] Range.NonEmptyRangeWorks 13: [ OK ] Range.NonEmptyRangeWorks (0 ms) 13: [ RUN ] Range.BeginEnd 13: [ OK ] Range.BeginEnd (0 ms) 13: [ RUN ] Range.IsInRangeWorks 13: [ OK ] Range.IsInRangeWorks (0 ms) 13: [ RUN ] Range.IteratorWorks 13: [ OK ] Range.IteratorWorks (0 ms) 13: [----------] 5 tests from Range (0 ms total) 13: 13: [----------] 7 tests from StringConvert 13: [ RUN ] StringConvert.NoResultFromEptyString 13: [ OK ] StringConvert.NoResultFromEptyString (0 ms) 13: [ RUN ] StringConvert.ThreeFloatsSuccessfully 13: [ OK ] StringConvert.ThreeFloatsSuccessfully (0 ms) 13: [ RUN ] StringConvert.OneIntSucessfully 13: [ OK ] StringConvert.OneIntSucessfully (0 ms) 13: [ RUN ] StringConvert.FloatAsStringToIntArrayThrows 13: [ OK ] StringConvert.FloatAsStringToIntArrayThrows (0 ms) 13: [ RUN ] StringConvert.ThrowsWhenWrongSize 13: [ OK ] StringConvert.ThrowsWhenWrongSize (0 ms) 13: [ RUN ] StringConvert.StringIdentityTransformWithArrayThrows 13: [ OK ] StringConvert.StringIdentityTransformWithArrayThrows (0 ms) 13: [ RUN ] StringConvert.StringIdentityTransformWithArrayOkay 13: [ OK ] StringConvert.StringIdentityTransformWithArrayOkay (0 ms) 13: [----------] 7 tests from StringConvert (0 ms total) 13: 13: [----------] 7 tests from StringToEnumValueConverterTest 13: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping 13: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping 13: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping 13: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping 13: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping 13: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping 13: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CustomConverterWorks 13: [ OK ] StringToEnumValueConverterTest.CustomConverterWorks (0 ms) 13: [----------] 7 tests from StringToEnumValueConverterTest (0 ms total) 13: 13: [----------] 9 tests from StringUtilityTest 13: [ RUN ] StringUtilityTest.StartsWith 13: [ OK ] StringUtilityTest.StartsWith (0 ms) 13: [ RUN ] StringUtilityTest.EndsWith 13: [ OK ] StringUtilityTest.EndsWith (0 ms) 13: [ RUN ] StringUtilityTest.StripSuffixIfPresent 13: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 13: [ RUN ] StringUtilityTest.StripString 13: [ OK ] StringUtilityTest.StripString (0 ms) 13: [ RUN ] StringUtilityTest.SplitString 13: [ OK ] StringUtilityTest.SplitString (0 ms) 13: [ RUN ] StringUtilityTest.SplitDelimitedString 13: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 13: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 13: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) 13: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive 13: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms) 13: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength 13: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms) 13: [----------] 9 tests from StringUtilityTest (0 ms total) 13: 13: [----------] 2 tests from FormatStringTest 13: [ RUN ] FormatStringTest.HandlesBasicFormatting 13: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 13: [ RUN ] FormatStringTest.HandlesLongStrings 13: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 13: [----------] 2 tests from FormatStringTest (0 ms total) 13: 13: [----------] 1 test from StringFormatterTest 13: [ RUN ] StringFormatterTest.HandlesBasicFormatting 13: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 13: [----------] 1 test from StringFormatterTest (0 ms total) 13: 13: [----------] 1 test from formatAndJoinTest 13: [ RUN ] formatAndJoinTest.Works 13: [ OK ] formatAndJoinTest.Works (0 ms) 13: [----------] 1 test from formatAndJoinTest (0 ms total) 13: 13: [----------] 1 test from JoinStringsTest 13: [ RUN ] JoinStringsTest.Works 13: [ OK ] JoinStringsTest.Works (0 ms) 13: [----------] 1 test from JoinStringsTest (0 ms total) 13: 13: [----------] 6 tests from ReplaceAllTest 13: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 13: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesNoMatches 13: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 13: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 13: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 13: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 13: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 13: [----------] 6 tests from ReplaceAllTest (0 ms total) 13: 13: [----------] 10 tests from TextLineWrapperTest 13: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 13: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 13: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 13: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 13: [ RUN ] TextLineWrapperTest.WrapsCorrectly 13: [ OK ] TextLineWrapperTest.WrapsCorrectly (3 ms) 13: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 13: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesIndent 13: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 13: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 13: [ OK ] TextLineWrapperTest.HandlesHangingIndent (2 ms) 13: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 13: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (4 ms) 13: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 13: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) 13: [----------] 10 tests from TextLineWrapperTest (12 ms total) 13: 13: [----------] 3 tests from TemplateMPTest 13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnum 13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnum (0 ms) 13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionBool 13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionBool (0 ms) 13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnumBool 13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnumBool (0 ms) 13: [----------] 3 tests from TemplateMPTest (0 ms total) 13: 13: [----------] 6 tests from TextWriterTest 13: [ RUN ] TextWriterTest.WritesLines 13: [ OK ] TextWriterTest.WritesLines (3 ms) 13: [ RUN ] TextWriterTest.WritesLinesInParts 13: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) 13: [ RUN ] TextWriterTest.WritesWrappedLines 13: [ OK ] TextWriterTest.WritesWrappedLines (0 ms) 13: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 13: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) 13: [ RUN ] TextWriterTest.TracksNewlines 13: [ OK ] TextWriterTest.TracksNewlines (0 ms) 13: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 13: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) 13: [----------] 6 tests from TextWriterTest (6 ms total) 13: 13: [----------] 1 test from TypeTraitsTest 13: [ RUN ] TypeTraitsTest.IsIntegralConstant 13: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 13: [----------] 1 test from TypeTraitsTest (0 ms total) 13: 13: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 13: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 13: 13: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 13: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 13: 13: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 13: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (3 ms total) 13: 13: [----------] 11 tests from WithInputPaths/PathSearchTest 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 (2 ms) 13: [----------] 11 tests from WithInputPaths/PathSearchTest (8 ms total) 13: 13: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 13: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (0 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 400 tests from 62 test suites ran. (54 ms total) 13: [ PASSED ] 400 tests. 13: 13: YOU HAVE 1 DISABLED TEST 13: 13/87 Test #13: UtilityUnitTests .......................... Passed 0.13 sec test 14 Start 14: UtilityMpiUnitTests 14: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/utility-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/UtilityMpiUnitTests.xml" 14: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests 14: Test timeout computed to be: 30 14: [==========] Running 2 tests from 1 test suite. 14: [----------] Global test environment set-up. 14: [----------] 2 tests from PhysicalNodeCommunicatorTest 14: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 14: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (6 ms) 14: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 14: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (3 ms) 14: [----------] 2 tests from PhysicalNodeCommunicatorTest (10 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 2 tests from 1 test suite ran. (10 ms total) 14: [ PASSED ] 2 tests. 14/87 Test #14: UtilityMpiUnitTests ....................... Passed 0.04 sec test 15 Start 15: GmxlibTests 15: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/nonbonded-fep-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/GmxlibTests.xml" 15: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxlib/nonbonded/tests 15: Test timeout computed to be: 30 15: [==========] Running 78 tests from 2 test suites. 15: [----------] Global test environment set-up. 15: [----------] 72 tests from NBInteraction/NonbondedFepTest 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/0 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/0 (4 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/1 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/1 (5 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/2 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/2 (2 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/3 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/3 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/4 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/4 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/5 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/5 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/6 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/6 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/7 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/7 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/8 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/8 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/9 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/9 (3 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/10 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/10 (3 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/11 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/11 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/12 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/12 (3 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/13 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/13 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/14 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/14 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/15 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/15 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/16 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/16 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/17 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/17 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/18 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/18 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/19 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/19 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/20 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/20 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/21 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/21 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/22 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/22 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/23 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/23 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/24 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/24 (2 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/25 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/25 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/26 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/26 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/27 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/27 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/28 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/28 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/29 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/29 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/30 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/30 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/31 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/31 (2 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/32 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/32 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/33 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/33 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/34 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/34 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/35 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/35 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/36 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/36 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/37 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/37 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/38 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/38 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/39 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/39 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/40 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/40 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/41 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/41 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/42 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/42 (2 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/43 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/43 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/44 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/44 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/45 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/45 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/46 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/46 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/47 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/47 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/48 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/48 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/49 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/49 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/50 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/50 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/51 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/51 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/52 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/52 (2 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/53 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/53 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/54 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/54 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/55 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/55 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/56 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/56 (2 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/57 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/57 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/58 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/58 (2 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/59 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/59 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/60 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/60 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/61 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/61 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/62 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/62 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/63 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/63 (2 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/64 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/64 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/65 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/65 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/66 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/66 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/67 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/67 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/68 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/68 (3 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/69 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/69 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/70 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/70 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/71 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/71 (0 ms) 15: [----------] 72 tests from NBInteraction/NonbondedFepTest (114 ms total) 15: 15: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 (4 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 (1 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 (2 ms) 15: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest (12 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 78 tests from 2 test suites ran. (127 ms total) 15: [ PASSED ] 78 tests. 15/87 Test #15: GmxlibTests ............................... Passed 0.19 sec test 16 Start 16: MdlibUnitTest 16: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdlib-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdlibUnitTest.xml" 16: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests 16: Test timeout computed to be: 30 16: [==========] Running 999 tests from 25 test suites. 16: [----------] Global test environment set-up. 16: [----------] 2 tests from EffectiveAtomDensity 16: [ RUN ] EffectiveAtomDensity.VolumeIndependence 16: [ OK ] EffectiveAtomDensity.VolumeIndependence (0 ms) 16: [ RUN ] EffectiveAtomDensity.WeightingWorks 16: [ OK ] EffectiveAtomDensity.WeightingWorks (0 ms) 16: [----------] 2 tests from EffectiveAtomDensity (0 ms total) 16: 16: [----------] 2 tests from AtomNonbondedAndKineticProperties 16: [ RUN ] AtomNonbondedAndKineticProperties.IsAccurate 16: [ OK ] AtomNonbondedAndKineticProperties.IsAccurate (0 ms) 16: [ RUN ] AtomNonbondedAndKineticProperties.ConstraintsWork 16: [ OK ] AtomNonbondedAndKineticProperties.ConstraintsWork (0 ms) 16: [----------] 2 tests from AtomNonbondedAndKineticProperties (0 ms total) 16: 16: [----------] 1 test from VerletBufferConstraintTest 16: [ RUN ] VerletBufferConstraintTest.EqualMasses 16: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) 16: [----------] 1 test from VerletBufferConstraintTest (0 ms total) 16: 16: [----------] 6 tests from CalcvirTest 16: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBox 16: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBox (1 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew 16: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew (1 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX (2 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ (1 ms) 16: [----------] 6 tests from CalcvirTest (8 ms total) 16: 16: [----------] 2 tests from PrEbinTest 16: [ RUN ] PrEbinTest.HandlesAverages 16: [ OK ] PrEbinTest.HandlesAverages (7 ms) 16: [ RUN ] PrEbinTest.HandlesEmptyAverages 16: [ OK ] PrEbinTest.HandlesEmptyAverages (0 ms) 16: [----------] 2 tests from PrEbinTest (8 ms total) 16: 16: [----------] 3 tests from EnergyDriftTracker 16: [ RUN ] EnergyDriftTracker.emptyWorks 16: [ OK ] EnergyDriftTracker.emptyWorks (0 ms) 16: [ RUN ] EnergyDriftTracker.onePointWorks 16: [ OK ] EnergyDriftTracker.onePointWorks (0 ms) 16: [ RUN ] EnergyDriftTracker.manyPointsWorks 16: [ OK ] EnergyDriftTracker.manyPointsWorks (0 ms) 16: [----------] 3 tests from EnergyDriftTracker (0 ms total) 16: 16: [----------] 4 tests from ShakeTest 16: [ RUN ] ShakeTest.ConstrainsOneBond 16: [ OK ] ShakeTest.ConstrainsOneBond (0 ms) 16: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 16: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 16: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 16: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 16: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 16: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 16: [----------] 4 tests from ShakeTest (0 ms total) 16: 16: [----------] 1 test from NullSignalTest 16: [ RUN ] NullSignalTest.NullSignallerWorks 16: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) 16: [----------] 1 test from NullSignalTest (0 ms total) 16: 16: [----------] 7 tests from SignalTest 16: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 16: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 16: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 16: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 16: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 16: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 16: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 16: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 16: [----------] 7 tests from SignalTest (0 ms total) 16: 16: [----------] 13 tests from UpdateGroupsTest 16: [ RUN ] UpdateGroupsTest.WithEthaneUA 16: [ OK ] UpdateGroupsTest.WithEthaneUA (0 ms) 16: [ RUN ] UpdateGroupsTest.WithMethane 16: [ OK ] UpdateGroupsTest.WithMethane (0 ms) 16: [ RUN ] UpdateGroupsTest.WithEthane 16: [ OK ] UpdateGroupsTest.WithEthane (0 ms) 16: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane 16: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane (0 ms) 16: [ RUN ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups 16: [ OK ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups (0 ms) 16: [ RUN ] UpdateGroupsTest.WithWaterThreeSite 16: [ OK ] UpdateGroupsTest.WithWaterThreeSite (0 ms) 16: [ RUN ] UpdateGroupsTest.WithWaterFourSite 16: [ OK ] UpdateGroupsTest.WithWaterFourSite (0 ms) 16: [ RUN ] UpdateGroupsTest.WithFourAtomsWithSettle 16: [ OK ] UpdateGroupsTest.WithFourAtomsWithSettle (0 ms) 16: [ RUN ] UpdateGroupsTest.WithWaterFlexAngle 16: [ OK ] UpdateGroupsTest.WithWaterFlexAngle (0 ms) 16: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle 16: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle (0 ms) 16: [ RUN ] UpdateGroupsTest.WithTwoMoltypes 16: [ OK ] UpdateGroupsTest.WithTwoMoltypes (0 ms) 16: [ RUN ] UpdateGroupsTest.LogsWhenSizesAreInvalid 16: [ OK ] UpdateGroupsTest.LogsWhenSizesAreInvalid (0 ms) 16: [ RUN ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful 16: [ OK ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful (0 ms) 16: [----------] 13 tests from UpdateGroupsTest (0 ms total) 16: 16: [----------] 1 test from UpdateGroupsCog 16: [ RUN ] UpdateGroupsCog.ComputesCogs 16: [ OK ] UpdateGroupsCog.ComputesCogs (7 ms) 16: [----------] 1 test from UpdateGroupsCog (7 ms total) 16: 16: [----------] 2 tests from WholeMoleculeTransform 16: [ RUN ] WholeMoleculeTransform.MakesMoleculesWhole 16: [ OK ] WholeMoleculeTransform.MakesMoleculesWhole (0 ms) 16: [ RUN ] WholeMoleculeTransform.HandlesReordering 16: [ OK ] WholeMoleculeTransform.HandlesReordering (0 ms) 16: [----------] 2 tests from WholeMoleculeTransform (0 ms total) 16: 16: [----------] 14 tests from WithParameters/ConstraintsTest 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 (1 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 (1 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 (4 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 (1 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 (9 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 (10 ms) 16: [----------] 14 tests from WithParameters/ConstraintsTest (47 ms total) 16: 16: [----------] 11 tests from WithParameters/EnergyOutputTest 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0 16: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (5 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1 16: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (6 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2 16: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (7 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3 16: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (1 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4 16: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as double precision energy file 16: Reading energy frame 0 time 10.100 Reading energy frame 1 time 27.500 Reading energy frame 2 time 44.900 Reading energy frame 3 time 62.300 Reading energy frame 4 time 79.700 Reading energy frame 5 time 97.100 Reading energy frame 6 time 114.500 Reading energy frame 7 time 131.900 Reading energy frame 8 time 149.300 Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (11 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5 16: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (8 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6 16: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (11 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7 16: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (3 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8 16: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (6 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9 16: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (2 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10 16: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (3 ms) 16: [----------] 11 tests from WithParameters/EnergyOutputTest (71 ms total) 16: 16: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (5 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms) 16: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (12 ms total) 16: 16: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms) 16: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (0 ms total) 16: 16: [----------] 23 tests from WithParameters/FreeEnergyParameterTest 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 (0 ms) 16: [----------] 23 tests from WithParameters/FreeEnergyParameterTest (0 ms total) 16: 16: [----------] 16 tests from WithParameters/LeapFrogTest 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (1 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (3 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (6 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (1 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (2 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (2 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (3 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (3 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (3 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (2 ms) 16: [----------] 16 tests from WithParameters/LeapFrogTest (58 ms total) 16: 16: [----------] 140 tests from Cubic/ParrRahmTest 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (9 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (10 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (6 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (5 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (2 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (2 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (4 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from Cubic/ParrRahmTest (165 ms total) 16: 16: [----------] 140 tests from Rectilinear/ParrRahmTest 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (4 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (2 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (4 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (2 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (2 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (6 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (2 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (8 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 (8 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 (7 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 (2 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (2 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (4 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (2 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (2 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (2 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (2 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (5 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (2 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (4 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (4 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (2 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (2 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 (2 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 (2 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 (6 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 (2 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from Rectilinear/ParrRahmTest (243 ms total) 16: 16: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (6 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (4 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (6 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 (6 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (4 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (4 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (4 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest (232 ms total) 16: 16: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (8 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (3 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (10 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (3 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (6 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 (4 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 (10 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (7 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (5 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (5 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (5 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (5 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (5 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (4 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (4 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (3 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (6 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 (6 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 (5 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest (263 ms total) 16: 16: [----------] 140 tests from TruncOct/ParrRahmTest 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (3 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (4 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (2 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (2 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (2 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (2 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (2 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (2 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (2 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (2 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (4 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (10 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 (6 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 (8 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 (3 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (3 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 (3 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (2 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (2 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (4 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (2 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (2 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (2 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (2 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (2 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (6 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (2 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (2 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (2 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 (2 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 (4 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (10 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 (3 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from TruncOct/ParrRahmTest (219 ms total) 16: 16: [----------] 140 tests from Other/ParrRahmTest 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (6 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (2 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (5 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (2 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (2 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (2 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (2 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (2 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (2 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (2 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (8 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 (3 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (3 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 (7 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (7 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (10 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (7 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (2 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (2 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (2 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (2 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (2 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (2 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 (2 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (1 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 (3 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (10 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 (2 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (8 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from Other/ParrRahmTest (227 ms total) 16: 16: [----------] 13 tests from WithParameters/SettleTest 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (4 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (10 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (5 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (1 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (2 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (2 ms) 16: [----------] 13 tests from WithParameters/SettleTest (39 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 999 tests from 25 test suites ran. (1608 ms total) 16: [ PASSED ] 999 tests. 16/87 Test #16: MdlibUnitTest ............................. Passed 1.84 sec test 17 Start 17: AwhTest 17: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/awh-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/AwhTest.xml" 17: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/awh/tests 17: Test timeout computed to be: 30 17: [==========] Running 27 tests from 10 test suites. 17: [----------] Global test environment set-up. 17: [----------] 3 tests from SerializationTest 17: [ RUN ] SerializationTest.CanSerializeDimParams 17: [ OK ] SerializationTest.CanSerializeDimParams (0 ms) 17: [ RUN ] SerializationTest.CanSerializeBiasParams 17: [ OK ] SerializationTest.CanSerializeBiasParams (0 ms) 17: [ RUN ] SerializationTest.CanSerializeAwhParams 17: [ OK ] SerializationTest.CanSerializeAwhParams (0 ms) 17: [----------] 3 tests from SerializationTest (0 ms total) 17: 17: [----------] 1 test from BiasTest 17: [ RUN ] BiasTest.DetectsCovering 17: [ OK ] BiasTest.DetectsCovering (4 ms) 17: [----------] 1 test from BiasTest (4 ms total) 17: 17: [----------] 1 test from biasGridTest 17: [ RUN ] biasGridTest.neighborhood 17: [ OK ] biasGridTest.neighborhood (0 ms) 17: [----------] 1 test from biasGridTest (0 ms total) 17: 17: [----------] 2 tests from BiasSharingTest 17: [ RUN ] BiasSharingTest.SharingWorks 17: [ OK ] BiasSharingTest.SharingWorks (82 ms) 17: [ RUN ] BiasSharingTest.SharingScalingByMetricWorks 17: [ OK ] BiasSharingTest.SharingScalingByMetricWorks (64 ms) 17: [----------] 2 tests from BiasSharingTest (147 ms total) 17: 17: [----------] 2 tests from BiasFepLambdaStateTest 17: [ RUN ] BiasFepLambdaStateTest.DetectsCovering 17: [ OK ] BiasFepLambdaStateTest.DetectsCovering (1 ms) 17: [ RUN ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy 17: [ OK ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy (0 ms) 17: [----------] 2 tests from BiasFepLambdaStateTest (7 ms total) 17: 17: [----------] 8 tests from WithParameters/BiasTest 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 (1 ms) 17: [----------] 8 tests from WithParameters/BiasTest (18 ms total) 17: 17: [----------] 2 tests from WithParameters/BiasStateTest 17: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 17: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (5 ms) 17: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 17: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (0 ms) 17: [----------] 2 tests from WithParameters/BiasStateTest (6 ms total) 17: 17: [----------] 1 test from WithParameters/UserInputTest 17: [ RUN ] WithParameters/UserInputTest.ParsesUser3DInput/0 17: [ OK ] WithParameters/UserInputTest.ParsesUser3DInput/0 (0 ms) 17: [----------] 1 test from WithParameters/UserInputTest (0 ms total) 17: 17: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 (4 ms) 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 (4 ms) 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 (5 ms) 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 (4 ms) 17: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest (30 ms total) 17: 17: [----------] 3 tests from WithParameters/FrictionMetricTest 17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/0 17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/0 (2 ms) 17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/1 17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/1 (0 ms) 17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/2 17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/2 (20 ms) 17: [----------] 3 tests from WithParameters/FrictionMetricTest (30 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 27 tests from 10 test suites ran. (248 ms total) 17: [ PASSED ] 27 tests. 17/87 Test #17: AwhTest ................................... Passed 0.28 sec test 18 Start 18: DensityFittingAppliedForcesUnitTest 18: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/density_fitting_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/DensityFittingAppliedForcesUnitTest.xml" 18: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests 18: Test timeout computed to be: 30 18: [==========] Running 18 tests from 4 test suites. 18: [----------] Global test environment set-up. 18: [----------] 2 tests from DensityFittingTest 18: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows 18: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (0 ms) 18: [ RUN ] DensityFittingTest.SingleAtom 18: [ OK ] DensityFittingTest.SingleAtom (1 ms) 18: [----------] 2 tests from DensityFittingTest (2 ms total) 18: 18: [----------] 7 tests from DensityFittingAmplitudeLookupTest 18: [ RUN ] DensityFittingAmplitudeLookupTest.Unity 18: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.Charge 18: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.Masses 18: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign 18: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct 18: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign 18: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct 18: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms) 18: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total) 18: 18: [----------] 1 test from DensityFittingForceProviderState 18: [ RUN ] DensityFittingForceProviderState.RoundTripSaving 18: [ OK ] DensityFittingForceProviderState.RoundTripSaving (0 ms) 18: [----------] 1 test from DensityFittingForceProviderState (0 ms total) 18: 18: [----------] 8 tests from DensityFittingOptionsTest 18: [ RUN ] DensityFittingOptionsTest.DefaultParameters 18: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms) 18: [ RUN ] DensityFittingOptionsTest.OptionSetsActive 18: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms) 18: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive 18: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 18: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive 18: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (0 ms) 18: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup 18: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 18: [ RUN ] DensityFittingOptionsTest.InternalsToKvt 18: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms) 18: [ RUN ] DensityFittingOptionsTest.KvtToInternal 18: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms) 18: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent 18: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms) 18: [----------] 8 tests from DensityFittingOptionsTest (0 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 18 tests from 4 test suites ran. (2 ms total) 18: [ PASSED ] 18 tests. 18/87 Test #18: DensityFittingAppliedForcesUnitTest ....... Passed 0.04 sec test 19 Start 19: QMMMAppliedForcesUnitTest 19: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/qmmm_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/QMMMAppliedForcesUnitTest.xml" 19: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests 19: Test timeout computed to be: 30 19: [==========] Running 21 tests from 5 test suites. 19: [----------] Global test environment set-up. 19: [----------] 3 tests from QMMMInputGeneratorTest 19: [ RUN ] QMMMInputGeneratorTest.CanConstruct 19: [ OK ] QMMMInputGeneratorTest.CanConstruct (0 ms) 19: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBENoLink 19: [ OK ] QMMMInputGeneratorTest.TwoWatersPBENoLink (0 ms) 19: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBEWithLink 19: [ OK ] QMMMInputGeneratorTest.TwoWatersPBEWithLink (0 ms) 19: [----------] 3 tests from QMMMInputGeneratorTest (1 ms total) 19: 19: [----------] 7 tests from QMMMTopologyPreprocessorTest 19: [ RUN ] QMMMTopologyPreprocessorTest.CanConstruct 19: [ OK ] QMMMTopologyPreprocessorTest.CanConstruct (0 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 21.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 19: Setting the LD random seed to -71334157 19: 19: Generated 10 of the 10 non-bonded parameter combinations 19: 19: Generated 10 of the 10 1-4 parameter combinations 19: 19: Excluding 2 bonded neighbours molecule type 'SOL' 19: Analysing residue names: 19: There are: 4 Water residues 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink (25 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 21.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 19: Setting the LD random seed to 1610610047 19: 19: Generated 10 of the 10 non-bonded parameter combinations 19: 19: Generated 10 of the 10 1-4 parameter combinations 19: 19: Excluding 2 bonded neighbours molecule type 'SOL' 19: Analysing residue names: 19: There are: 4 Water residues 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink (6 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 21.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 19: Setting the LD random seed to 788362943 19: 19: Generated 10 of the 10 non-bonded parameter combinations 19: 19: Generated 10 of the 10 1-4 parameter combinations 19: 19: Excluding 2 bonded neighbours molecule type 'SOL' 19: Analysing residue names: 19: There are: 4 Water residues 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink (7 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 63.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 19: NVE simulation: will use the initial temperature of 129.093 K for 19: determining the Verlet buffer size 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 19: Setting the LD random seed to -67639713 19: 19: Generated 2145 of the 2145 non-bonded parameter combinations 19: 19: Generated 2145 of the 2145 1-4 parameter combinations 19: 19: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 19: Analysing residue names: 19: There are: 3 Protein residues 19: Analysing Protein... 19: 19: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 19: 19: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 19: 19: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 19: 19: Note that mdrun will redetermine rlist based on the actual pair-list setup 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints (34 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: 19: NOTE 2 [file unknown]: 19: You are using constraints on all bonds, whereas the forcefield has been 19: parametrized only with constraints involving hydrogen atoms. We suggest 19: using constraints = h-bonds instead, this will also improve performance. 19: 19: 19: NOTE 3 [file unknown]: 19: For energy conservation with LINCS, lincs_iter should be 2 or larger. 19: 19: 19: Number of degrees of freedom in T-Coupling group rest is 42.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 19: NVE simulation: will use the initial temperature of 193.640 K for 19: determining the Verlet buffer size 19: 19: 19: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 5 NOTEs 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 19: Setting the LD random seed to -67260945 19: 19: Generated 2145 of the 2145 non-bonded parameter combinations 19: 19: Generated 2145 of the 2145 1-4 parameter combinations 19: 19: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 19: 19: turning all bonds into constraints... 19: Analysing residue names: 19: There are: 3 Protein residues 19: Analysing Protein... 19: 19: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 19: 19: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 19: 19: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 19: 19: Note that mdrun will redetermine rlist based on the actual pair-list setup 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints (24 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.RemovingQMVsites 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Number of degrees of freedom in T-Coupling group rest is 45.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 19: Setting the LD random seed to -8656261 19: 19: Generated 3 of the 6 non-bonded parameter combinations 19: 19: Excluding 3 bonded neighbours molecule type 'VSTEST' 19: 19: Cleaning up constraints and constant bonded interactions with virtual sites 19: Analysing residue names: 19: There are: 1 Other residues 19: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.RemovingQMVsites (15 ms) 19: [----------] 7 tests from QMMMTopologyPreprocessorTest (118 ms total) 19: 19: [----------] 9 tests from QMMMOptionsTest 19: [ RUN ] QMMMOptionsTest.DefaultParameters 19: [ OK ] QMMMOptionsTest.DefaultParameters (0 ms) 19: [ RUN ] QMMMOptionsTest.OptionSetsActive 19: [ OK ] QMMMOptionsTest.OptionSetsActive (0 ms) 19: [ RUN ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive 19: [ OK ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive (1 ms) 19: [ RUN ] QMMMOptionsTest.OutputDefaultValuesWhenActive 19: [ OK ] QMMMOptionsTest.OutputDefaultValuesWhenActive (0 ms) 19: [ RUN ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup 19: [ OK ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 19: [ RUN ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup 19: [ OK ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup (1 ms) 19: [ RUN ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup 19: [ OK ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup (0 ms) 19: [ RUN ] QMMMOptionsTest.InternalsToKvtAndBack 19: [ OK ] QMMMOptionsTest.InternalsToKvtAndBack (0 ms) 19: [ RUN ] QMMMOptionsTest.CP2KInputProcessing 19: [ OK ] QMMMOptionsTest.CP2KInputProcessing (4 ms) 19: [----------] 9 tests from QMMMOptionsTest (14 ms total) 19: 19: [----------] 1 test from QMMMForceProviderTest 19: [ RUN ] QMMMForceProviderTest.CanConstructOrNot 19: [ OK ] QMMMForceProviderTest.CanConstructOrNot (0 ms) 19: [----------] 1 test from QMMMForceProviderTest (0 ms total) 19: 19: [----------] 1 test from QMMMTest 19: [ RUN ] QMMMTest.ForceProviderLackingInputThrows 19: [ OK ] QMMMTest.ForceProviderLackingInputThrows (0 ms) 19: [----------] 1 test from QMMMTest (0 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 21 tests from 5 test suites ran. (136 ms total) 19: [ PASSED ] 21 tests. 19/87 Test #19: QMMMAppliedForcesUnitTest ................. Passed 0.20 sec test 20 Start 20: ColvarsAppliedForcesUnitTest 20: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/colvars_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/ColvarsAppliedForcesUnitTest.xml" 20: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests 20: Test timeout computed to be: 30 20: [==========] Running 16 tests from 4 test suites. 20: [----------] Global test environment set-up. 20: [----------] 1 test from ColvarsTest 20: [ RUN ] ColvarsTest.ForceProviderLackingInputThrows 20: [ OK ] ColvarsTest.ForceProviderLackingInputThrows (0 ms) 20: [----------] 1 test from ColvarsTest (0 ms total) 20: 20: [----------] 6 tests from ColvarsOptionsTest 20: [ RUN ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive 20: [ OK ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive (11 ms) 20: [ RUN ] ColvarsOptionsTest.OutputDefaultValuesWhenActive 20: [ OK ] ColvarsOptionsTest.OutputDefaultValuesWhenActive (0 ms) 20: [ RUN ] ColvarsOptionsTest.OutputValuesWhenActive 20: [ OK ] ColvarsOptionsTest.OutputValuesWhenActive (2 ms) 20: [ RUN ] ColvarsOptionsTest.OptionSetsActive 20: [ OK ] ColvarsOptionsTest.OptionSetsActive (0 ms) 20: [ RUN ] ColvarsOptionsTest.InternalsToKvtAndBack 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 20: Setting the LD random seed to -8655117 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsOptionsTest.InternalsToKvtAndBack (66 ms) 20: [ RUN ] ColvarsOptionsTest.RetrieveEdrFilename 20: [ OK ] ColvarsOptionsTest.RetrieveEdrFilename (0 ms) 20: [----------] 6 tests from ColvarsOptionsTest (81 ms total) 20: 20: [----------] 4 tests from ColvarsPreProcessorTest 20: [ RUN ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 20: Setting the LD random seed to 1466889083 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess (5 ms) 20: [ RUN ] ColvarsPreProcessorTest.CheckValuesFourWaters 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 20: Setting the LD random seed to -1619013746 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.CheckValuesFourWaters (32 ms) 20: [ RUN ] ColvarsPreProcessorTest.CheckNestedInputFiles 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 20: Setting the LD random seed to -1073750273 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.CheckNestedInputFiles (14 ms) 20: [ RUN ] ColvarsPreProcessorTest.WrongColvarsInput 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 20: Setting the LD random seed to -537139217 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.WrongColvarsInput (23 ms) 20: [----------] 4 tests from ColvarsPreProcessorTest (77 ms total) 20: 20: [----------] 5 tests from ColvarsForceProviderTest 20: [ RUN ] ColvarsForceProviderTest.CanConstructOrNot 20: [ OK ] ColvarsForceProviderTest.CanConstructOrNot (0 ms) 20: [ RUN ] ColvarsForceProviderTest.SimpleInputs 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 20: Setting the LD random seed to -85002753 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.SimpleInputs (9 ms) 20: [ RUN ] ColvarsForceProviderTest.WrongColvarsInput 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 20: Setting the LD random seed to -268436737 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.WrongColvarsInput (16 ms) 20: [ RUN ] ColvarsForceProviderTest.CalculateForces4water 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 20: Setting the LD random seed to -25633 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.CalculateForces4water (89 ms) 20: [ RUN ] ColvarsForceProviderTest.CalculateForcesAlanine 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 66.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 20: NVE simulation: will use the initial temperature of 300.368 K for 20: determining the Verlet buffer size 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 20: Setting the LD random seed to -1258815501 20: 20: Generated 2211 of the 2211 non-bonded parameter combinations 20: 20: Generated 2211 of the 2211 1-4 parameter combinations 20: 20: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 20: Analysing residue names: 20: There are: 2 Protein residues 20: Analysing Protein... 20: 20: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 20: 20: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 20: 20: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 20: 20: Note that mdrun will redetermine rlist based on the actual pair-list setup 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.CalculateForcesAlanine (155 ms) 20: [----------] 5 tests from ColvarsForceProviderTest (272 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 16 tests from 4 test suites ran. (432 ms total) 20: [ PASSED ] 16 tests. 20/87 Test #20: ColvarsAppliedForcesUnitTest .............. Passed 0.50 sec test 21 Start 21: AppliedForcesUnitTest 21: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/AppliedForcesUnitTest.xml" 21: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/tests 21: Test timeout computed to be: 30 21: [==========] Running 3 tests from 1 test suite. 21: [----------] Global test environment set-up. 21: [----------] 3 tests from ElectricFieldTest 21: [ RUN ] ElectricFieldTest.Static 21: [ OK ] ElectricFieldTest.Static (0 ms) 21: [ RUN ] ElectricFieldTest.Oscillating 21: [ OK ] ElectricFieldTest.Oscillating (0 ms) 21: [ RUN ] ElectricFieldTest.Pulsed 21: [ OK ] ElectricFieldTest.Pulsed (0 ms) 21: [----------] 3 tests from ElectricFieldTest (0 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 3 tests from 1 test suite ran. (0 ms total) 21: [ PASSED ] 3 tests. 21/87 Test #21: AppliedForcesUnitTest ..................... Passed 0.03 sec test 22 Start 22: ListedForcesTest 22: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/listed_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/ListedForcesTest.xml" 22: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/listed_forces/tests 22: Test timeout computed to be: 30 22: [==========] Running 132 tests from 9 test suites. 22: [----------] Global test environment set-up. 22: [----------] 24 tests from Bond/ListedForcesTest 22: [ RUN ] Bond/ListedForcesTest.Ifunc/0 22: [ OK ] Bond/ListedForcesTest.Ifunc/0 (3 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/1 22: [ OK ] Bond/ListedForcesTest.Ifunc/1 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/2 22: [ OK ] Bond/ListedForcesTest.Ifunc/2 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/3 22: [ OK ] Bond/ListedForcesTest.Ifunc/3 (1 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/4 22: [ OK ] Bond/ListedForcesTest.Ifunc/4 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/5 22: [ OK ] Bond/ListedForcesTest.Ifunc/5 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/6 22: [ OK ] Bond/ListedForcesTest.Ifunc/6 (3 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/7 22: [ OK ] Bond/ListedForcesTest.Ifunc/7 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/8 22: [ OK ] Bond/ListedForcesTest.Ifunc/8 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/9 22: [ OK ] Bond/ListedForcesTest.Ifunc/9 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/10 22: [ OK ] Bond/ListedForcesTest.Ifunc/10 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/11 22: [ OK ] Bond/ListedForcesTest.Ifunc/11 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/12 22: [ OK ] Bond/ListedForcesTest.Ifunc/12 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/13 22: [ OK ] Bond/ListedForcesTest.Ifunc/13 (1 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/14 22: [ OK ] Bond/ListedForcesTest.Ifunc/14 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/15 22: [ OK ] Bond/ListedForcesTest.Ifunc/15 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/16 22: [ OK ] Bond/ListedForcesTest.Ifunc/16 (1 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/17 22: [ OK ] Bond/ListedForcesTest.Ifunc/17 (1 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/18 22: [ OK ] Bond/ListedForcesTest.Ifunc/18 (2 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/19 22: [ OK ] Bond/ListedForcesTest.Ifunc/19 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/20 22: [ OK ] Bond/ListedForcesTest.Ifunc/20 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/21 22: [ OK ] Bond/ListedForcesTest.Ifunc/21 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/22 22: [ OK ] Bond/ListedForcesTest.Ifunc/22 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/23 22: [ OK ] Bond/ListedForcesTest.Ifunc/23 (0 ms) 22: [----------] 24 tests from Bond/ListedForcesTest (31 ms total) 22: 22: [----------] 33 tests from Angle/ListedForcesTest 22: [ RUN ] Angle/ListedForcesTest.Ifunc/0 22: [ OK ] Angle/ListedForcesTest.Ifunc/0 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/1 22: [ OK ] Angle/ListedForcesTest.Ifunc/1 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/2 22: [ OK ] Angle/ListedForcesTest.Ifunc/2 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/3 22: [ OK ] Angle/ListedForcesTest.Ifunc/3 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/4 22: [ OK ] Angle/ListedForcesTest.Ifunc/4 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/5 22: [ OK ] Angle/ListedForcesTest.Ifunc/5 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/6 22: [ OK ] Angle/ListedForcesTest.Ifunc/6 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/7 22: [ OK ] Angle/ListedForcesTest.Ifunc/7 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/8 22: [ OK ] Angle/ListedForcesTest.Ifunc/8 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/9 22: [ OK ] Angle/ListedForcesTest.Ifunc/9 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/10 22: [ OK ] Angle/ListedForcesTest.Ifunc/10 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/11 22: [ OK ] Angle/ListedForcesTest.Ifunc/11 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/12 22: [ OK ] Angle/ListedForcesTest.Ifunc/12 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/13 22: [ OK ] Angle/ListedForcesTest.Ifunc/13 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/14 22: [ OK ] Angle/ListedForcesTest.Ifunc/14 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/15 22: [ OK ] Angle/ListedForcesTest.Ifunc/15 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/16 22: [ OK ] Angle/ListedForcesTest.Ifunc/16 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/17 22: [ OK ] Angle/ListedForcesTest.Ifunc/17 (2 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/18 22: [ OK ] Angle/ListedForcesTest.Ifunc/18 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/19 22: [ OK ] Angle/ListedForcesTest.Ifunc/19 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/20 22: [ OK ] Angle/ListedForcesTest.Ifunc/20 (6 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/21 22: [ OK ] Angle/ListedForcesTest.Ifunc/21 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/22 22: [ OK ] Angle/ListedForcesTest.Ifunc/22 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/23 22: [ OK ] Angle/ListedForcesTest.Ifunc/23 (2 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/24 22: [ OK ] Angle/ListedForcesTest.Ifunc/24 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/25 22: [ OK ] Angle/ListedForcesTest.Ifunc/25 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/26 22: [ OK ] Angle/ListedForcesTest.Ifunc/26 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/27 22: [ OK ] Angle/ListedForcesTest.Ifunc/27 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/28 22: [ OK ] Angle/ListedForcesTest.Ifunc/28 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/29 22: [ OK ] Angle/ListedForcesTest.Ifunc/29 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/30 22: [ OK ] Angle/ListedForcesTest.Ifunc/30 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/31 22: [ OK ] Angle/ListedForcesTest.Ifunc/31 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/32 22: [ OK ] Angle/ListedForcesTest.Ifunc/32 (0 ms) 22: [----------] 33 tests from Angle/ListedForcesTest (49 ms total) 22: 22: [----------] 18 tests from Dihedral/ListedForcesTest 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/0 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/0 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/1 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/1 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/2 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/2 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/3 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/3 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/4 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/4 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/5 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/5 (4 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/6 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/6 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/7 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/7 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/8 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/8 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/9 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/9 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/10 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/10 (4 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/11 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/11 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/12 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/12 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/13 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/13 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/14 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/14 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/15 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/15 (4 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/16 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/16 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/17 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/17 (0 ms) 22: [----------] 18 tests from Dihedral/ListedForcesTest (30 ms total) 22: 22: [----------] 12 tests from Polarize/ListedForcesTest 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/0 22: [ OK ] Polarize/ListedForcesTest.Ifunc/0 (0 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/1 22: [ OK ] Polarize/ListedForcesTest.Ifunc/1 (0 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/2 22: [ OK ] Polarize/ListedForcesTest.Ifunc/2 (0 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/3 22: [ OK ] Polarize/ListedForcesTest.Ifunc/3 (3 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/4 22: [ OK ] Polarize/ListedForcesTest.Ifunc/4 (0 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/5 22: [ OK ] Polarize/ListedForcesTest.Ifunc/5 (0 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/6 22: [ OK ] Polarize/ListedForcesTest.Ifunc/6 (0 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/7 22: [ OK ] Polarize/ListedForcesTest.Ifunc/7 (0 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/8 22: [ OK ] Polarize/ListedForcesTest.Ifunc/8 (0 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/9 22: [ OK ] Polarize/ListedForcesTest.Ifunc/9 (1 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/10 22: [ OK ] Polarize/ListedForcesTest.Ifunc/10 (1 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/11 22: [ OK ] Polarize/ListedForcesTest.Ifunc/11 (1 ms) 22: [----------] 12 tests from Polarize/ListedForcesTest (15 ms total) 22: 22: [----------] 18 tests from Restraints/ListedForcesTest 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/0 22: [ OK ] Restraints/ListedForcesTest.Ifunc/0 (1 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/1 22: [ OK ] Restraints/ListedForcesTest.Ifunc/1 (1 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/2 22: [ OK ] Restraints/ListedForcesTest.Ifunc/2 (2 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/3 22: [ OK ] Restraints/ListedForcesTest.Ifunc/3 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/4 22: [ OK ] Restraints/ListedForcesTest.Ifunc/4 (1 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/5 22: [ OK ] Restraints/ListedForcesTest.Ifunc/5 (4 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/6 22: [ OK ] Restraints/ListedForcesTest.Ifunc/6 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/7 22: [ OK ] Restraints/ListedForcesTest.Ifunc/7 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/8 22: [ OK ] Restraints/ListedForcesTest.Ifunc/8 (1 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/9 22: [ OK ] Restraints/ListedForcesTest.Ifunc/9 (1 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/10 22: [ OK ] Restraints/ListedForcesTest.Ifunc/10 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/11 22: [ OK ] Restraints/ListedForcesTest.Ifunc/11 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/12 22: [ OK ] Restraints/ListedForcesTest.Ifunc/12 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/13 22: [ OK ] Restraints/ListedForcesTest.Ifunc/13 (4 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/14 22: [ OK ] Restraints/ListedForcesTest.Ifunc/14 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/15 22: [ OK ] Restraints/ListedForcesTest.Ifunc/15 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/16 22: [ OK ] Restraints/ListedForcesTest.Ifunc/16 (1 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/17 22: [ OK ] Restraints/ListedForcesTest.Ifunc/17 (1 ms) 22: [----------] 18 tests from Restraints/ListedForcesTest (35 ms total) 22: 22: [----------] 3 tests from BondZeroLength/ListedForcesTest 22: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/0 22: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/0 (0 ms) 22: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/1 22: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/1 (1 ms) 22: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/2 22: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/2 (1 ms) 22: [----------] 3 tests from BondZeroLength/ListedForcesTest (4 ms total) 22: 22: [----------] 3 tests from AngleZero/ListedForcesTest 22: [ RUN ] AngleZero/ListedForcesTest.Ifunc/0 22: [ OK ] AngleZero/ListedForcesTest.Ifunc/0 (1 ms) 22: [ RUN ] AngleZero/ListedForcesTest.Ifunc/1 22: [ OK ] AngleZero/ListedForcesTest.Ifunc/1 (5 ms) 22: [ RUN ] AngleZero/ListedForcesTest.Ifunc/2 22: [ OK ] AngleZero/ListedForcesTest.Ifunc/2 (3 ms) 22: [----------] 3 tests from AngleZero/ListedForcesTest (11 ms total) 22: 22: [----------] 12 tests from 14Interaction/ListedForcesPairsTest 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/0 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/0 (0 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/1 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/1 (0 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/2 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/2 (0 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/3 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/3 (1 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/4 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/4 (2 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/5 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/5 (1 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/6 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/6 (1 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/7 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/7 (3 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/8 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/8 (3 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/9 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/9 (4 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/10 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/10 (15 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/11 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/11 (3 ms) 22: [----------] 12 tests from 14Interaction/ListedForcesPairsTest (43 ms total) 22: 22: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest 22: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 22: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 (6 ms) 22: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 22: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 (0 ms) 22: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 22: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 (0 ms) 22: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 22: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 (0 ms) 22: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 22: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 (1 ms) 22: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 22: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 (0 ms) 22: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 22: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 (1 ms) 22: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 22: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 (1 ms) 22: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 22: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 (1 ms) 22: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest (20 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 132 tests from 9 test suites ran. (251 ms total) 22: [ PASSED ] 132 tests. 22/87 Test #22: ListedForcesTest .......................... Passed 0.29 sec test 23 Start 23: NbnxmTests 23: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/nbnxm-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/NbnxmTests.xml" 23: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/nbnxm/tests 23: Test timeout computed to be: 30 23: [==========] Running 80 tests from 3 test suites. 23: [----------] Global test environment set-up. 23: [----------] 18 tests from KernelSetupTest 23: [ RUN ] KernelSetupTest.getCoulombKernelTypeRF 23: [ OK ] KernelSetupTest.getCoulombKernelTypeRF (0 ms) 23: [ RUN ] KernelSetupTest.getCoulombKernelTypeCut 23: [ OK ] KernelSetupTest.getCoulombKernelTypeCut (0 ms) 23: [ RUN ] KernelSetupTest.getCoulombKernelTypeTable 23: [ OK ] KernelSetupTest.getCoulombKernelTypeTable (0 ms) 23: [ RUN ] KernelSetupTest.getCoulombKernelTypeTableTwin 23: [ OK ] KernelSetupTest.getCoulombKernelTypeTableTwin (0 ms) 23: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwald 23: [ OK ] KernelSetupTest.getCoulombKernelTypeEwald (0 ms) 23: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwaldTwin 23: [ OK ] KernelSetupTest.getCoulombKernelTypeEwaldTwin (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone 23: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift 23: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone 23: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift 23: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone 23: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift 23: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutThrows 23: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutThrows (5 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch 23: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypePmeGeom 23: [ OK ] KernelSetupTest.getVdwKernelTypePmeGeom (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypePmeNone 23: [ OK ] KernelSetupTest.getVdwKernelTypePmeNone (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch 23: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypeAllCountThrows 23: [ OK ] KernelSetupTest.getVdwKernelTypeAllCountThrows (0 ms) 23: [----------] 18 tests from KernelSetupTest (5 ms total) 23: 23: [----------] 60 tests from NbnxmKernelTest 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwCutCombGeom 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwCutCombGeom (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwCutCombLB 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwCutCombLB (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwCutCombNone 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwCutCombNone (29 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwForceSwitch 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwForceSwitch (30 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwPotSwitch 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwPotSwitch (35 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwEwaldCombGeom 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwEwaldCombGeom (20 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwCutCombGeom 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwCutCombGeom (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwCutCombLB 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwCutCombLB (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwCutCombNone 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwCutCombNone (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwForceSwitch 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwForceSwitch (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwPotSwitch 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwPotSwitch (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwEwaldCombGeom 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwEwaldCombGeom (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwCutCombGeom 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwCutCombLB 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwCutCombLB (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwCutCombNone 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwCutCombNone (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwForceSwitch 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwForceSwitch (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwPotSwitch 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwPotSwitch (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwEwaldCombGeom 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwCutCombGeom 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwCutCombGeom (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwCutCombLB 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwCutCombLB (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwCutCombNone 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwCutCombNone (22 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwForceSwitch 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwForceSwitch (19 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwPotSwitch 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwPotSwitch (25 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwEwaldCombGeom 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwEwaldCombGeom (26 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwCutCombGeom 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwCutCombLB 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwCutCombLB (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwCutCombNone 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwCutCombNone (14 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwForceSwitch 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwForceSwitch (21 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwPotSwitch 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwPotSwitch (16 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwEwaldCombGeom 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwEwaldCombGeom (18 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwCutCombGeom 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwCutCombGeom (16 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwCutCombLB 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwCutCombLB (16 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwCutCombNone 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwCutCombNone (11 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwForceSwitch 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwForceSwitch (2 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwPotSwitch 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwPotSwitch (13 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwEwaldCombGeom 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwEwaldCombGeom (12 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwCutCombGeom 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwCutCombGeom (21 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwCutCombLB 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwCutCombLB (26 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwCutCombNone 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwCutCombNone (9 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwForceSwitch 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwForceSwitch (15 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwPotSwitch 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwPotSwitch (11 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwEwaldCombGeom 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwEwaldCombGeom (14 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwCutCombGeom 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwCutCombGeom (20 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwCutCombLB 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwCutCombLB (5 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwCutCombNone 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwCutCombNone (9 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwForceSwitch 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwForceSwitch (12 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwPotSwitch 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwPotSwitch (11 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwEwaldCombGeom 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwEwaldCombGeom (11 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwCutCombGeom 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwCutCombGeom (16 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwCutCombLB 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwCutCombLB (3 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwCutCombNone 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwCutCombNone (8 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwForceSwitch 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwForceSwitch (3 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwPotSwitch 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwPotSwitch (3 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwEwaldCombGeom 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwEwaldCombGeom (3 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwCutCombGeom 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwCutCombGeom (11 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwCutCombLB 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwCutCombLB (3 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwCutCombNone 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwCutCombNone (12 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwForceSwitch 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwForceSwitch (11 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwPotSwitch 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwPotSwitch (11 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwEwaldCombGeom 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwEwaldCombGeom (3 ms) 23: [----------] 60 tests from NbnxmKernelTest (737 ms total) 23: 23: [----------] 2 tests from WithParameters/CpuListDiagonalExclusionsTest 23: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 23: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 (0 ms) 23: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 23: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 (0 ms) 23: [----------] 2 tests from WithParameters/CpuListDiagonalExclusionsTest (0 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 80 tests from 3 test suites ran. (743 ms total) 23: [ PASSED ] 80 tests. 23/87 Test #23: NbnxmTests ................................ Passed 0.86 sec test 24 Start 24: CommandLineUnitTests 24: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/commandline-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/CommandLineUnitTests.xml" 24: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/commandline/tests 24: Test timeout computed to be: 30 24: [==========] Running 60 tests from 7 test suites. 24: [----------] Global test environment set-up. 24: [----------] 3 tests from CommandLineHelpModuleTest 24: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 24: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (3 ms) 24: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 24: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (0 ms) 24: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 24: [ OK ] CommandLineHelpModuleTest.ExportsHelp (1 ms) 24: [----------] 3 tests from CommandLineHelpModuleTest (5 ms total) 24: 24: [----------] 7 tests from CommandLineHelpWriterTest 24: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 24: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (0 ms) 24: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 24: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms) 24: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 24: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms) 24: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 24: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms) 24: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 24: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) 24: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 24: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms) 24: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues 24: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms) 24: [----------] 7 tests from CommandLineHelpWriterTest (4 ms total) 24: 24: [----------] 6 tests from CommandLineModuleManagerTest 24: [ RUN ] CommandLineModuleManagerTest.RunsModule 24: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms) 24: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 24: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 24: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 24: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 24: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 24: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) 24: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 24: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 24: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 24: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 24: [----------] 6 tests from CommandLineModuleManagerTest (1 ms total) 24: 24: [----------] 13 tests from CommandLineParserTest 24: [ RUN ] CommandLineParserTest.HandlesSingleValues 24: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 24: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 24: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 24: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 24: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 24: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 24: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms) 24: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 24: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 24: [ RUN ] CommandLineParserTest.HandlesString 24: [ OK ] CommandLineParserTest.HandlesString (0 ms) 24: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 24: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) 24: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 24: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 24: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 24: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 24: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 24: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 24: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 24: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 24: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 24: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 24: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 24: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 24: [----------] 13 tests from CommandLineParserTest (0 ms total) 24: 24: [----------] 6 tests from CommandLineProgramContextTest 24: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 24: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (1 ms) 24: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 24: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 24: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 24: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 24: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 24: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 24: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 24: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) 24: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 24: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 24: [----------] 6 tests from CommandLineProgramContextTest (7 ms total) 24: 24: [----------] 3 tests from OutputNamesTest 24: [ RUN ] OutputNamesTest.CanBeSuffixed 24: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms) 24: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend 24: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms) 24: [ RUN ] OutputNamesTest.CanHavePartNumberAdded 24: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms) 24: [----------] 3 tests from OutputNamesTest (0 ms total) 24: 24: [----------] 22 tests from ParseCommonArgsTest 24: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 24: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 24: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 24: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 24: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 24: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum 24: [ OK ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 24: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 24: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 24: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 24: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 24: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 24: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 24: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 24: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 24: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 24: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 24: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 24: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 24: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 24: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 24: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 24: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (1 ms) 24: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 24: Value is /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary/ParseCommonArgsTest_AcceptsUnknownTrajectoryExtension.foo 24: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) 24: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 24: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (0 ms) 24: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 24: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (5 ms) 24: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 24: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 24: [----------] 22 tests from ParseCommonArgsTest (7 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 60 tests from 7 test suites ran. (27 ms total) 24: [ PASSED ] 60 tests. 24/87 Test #24: CommandLineUnitTests ...................... Passed 0.06 sec test 25 Start 25: DomDecTests 25: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/domdec-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/DomDecTests.xml" 25: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/domdec/tests 25: Test timeout computed to be: 30 25: [==========] Running 9 tests from 2 test suites. 25: [----------] Global test environment set-up. 25: [----------] 7 tests from HashedMap 25: [ RUN ] HashedMap.InsertsFinds 25: [ OK ] HashedMap.InsertsFinds (0 ms) 25: [ RUN ] HashedMap.NegativeKeysWork 25: [ OK ] HashedMap.NegativeKeysWork (0 ms) 25: [ RUN ] HashedMap.InsertsErases 25: [ OK ] HashedMap.InsertsErases (0 ms) 25: [ RUN ] HashedMap.InsertsOrAssigns 25: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 25: [ RUN ] HashedMap.Clears 25: [ OK ] HashedMap.Clears (0 ms) 25: [ RUN ] HashedMap.LinkedEntries 25: [ OK ] HashedMap.LinkedEntries (0 ms) 25: [ RUN ] HashedMap.ResizesTable 25: [ OK ] HashedMap.ResizesTable (0 ms) 25: [----------] 7 tests from HashedMap (0 ms total) 25: 25: [----------] 2 tests from LocalAtomSetManager 25: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 25: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 25: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 25: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 25: [----------] 2 tests from LocalAtomSetManager (0 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 9 tests from 2 test suites ran. (0 ms total) 25: [ PASSED ] 9 tests. 25/87 Test #25: DomDecTests ............................... Passed 0.05 sec test 26 Start 26: DomDecMpiTests 26: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/domdec-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/DomDecMpiTests.xml" 26: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/domdec/tests 26: Test timeout computed to be: 30 26: [==========] Running 4 tests from 1 test suite. 26: [----------] Global test environment set-up. 26: [----------] 4 tests from HaloExchangeTest 26: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith1Pulse 26: [ OK ] HaloExchangeTest.Coordinates1dHaloWith1Pulse (23 ms) 26: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith2Pulses 26: [ OK ] HaloExchangeTest.Coordinates1dHaloWith2Pulses (19 ms) 26: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim 26: [ OK ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim (15 ms) 26: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 26: [ OK ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 (27 ms) 26: [----------] 4 tests from HaloExchangeTest (87 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 4 tests from 1 test suite ran. (87 ms total) 26: [ PASSED ] 4 tests. 26/87 Test #26: DomDecMpiTests ............................ Passed 0.17 sec test 27 Start 27: EwaldUnitTests 27: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/ewald-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/EwaldUnitTests.xml" 27: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/ewald/tests 27: Test timeout computed to be: 30 27: [==========] Running 407 tests from 9 test suites. 27: [----------] Global test environment set-up. 27: [----------] 6 tests from SeparatePmeRanksPermittedTest 27: [ RUN ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons 27: [ OK ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons (0 ms) 27: [ RUN ] SeparatePmeRanksPermittedTest.CanBeDisabled 27: [ OK ] SeparatePmeRanksPermittedTest.CanBeDisabled (0 ms) 27: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag 27: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag (0 ms) 27: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonText 27: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonText (0 ms) 27: [ RUN ] SeparatePmeRanksPermittedTest.TwoDisableReasonText 27: [ OK ] SeparatePmeRanksPermittedTest.TwoDisableReasonText (0 ms) 27: [ RUN ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText 27: [ OK ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText (0 ms) 27: [----------] 6 tests from SeparatePmeRanksPermittedTest (0 ms total) 27: 27: [----------] 108 tests from Pme_SplineAndSpreadTest 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline (20 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline (2 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline (5 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline (2 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline (4 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline (7 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline (6 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline (6 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline (3 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline (5 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline (4 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread (2 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (2 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline (6 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread (2 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (2 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline (2 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline (2 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline (2 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline (5 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline (5 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline (5 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline (8 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline (11 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline (13 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline (16 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline (7 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline (3 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (2 ms) 27: [----------] 108 tests from Pme_SplineAndSpreadTest (317 ms total) 27: 27: [----------] 64 tests from Pme_SolveTest 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (2 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (1 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (4 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (3 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (5 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (3 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (1 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (8 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (1 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (8 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [----------] 64 tests from Pme_SolveTest (68 ms total) 27: 27: [----------] 32 tests from PmeDiffEwaldQ_SolveTest 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (7 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (5 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (5 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (3 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (6 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (7 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [----------] 32 tests from PmeDiffEwaldQ_SolveTest (49 ms total) 27: 27: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (1 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (7 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (3 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (7 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (7 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (7 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (7 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (7 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 27: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest (54 ms total) 27: 27: [----------] 64 tests from PmeDiffEps_SolveTest 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (7 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (7 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (11 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (7 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (11 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (7 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (7 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (1 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (7 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (7 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (3 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (7 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (7 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (7 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [----------] 64 tests from PmeDiffEps_SolveTest (116 ms total) 27: 27: [----------] 72 tests from Pme_GatherTest 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom (3 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (3 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom (3 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom (7 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (2 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (9 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (9 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom (4 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (3 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (2 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom (9 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom (1 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (8 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (6 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (2 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom (1 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (3 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (4 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (1 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom (3 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom (4 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (10 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 27: [----------] 72 tests from Pme_GatherTest (166 ms total) 27: 27: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 27: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 27: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms) 27: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 27: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 27: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 27: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 27: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 27: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (2 ms) 27: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 27: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 27: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (5 ms total) 27: 27: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (8 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (7 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (11 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (3 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (1 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (3 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (2 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (4 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (5 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (4 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (10 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (4 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (8 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (5 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (7 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (1 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (3 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (7 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (3 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (7 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (7 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (3 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (3 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (4 ms) 27: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (148 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 407 tests from 9 test suites ran. (926 ms total) 27: [ PASSED ] 311 tests. 27: [ SKIPPED ] 96 tests, listed below: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27/87 Test #27: EwaldUnitTests ............................ Passed 1.03 sec test 28 Start 28: FFTUnitTests 28: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/fft-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/FFTUnitTests.xml" 28: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fft/tests 28: Test timeout computed to be: 1920 28: [==========] Running 15 tests from 4 test suites. 28: [----------] Global test environment set-up. 28: [----------] 2 tests from ManyFFTTest 28: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 28: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (11 ms) 28: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 28: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (24 ms) 28: [----------] 2 tests from ManyFFTTest (36 ms total) 28: 28: [----------] 1 test from FFTTest 28: [ RUN ] FFTTest.Real2DLength18_15Test 28: [ OK ] FFTTest.Real2DLength18_15Test (4 ms) 28: [----------] 1 test from FFTTest (10 ms total) 28: 28: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 28: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 28: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (1 ms) 28: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 28: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (1 ms) 28: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 28: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (1 ms) 28: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 28: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (2 ms) 28: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 28: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (5 ms) 28: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 28: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (1 ms) 28: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 28: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (1 ms) 28: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 28: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (5 ms) 28: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 28: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (11 ms) 28: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 28: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (13 ms) 28: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (55 ms total) 28: 28: [----------] 2 tests from Works/ParameterizedFFTTest3D 28: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 28: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 (4 ms) 28: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 28: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 (1 ms) 28: [----------] 2 tests from Works/ParameterizedFFTTest3D (11 ms total) 28: 28: [----------] Global test environment tear-down 28: [==========] 15 tests from 4 test suites ran. (114 ms total) 28: [ PASSED ] 15 tests. 28/87 Test #28: FFTUnitTests .............................. Passed 0.19 sec test 29 Start 29: GpuUtilsUnitTests 29: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/gpu_utils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/GpuUtilsUnitTests.xml" 29: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gpu_utils/tests 29: Test timeout computed to be: 30 29: [==========] Running 64 tests from 22 test suites. 29: [----------] Global test environment set-up. 29: [----------] 2 tests from ClfftInitializer 29: [ RUN ] ClfftInitializer.SingleInitializationWorks 29: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms) 29: [ RUN ] ClfftInitializer.TwoInitializationsWork 29: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms) 29: [----------] 2 tests from ClfftInitializer (0 ms total) 29: 29: [----------] 1 test from DevicesAvailable 29: [ RUN ] DevicesAvailable.ShouldBeAbleToRunOnDevice 29: [ OK ] DevicesAvailable.ShouldBeAbleToRunOnDevice (0 ms) 29: [----------] 1 test from DevicesAvailable (0 ms total) 29: 29: [----------] 1 test from DeviceStreamManagerTest 29: [ RUN ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice 29: [ OK ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice (0 ms) 29: [----------] 1 test from DeviceStreamManagerTest (0 ms total) 29: 29: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 29: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 29: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 29: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 29: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 29: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 29: 29: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = double 29: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 29: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 29: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 29: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 29: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 29: 29: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 29: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 29: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 29: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 29: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 29: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 29: 29: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 29: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 29: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 29: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 29: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 29: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 29: 29: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 29: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 29: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 29: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 29: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 29: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 29: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 29: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 29: 29: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = double 29: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 29: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 29: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 29: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 29: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 29: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 29: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 29: 29: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 29: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 29: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 29: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 29: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 29: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 29: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 29: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 29: 29: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 29: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 29: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 29: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 29: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/0.Swap 29: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/0.Comparison 29: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 29: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 29: 29: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = double 29: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 29: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 29: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 29: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/1.Swap 29: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/1.Comparison 29: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 29: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 29: 29: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 29: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 29: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 29: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 29: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/2.Swap 29: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/2.Comparison 29: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 29: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 29: 29: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 29: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 29: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 29: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 29: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/3.Swap 29: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/3.Comparison 29: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 29: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 29: 29: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 29: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 29: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 29: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 29: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 29: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 29: 29: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = double 29: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 29: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 29: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 29: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 29: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 29: 29: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 29: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 29: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 29: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 29: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 29: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 29: 29: [----------] 1 test from HostAllocatorUntypedTest 29: [ RUN ] HostAllocatorUntypedTest.Comparison 29: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 29: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 29: 29: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 29: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 29: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 29: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 29: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/0.Move 29: [ OK ] AllocatorTest/0.Move (0 ms) 29: [----------] 4 tests from AllocatorTest/0 (0 ms total) 29: 29: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 29: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 29: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 29: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 29: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/1.Move 29: [ OK ] AllocatorTest/1.Move (0 ms) 29: [----------] 4 tests from AllocatorTest/1 (0 ms total) 29: 29: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> 29: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 29: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 29: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 29: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/2.Move 29: [ OK ] AllocatorTest/2.Move (0 ms) 29: [----------] 4 tests from AllocatorTest/2 (0 ms total) 29: 29: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 29: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 29: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 29: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 29: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/3.Move 29: [ OK ] AllocatorTest/3.Move (0 ms) 29: [----------] 4 tests from AllocatorTest/3 (0 ms total) 29: 29: [----------] Global test environment tear-down 29: [==========] 64 tests from 22 test suites ran. (0 ms total) 29: [ PASSED ] 64 tests. 29/87 Test #29: GpuUtilsUnitTests ......................... Passed 0.08 sec test 30 Start 30: HardwareUnitTests 30: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/hardware-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/HardwareUnitTests.xml" 30: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/hardware/tests 30: Test timeout computed to be: 30 30: [==========] Running 21 tests from 9 test suites. 30: [----------] Global test environment set-up. 30: [----------] 1 test from CpuInfoTest 30: [ RUN ] CpuInfoTest.SupportLevel 30: [ OK ] CpuInfoTest.SupportLevel (16 ms) 30: [----------] 1 test from CpuInfoTest (16 ms total) 30: 30: [----------] 4 tests from HardwareTopologyTest 30: [ RUN ] HardwareTopologyTest.Execute 30: [ OK ] HardwareTopologyTest.Execute (35 ms) 30: [ RUN ] HardwareTopologyTest.HwlocExecute 30: [ OK ] HardwareTopologyTest.HwlocExecute (44 ms) 30: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 30: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (27 ms) 30: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 30: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (28 ms) 30: [----------] 4 tests from HardwareTopologyTest (135 ms total) 30: 30: [----------] 1 test from DevicesManagerTest 30: [ RUN ] DevicesManagerTest.Serialization 30: [ OK ] DevicesManagerTest.Serialization (0 ms) 30: [----------] 1 test from DevicesManagerTest (0 ms total) 30: 30: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest 30: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 30: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 (12 ms) 30: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 30: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 (4 ms) 30: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 30: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 (1 ms) 30: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 30: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) 30: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 30: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) 30: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest (25 ms total) 30: 30: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest 30: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 30: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 (6 ms) 30: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 30: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 (1 ms) 30: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 30: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) 30: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 30: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) 30: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 30: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) 30: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest (14 ms total) 30: 30: [----------] 2 tests from Core12900K/MockHardwareTopologyTest 30: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 30: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 (9 ms) 30: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 30: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 (14 ms) 30: [----------] 2 tests from Core12900K/MockHardwareTopologyTest (24 ms total) 30: 30: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest 30: [ RUN ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 30: [ OK ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (36 ms) 30: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest (36 ms total) 30: 30: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest 30: [ RUN ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 30: [ OK ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (145 ms) 30: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest (145 ms total) 30: 30: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest 30: [ RUN ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 30: [ OK ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (224 ms) 30: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest (224 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 21 tests from 9 test suites ran. (624 ms total) 30: [ PASSED ] 21 tests. 30/87 Test #30: HardwareUnitTests ......................... Passed 0.65 sec test 31 Start 31: MathUnitTests 31: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/math-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MathUnitTests.xml" 31: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/math/tests 31: Test timeout computed to be: 30 31: [==========] Running 304 tests from 38 test suites. 31: [----------] Global test environment set-up. 31: [----------] 1 test from EmptyArrayRefWithPaddingTest 31: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 31: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 31: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 31: 31: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 31: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 31: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 31: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 31: 31: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 31: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 31: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 31: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 31: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 31: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 31: 31: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 31: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 31: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 31: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 31: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 31: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 31: 31: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 31: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 31: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 31: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 31: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 31: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 31: 31: [----------] 2 tests from InvertBoxMatrixTest 31: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 31: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 31: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 31: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 31: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 31: 31: [----------] 11 tests from TranslateAndScaleTest 31: [ RUN ] TranslateAndScaleTest.identityTransformation 31: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms) 31: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling 31: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms) 31: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation 31: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms) 31: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial 31: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms) 31: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector 31: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector (0 ms) 31: [ RUN ] TranslateAndScaleTest.scalingIdentity 31: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms) 31: [ RUN ] TranslateAndScaleTest.scalingNonTrivial 31: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms) 31: [ RUN ] TranslateAndScaleTest.scalingNonTrivialSingleVector 31: [ OK ] TranslateAndScaleTest.scalingNonTrivialSingleVector (0 ms) 31: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero 31: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms) 31: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero 31: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms) 31: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector 31: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector (0 ms) 31: [----------] 11 tests from TranslateAndScaleTest (0 ms total) 31: 31: [----------] 3 tests from AffineTransformationTest 31: [ RUN ] AffineTransformationTest.identityTransformYieldsSameVectors 31: [ OK ] AffineTransformationTest.identityTransformYieldsSameVectors (0 ms) 31: [ RUN ] AffineTransformationTest.applyTransformationToVectors 31: [ OK ] AffineTransformationTest.applyTransformationToVectors (0 ms) 31: [ RUN ] AffineTransformationTest.retrieveGradient 31: [ OK ] AffineTransformationTest.retrieveGradient (0 ms) 31: [----------] 3 tests from AffineTransformationTest (0 ms total) 31: 31: [----------] 14 tests from DensitySimilarityTest 31: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect 31: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms) 31: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect 31: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms) 31: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch 31: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (1 ms) 31: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch 31: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms) 31: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect 31: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms) 31: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero 31: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms) 31: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect 31: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms) 31: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect 31: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (0 ms) 31: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne 31: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (33 ms) 31: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated 31: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (32 ms) 31: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated 31: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (1 ms) 31: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect 31: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (0 ms) 31: [ RUN ] DensitySimilarityTest.NormalizationCorrect 31: [ OK ] DensitySimilarityTest.NormalizationCorrect (0 ms) 31: [ RUN ] DensitySimilarityTest.NormalizationAllNonPositive 31: [ OK ] DensitySimilarityTest.NormalizationAllNonPositive (0 ms) 31: [----------] 14 tests from DensitySimilarityTest (76 ms total) 31: 31: [----------] 6 tests from StructureSimilarityTest 31: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 31: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 31: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 31: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 31: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 31: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 31: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 31: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 31: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 31: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 31: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 31: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 31: [----------] 6 tests from StructureSimilarityTest (0 ms total) 31: 31: [----------] 8 tests from ExponentialMovingAverage 31: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero 31: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms) 31: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative 31: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms) 31: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue 31: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms) 31: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue 31: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms) 31: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly 31: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms) 31: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing 31: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms) 31: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect 31: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms) 31: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree 31: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms) 31: [----------] 8 tests from ExponentialMovingAverage (0 ms total) 31: 31: [----------] 21 tests from FunctionTest 31: [ RUN ] FunctionTest.StaticLog2 31: [ OK ] FunctionTest.StaticLog2 (0 ms) 31: [ RUN ] FunctionTest.Log2I32Bit 31: [ OK ] FunctionTest.Log2I32Bit (0 ms) 31: [ RUN ] FunctionTest.Log2I64Bit 31: [ OK ] FunctionTest.Log2I64Bit (0 ms) 31: [ RUN ] FunctionTest.GreatestCommonDivisor 31: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 31: [ RUN ] FunctionTest.InvsqrtFloat 31: [ OK ] FunctionTest.InvsqrtFloat (0 ms) 31: [ RUN ] FunctionTest.InvsqrtDouble 31: [ OK ] FunctionTest.InvsqrtDouble (0 ms) 31: [ RUN ] FunctionTest.InvsqrtInteger 31: [ OK ] FunctionTest.InvsqrtInteger (0 ms) 31: [ RUN ] FunctionTest.InvcbrtFloat 31: [ OK ] FunctionTest.InvcbrtFloat (0 ms) 31: [ RUN ] FunctionTest.InvcbrtDouble 31: [ OK ] FunctionTest.InvcbrtDouble (0 ms) 31: [ RUN ] FunctionTest.InvcbrtInteger 31: [ OK ] FunctionTest.InvcbrtInteger (0 ms) 31: [ RUN ] FunctionTest.SixthrootFloat 31: [ OK ] FunctionTest.SixthrootFloat (0 ms) 31: [ RUN ] FunctionTest.SixthrootDouble 31: [ OK ] FunctionTest.SixthrootDouble (0 ms) 31: [ RUN ] FunctionTest.SixthrootInteger 31: [ OK ] FunctionTest.SixthrootInteger (0 ms) 31: [ RUN ] FunctionTest.InvsixthrootFloat 31: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) 31: [ RUN ] FunctionTest.InvsixthrootDouble 31: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) 31: [ RUN ] FunctionTest.InvsixthrootInteger 31: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) 31: [ RUN ] FunctionTest.Powers 31: [ OK ] FunctionTest.Powers (0 ms) 31: [ RUN ] FunctionTest.ErfInvFloat 31: [ OK ] FunctionTest.ErfInvFloat (0 ms) 31: [ RUN ] FunctionTest.ErfInvDouble 31: [ OK ] FunctionTest.ErfInvDouble (0 ms) 31: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 31: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) 31: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 31: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms) 31: [----------] 21 tests from FunctionTest (17 ms total) 31: 31: [----------] 1 test from FunctionTestIntegerTypes/0, where TypeParam = char 31: [ RUN ] FunctionTestIntegerTypes/0.IsPowerOfTwo 31: [ OK ] FunctionTestIntegerTypes/0.IsPowerOfTwo (0 ms) 31: [----------] 1 test from FunctionTestIntegerTypes/0 (0 ms total) 31: 31: [----------] 1 test from FunctionTestIntegerTypes/1, where TypeParam = unsigned char 31: [ RUN ] FunctionTestIntegerTypes/1.IsPowerOfTwo 31: [ OK ] FunctionTestIntegerTypes/1.IsPowerOfTwo (0 ms) 31: [----------] 1 test from FunctionTestIntegerTypes/1 (0 ms total) 31: 31: [----------] 1 test from FunctionTestIntegerTypes/2, where TypeParam = int 31: [ RUN ] FunctionTestIntegerTypes/2.IsPowerOfTwo 31: [ OK ] FunctionTestIntegerTypes/2.IsPowerOfTwo (0 ms) 31: [----------] 1 test from FunctionTestIntegerTypes/2 (0 ms total) 31: 31: [----------] 1 test from FunctionTestIntegerTypes/3, where TypeParam = unsigned int 31: [ RUN ] FunctionTestIntegerTypes/3.IsPowerOfTwo 31: [ OK ] FunctionTestIntegerTypes/3.IsPowerOfTwo (0 ms) 31: [----------] 1 test from FunctionTestIntegerTypes/3 (0 ms total) 31: 31: [----------] 1 test from FunctionTestIntegerTypes/4, where TypeParam = long 31: [ RUN ] FunctionTestIntegerTypes/4.IsPowerOfTwo 31: [ OK ] FunctionTestIntegerTypes/4.IsPowerOfTwo (0 ms) 31: [----------] 1 test from FunctionTestIntegerTypes/4 (0 ms total) 31: 31: [----------] 1 test from FunctionTestIntegerTypes/5, where TypeParam = unsigned long 31: [ RUN ] FunctionTestIntegerTypes/5.IsPowerOfTwo 31: [ OK ] FunctionTestIntegerTypes/5.IsPowerOfTwo (0 ms) 31: [----------] 1 test from FunctionTestIntegerTypes/5 (0 ms total) 31: 31: [----------] 4 tests from GaussianOn1DLattice 31: [ RUN ] GaussianOn1DLattice.sumsCloseToOne 31: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms) 31: [ RUN ] GaussianOn1DLattice.isCorrect 31: [ OK ] GaussianOn1DLattice.isCorrect (0 ms) 31: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero 31: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms) 31: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange 31: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms) 31: [----------] 4 tests from GaussianOn1DLattice (0 ms total) 31: 31: [----------] 9 tests from GaussTransformTest 31: [ RUN ] GaussTransformTest.isZeroUponConstruction 31: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms) 31: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss 31: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms) 31: [ RUN ] GaussTransformTest.isZeroAfterSettingZero 31: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms) 31: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX 31: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms) 31: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY 31: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms) 31: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ 31: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms) 31: [ RUN ] GaussTransformTest.complementaryGaussAddToZero 31: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms) 31: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues 31: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (1 ms) 31: [ RUN ] GaussTransformTest.view 31: [ OK ] GaussTransformTest.view (0 ms) 31: [----------] 9 tests from GaussTransformTest (1 ms total) 31: 31: [----------] 3 tests from DensityFittingForce 31: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity 31: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms) 31: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections 31: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms) 31: [ RUN ] DensityFittingForce.pullsTowardsDerivative 31: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms) 31: [----------] 3 tests from DensityFittingForce (0 ms total) 31: 31: [----------] 2 tests from InvertMatrixTest 31: [ RUN ] InvertMatrixTest.IdentityIsImpotent 31: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 31: [ RUN ] InvertMatrixTest.ComputesInverse 31: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 31: [----------] 2 tests from InvertMatrixTest (0 ms total) 31: 31: [----------] 17 tests from MatrixTest 31: [ RUN ] MatrixTest.canSetFromArray 31: [ OK ] MatrixTest.canSetFromArray (0 ms) 31: [ RUN ] MatrixTest.canSetStaticallyFromList 31: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms) 31: [ RUN ] MatrixTest.canConstructAndFill 31: [ OK ] MatrixTest.canConstructAndFill (0 ms) 31: [ RUN ] MatrixTest.canSetValues 31: [ OK ] MatrixTest.canSetValues (0 ms) 31: [ RUN ] MatrixTest.canCopyAssign 31: [ OK ] MatrixTest.canCopyAssign (0 ms) 31: [ RUN ] MatrixTest.canSwap 31: [ OK ] MatrixTest.canSwap (0 ms) 31: [ RUN ] MatrixTest.staticMultiDimArrayExtent 31: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms) 31: [ RUN ] MatrixTest.determinantWorks 31: [ OK ] MatrixTest.determinantWorks (0 ms) 31: [ RUN ] MatrixTest.noninvertableDeterminantIsZero 31: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms) 31: [ RUN ] MatrixTest.determinantOfDiagonalMatrix 31: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms) 31: [ RUN ] MatrixTest.traceWorks 31: [ OK ] MatrixTest.traceWorks (0 ms) 31: [ RUN ] MatrixTest.transposeWorks 31: [ OK ] MatrixTest.transposeWorks (0 ms) 31: [ RUN ] MatrixTest.transposeOfSymmetricMatrix 31: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms) 31: [ RUN ] MatrixTest.canCreateFromLegacyMatrix 31: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms) 31: [ RUN ] MatrixTest.canFillLegacyMatrix 31: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms) 31: [ RUN ] MatrixTest.IdentityMatrix 31: [ OK ] MatrixTest.IdentityMatrix (0 ms) 31: [ RUN ] MatrixTest.MatrixVectorMultiplication 31: [ OK ] MatrixTest.MatrixVectorMultiplication (0 ms) 31: [----------] 17 tests from MatrixTest (0 ms total) 31: 31: [----------] 25 tests from MultiDimArrayTest 31: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic 31: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms) 31: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic 31: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms) 31: [ RUN ] MultiDimArrayTest.canSetValuesInStatic 31: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms) 31: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic 31: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms) 31: [ RUN ] MultiDimArrayTest.canMoveConstructStatic 31: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms) 31: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic 31: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms) 31: [ RUN ] MultiDimArrayTest.canMoveAssignStatic 31: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms) 31: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic 31: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms) 31: [ RUN ] MultiDimArrayTest.canCopyConstructStatic 31: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms) 31: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic 31: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms) 31: [ RUN ] MultiDimArrayTest.canCopyAssignStatic 31: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms) 31: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic 31: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms) 31: [ RUN ] MultiDimArrayTest.canSwapStatic 31: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms) 31: [ RUN ] MultiDimArrayTest.canSwapDynamic 31: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms) 31: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent 31: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms) 31: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent 31: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms) 31: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent 31: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms) 31: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue 31: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms) 31: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray 31: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms) 31: [ RUN ] MultiDimArrayTest.conversionToView 31: [ OK ] MultiDimArrayTest.conversionToView (0 ms) 31: [ RUN ] MultiDimArrayTest.conversionToConstView 31: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms) 31: [ RUN ] MultiDimArrayTest.viewBegin 31: [ OK ] MultiDimArrayTest.viewBegin (0 ms) 31: [ RUN ] MultiDimArrayTest.viewEnd 31: [ OK ] MultiDimArrayTest.viewEnd (0 ms) 31: [ RUN ] MultiDimArrayTest.constViewConstBegin 31: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms) 31: [ RUN ] MultiDimArrayTest.constViewConstEnd 31: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms) 31: [----------] 25 tests from MultiDimArrayTest (0 ms total) 31: 31: [----------] 4 tests from MultiDimArrayToMdSpanTest 31: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan 31: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms) 31: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan 31: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms) 31: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan 31: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms) 31: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan 31: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms) 31: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total) 31: 31: [----------] 9 tests from NelderMeadSimplexTest 31: [ RUN ] NelderMeadSimplexTest.BestVertex 31: [ OK ] NelderMeadSimplexTest.BestVertex (0 ms) 31: [ RUN ] NelderMeadSimplexTest.WorstVertex 31: [ OK ] NelderMeadSimplexTest.WorstVertex (0 ms) 31: [ RUN ] NelderMeadSimplexTest.SecondWorstValue 31: [ OK ] NelderMeadSimplexTest.SecondWorstValue (0 ms) 31: [ RUN ] NelderMeadSimplexTest.ReflectionPoint 31: [ OK ] NelderMeadSimplexTest.ReflectionPoint (0 ms) 31: [ RUN ] NelderMeadSimplexTest.EvaluateExpansionPoint 31: [ OK ] NelderMeadSimplexTest.EvaluateExpansionPoint (0 ms) 31: [ RUN ] NelderMeadSimplexTest.EvaluateContractionPoint 31: [ OK ] NelderMeadSimplexTest.EvaluateContractionPoint (0 ms) 31: [ RUN ] NelderMeadSimplexTest.SwapOutWorst 31: [ OK ] NelderMeadSimplexTest.SwapOutWorst (0 ms) 31: [ RUN ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest 31: [ OK ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest (0 ms) 31: [ RUN ] NelderMeadSimplexTest.OrientedLength 31: [ OK ] NelderMeadSimplexTest.OrientedLength (0 ms) 31: [----------] 9 tests from NelderMeadSimplexTest (0 ms total) 31: 31: [----------] 2 tests from NelderMead 31: [ RUN ] NelderMead.Optimizes2DFunctionCorrectly 31: [ OK ] NelderMead.Optimizes2DFunctionCorrectly (0 ms) 31: [ RUN ] NelderMead.Optimizes3DFunctorCorrectly 31: [ OK ] NelderMead.Optimizes3DFunctorCorrectly (0 ms) 31: [----------] 2 tests from NelderMead (0 ms total) 31: 31: [----------] 11 tests from PaddedVectorTest/0, where TypeParam = std::allocator 31: [ RUN ] PaddedVectorTest/0.DefaultConstructorWorks 31: [ OK ] PaddedVectorTest/0.DefaultConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/0.ResizeWorks 31: [ OK ] PaddedVectorTest/0.ResizeWorks (1 ms) 31: [ RUN ] PaddedVectorTest/0.ReserveWorks 31: [ OK ] PaddedVectorTest/0.ReserveWorks (0 ms) 31: [ RUN ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve 31: [ OK ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve (0 ms) 31: [ RUN ] PaddedVectorTest/0.MoveConstructorWorks 31: [ OK ] PaddedVectorTest/0.MoveConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks 31: [ OK ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/0.MoveAssignmentWorks 31: [ OK ] PaddedVectorTest/0.MoveAssignmentWorks (0 ms) 31: [ RUN ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical 31: [ OK ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical (0 ms) 31: [ RUN ] PaddedVectorTest/0.CanCopyAssign 31: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 31: [ RUN ] PaddedVectorTest/0.CanMoveAssign 31: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 31: [ RUN ] PaddedVectorTest/0.CanSwap 31: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 31: [----------] 11 tests from PaddedVectorTest/0 (1 ms total) 31: 31: [----------] 11 tests from PaddedVectorTest/1, where TypeParam = std::allocator 31: [ RUN ] PaddedVectorTest/1.DefaultConstructorWorks 31: [ OK ] PaddedVectorTest/1.DefaultConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/1.ResizeWorks 31: [ OK ] PaddedVectorTest/1.ResizeWorks (0 ms) 31: [ RUN ] PaddedVectorTest/1.ReserveWorks 31: [ OK ] PaddedVectorTest/1.ReserveWorks (0 ms) 31: [ RUN ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve 31: [ OK ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve (0 ms) 31: [ RUN ] PaddedVectorTest/1.MoveConstructorWorks 31: [ OK ] PaddedVectorTest/1.MoveConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks 31: [ OK ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/1.MoveAssignmentWorks 31: [ OK ] PaddedVectorTest/1.MoveAssignmentWorks (0 ms) 31: [ RUN ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical 31: [ OK ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical (0 ms) 31: [ RUN ] PaddedVectorTest/1.CanCopyAssign 31: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 31: [ RUN ] PaddedVectorTest/1.CanMoveAssign 31: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 31: [ RUN ] PaddedVectorTest/1.CanSwap 31: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 31: [----------] 11 tests from PaddedVectorTest/1 (0 ms total) 31: 31: [----------] 11 tests from PaddedVectorTest/2, where TypeParam = std::allocator 31: [ RUN ] PaddedVectorTest/2.DefaultConstructorWorks 31: [ OK ] PaddedVectorTest/2.DefaultConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/2.ResizeWorks 31: [ OK ] PaddedVectorTest/2.ResizeWorks (0 ms) 31: [ RUN ] PaddedVectorTest/2.ReserveWorks 31: [ OK ] PaddedVectorTest/2.ReserveWorks (0 ms) 31: [ RUN ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve 31: [ OK ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve (0 ms) 31: [ RUN ] PaddedVectorTest/2.MoveConstructorWorks 31: [ OK ] PaddedVectorTest/2.MoveConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks 31: [ OK ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/2.MoveAssignmentWorks 31: [ OK ] PaddedVectorTest/2.MoveAssignmentWorks (0 ms) 31: [ RUN ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical 31: [ OK ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical (0 ms) 31: [ RUN ] PaddedVectorTest/2.CanCopyAssign 31: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 31: [ RUN ] PaddedVectorTest/2.CanMoveAssign 31: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 31: [ RUN ] PaddedVectorTest/2.CanSwap 31: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 31: [----------] 11 tests from PaddedVectorTest/2 (0 ms total) 31: 31: [----------] 11 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 31: [ RUN ] PaddedVectorTest/3.DefaultConstructorWorks 31: [ OK ] PaddedVectorTest/3.DefaultConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/3.ResizeWorks 31: [ OK ] PaddedVectorTest/3.ResizeWorks (0 ms) 31: [ RUN ] PaddedVectorTest/3.ReserveWorks 31: [ OK ] PaddedVectorTest/3.ReserveWorks (0 ms) 31: [ RUN ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve 31: [ OK ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve (0 ms) 31: [ RUN ] PaddedVectorTest/3.MoveConstructorWorks 31: [ OK ] PaddedVectorTest/3.MoveConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks 31: [ OK ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/3.MoveAssignmentWorks 31: [ OK ] PaddedVectorTest/3.MoveAssignmentWorks (0 ms) 31: [ RUN ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical 31: [ OK ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical (0 ms) 31: [ RUN ] PaddedVectorTest/3.CanCopyAssign 31: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 31: [ RUN ] PaddedVectorTest/3.CanMoveAssign 31: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 31: [ RUN ] PaddedVectorTest/3.CanSwap 31: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 31: [----------] 11 tests from PaddedVectorTest/3 (0 ms total) 31: 31: [----------] 11 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 31: [ RUN ] PaddedVectorTest/4.DefaultConstructorWorks 31: [ OK ] PaddedVectorTest/4.DefaultConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/4.ResizeWorks 31: [ OK ] PaddedVectorTest/4.ResizeWorks (0 ms) 31: [ RUN ] PaddedVectorTest/4.ReserveWorks 31: [ OK ] PaddedVectorTest/4.ReserveWorks (0 ms) 31: [ RUN ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve 31: [ OK ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve (0 ms) 31: [ RUN ] PaddedVectorTest/4.MoveConstructorWorks 31: [ OK ] PaddedVectorTest/4.MoveConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks 31: [ OK ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/4.MoveAssignmentWorks 31: [ OK ] PaddedVectorTest/4.MoveAssignmentWorks (0 ms) 31: [ RUN ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical 31: [ OK ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical (0 ms) 31: [ RUN ] PaddedVectorTest/4.CanCopyAssign 31: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 31: [ RUN ] PaddedVectorTest/4.CanMoveAssign 31: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 31: [ RUN ] PaddedVectorTest/4.CanSwap 31: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 31: [----------] 11 tests from PaddedVectorTest/4 (0 ms total) 31: 31: [----------] 11 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 31: [ RUN ] PaddedVectorTest/5.DefaultConstructorWorks 31: [ OK ] PaddedVectorTest/5.DefaultConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/5.ResizeWorks 31: [ OK ] PaddedVectorTest/5.ResizeWorks (0 ms) 31: [ RUN ] PaddedVectorTest/5.ReserveWorks 31: [ OK ] PaddedVectorTest/5.ReserveWorks (0 ms) 31: [ RUN ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve 31: [ OK ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve (0 ms) 31: [ RUN ] PaddedVectorTest/5.MoveConstructorWorks 31: [ OK ] PaddedVectorTest/5.MoveConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks 31: [ OK ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/5.MoveAssignmentWorks 31: [ OK ] PaddedVectorTest/5.MoveAssignmentWorks (0 ms) 31: [ RUN ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical 31: [ OK ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical (0 ms) 31: [ RUN ] PaddedVectorTest/5.CanCopyAssign 31: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 31: [ RUN ] PaddedVectorTest/5.CanMoveAssign 31: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 31: [ RUN ] PaddedVectorTest/5.CanSwap 31: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 31: [----------] 11 tests from PaddedVectorTest/5 (0 ms total) 31: 31: [----------] 11 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 31: [ RUN ] PaddedVectorTest/6.DefaultConstructorWorks 31: [ OK ] PaddedVectorTest/6.DefaultConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/6.ResizeWorks 31: [ OK ] PaddedVectorTest/6.ResizeWorks (0 ms) 31: [ RUN ] PaddedVectorTest/6.ReserveWorks 31: [ OK ] PaddedVectorTest/6.ReserveWorks (0 ms) 31: [ RUN ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve 31: [ OK ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve (0 ms) 31: [ RUN ] PaddedVectorTest/6.MoveConstructorWorks 31: [ OK ] PaddedVectorTest/6.MoveConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks 31: [ OK ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/6.MoveAssignmentWorks 31: [ OK ] PaddedVectorTest/6.MoveAssignmentWorks (0 ms) 31: [ RUN ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical 31: [ OK ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical (0 ms) 31: [ RUN ] PaddedVectorTest/6.CanCopyAssign 31: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 31: [ RUN ] PaddedVectorTest/6.CanMoveAssign 31: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 31: [ RUN ] PaddedVectorTest/6.CanSwap 31: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 31: [----------] 11 tests from PaddedVectorTest/6 (0 ms total) 31: 31: [----------] 11 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 31: [ RUN ] PaddedVectorTest/7.DefaultConstructorWorks 31: [ OK ] PaddedVectorTest/7.DefaultConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/7.ResizeWorks 31: [ OK ] PaddedVectorTest/7.ResizeWorks (0 ms) 31: [ RUN ] PaddedVectorTest/7.ReserveWorks 31: [ OK ] PaddedVectorTest/7.ReserveWorks (0 ms) 31: [ RUN ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve 31: [ OK ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve (0 ms) 31: [ RUN ] PaddedVectorTest/7.MoveConstructorWorks 31: [ OK ] PaddedVectorTest/7.MoveConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks 31: [ OK ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/7.MoveAssignmentWorks 31: [ OK ] PaddedVectorTest/7.MoveAssignmentWorks (0 ms) 31: [ RUN ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical 31: [ OK ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical (0 ms) 31: [ RUN ] PaddedVectorTest/7.CanCopyAssign 31: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 31: [ RUN ] PaddedVectorTest/7.CanMoveAssign 31: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 31: [ RUN ] PaddedVectorTest/7.CanSwap 31: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 31: [----------] 11 tests from PaddedVectorTest/7 (0 ms total) 31: 31: [----------] 11 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 31: [ RUN ] PaddedVectorTest/8.DefaultConstructorWorks 31: [ OK ] PaddedVectorTest/8.DefaultConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/8.ResizeWorks 31: [ OK ] PaddedVectorTest/8.ResizeWorks (0 ms) 31: [ RUN ] PaddedVectorTest/8.ReserveWorks 31: [ OK ] PaddedVectorTest/8.ReserveWorks (0 ms) 31: [ RUN ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve 31: [ OK ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve (0 ms) 31: [ RUN ] PaddedVectorTest/8.MoveConstructorWorks 31: [ OK ] PaddedVectorTest/8.MoveConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks 31: [ OK ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/8.MoveAssignmentWorks 31: [ OK ] PaddedVectorTest/8.MoveAssignmentWorks (0 ms) 31: [ RUN ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical 31: [ OK ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical (0 ms) 31: [ RUN ] PaddedVectorTest/8.CanCopyAssign 31: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 31: [ RUN ] PaddedVectorTest/8.CanMoveAssign 31: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 31: [ RUN ] PaddedVectorTest/8.CanSwap 31: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 31: [----------] 11 tests from PaddedVectorTest/8 (0 ms total) 31: 31: [----------] 11 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 31: [ RUN ] PaddedVectorTest/9.DefaultConstructorWorks 31: [ OK ] PaddedVectorTest/9.DefaultConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/9.ResizeWorks 31: [ OK ] PaddedVectorTest/9.ResizeWorks (0 ms) 31: [ RUN ] PaddedVectorTest/9.ReserveWorks 31: [ OK ] PaddedVectorTest/9.ReserveWorks (0 ms) 31: [ RUN ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve 31: [ OK ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve (0 ms) 31: [ RUN ] PaddedVectorTest/9.MoveConstructorWorks 31: [ OK ] PaddedVectorTest/9.MoveConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks 31: [ OK ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/9.MoveAssignmentWorks 31: [ OK ] PaddedVectorTest/9.MoveAssignmentWorks (0 ms) 31: [ RUN ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical 31: [ OK ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical (0 ms) 31: [ RUN ] PaddedVectorTest/9.CanCopyAssign 31: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 31: [ RUN ] PaddedVectorTest/9.CanMoveAssign 31: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 31: [ RUN ] PaddedVectorTest/9.CanSwap 31: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 31: [----------] 11 tests from PaddedVectorTest/9 (0 ms total) 31: 31: [----------] 40 tests from RVecTest 31: [ RUN ] RVecTest.CanBeStoredInVector 31: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 31: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 31: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 31: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 31: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 31: [ RUN ] RVecTest.WorksAsMutable_rvec 31: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 31: [ RUN ] RVecTest.WorksAs_rvec_Array 31: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 31: [ RUN ] RVecTest.ComparesEqual 31: [ OK ] RVecTest.ComparesEqual (0 ms) 31: [ RUN ] RVecTest.ComparesUnequal 31: [ OK ] RVecTest.ComparesUnequal (0 ms) 31: [ RUN ] RVecTest.CanAddRVecToRvec 31: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 31: [ RUN ] RVecTest.CanAddAssignRVecToRvec 31: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 31: [ RUN ] RVecTest.CanSubtractRVecFromRvec 31: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 31: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 31: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 31: [ RUN ] RVecTest.CanDotProductRVecByRvec 31: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 31: [ RUN ] RVecTest.CanCrossProductRVecByRvec 31: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 31: [ RUN ] RVecTest.CanDivideRVecInplace 31: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 31: [ RUN ] RVecTest.CanScaleRVec 31: [ OK ] RVecTest.CanScaleRVec (0 ms) 31: [ RUN ] RVecTest.CanDivideRVec 31: [ OK ] RVecTest.CanDivideRVec (0 ms) 31: [ RUN ] RVecTest.CanDoUnitvFromRVec 31: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 31: [ RUN ] RVecTest.CanSqLengthOfRVec 31: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 31: [ RUN ] RVecTest.CanLengthOfRVec 31: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 31: [ RUN ] RVecTest.CanCastToRVec 31: [ OK ] RVecTest.CanCastToRVec (0 ms) 31: [ RUN ] RVecTest.CanCastToDVec 31: [ OK ] RVecTest.CanCastToDVec (0 ms) 31: [ RUN ] RVecTest.CanLeftScalarMultiply 31: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 31: [ RUN ] RVecTest.CanRightScalarMultiply 31: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 31: [ RUN ] RVecTest.CanGetUnitvFromRVec 31: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 31: [ RUN ] RVecTest.CanGetSqLengthOfRVec 31: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 31: [ RUN ] RVecTest.CanGetLengthOfRVec 31: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 31: [ RUN ] RVecTest.CanDoCrossProductOfRVec 31: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 31: [ RUN ] RVecTest.CanDoDotProductOfRVec 31: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 31: [ RUN ] RVecTest.CanScaleByVector 31: [ OK ] RVecTest.CanScaleByVector (0 ms) 31: [ RUN ] RVecTest.CanNegate 31: [ OK ] RVecTest.CanNegate (0 ms) 31: [ RUN ] RVecTest.asIVec 31: [ OK ] RVecTest.asIVec (0 ms) 31: [ RUN ] RVecTest.elementWiseMin 31: [ OK ] RVecTest.elementWiseMin (0 ms) 31: [ RUN ] RVecTest.elementWiseMax 31: [ OK ] RVecTest.elementWiseMax (0 ms) 31: [ RUN ] RVecTest.WorksAs_dvec_Reference 31: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 31: [ RUN ] RVecTest.WorksAs_ivec_Reference 31: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 31: [ RUN ] RVecTest.WorksAs_rvec_Reference 31: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 31: [ RUN ] RVecTest.CopyConstructorWorks 31: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 31: [ RUN ] RVecTest.CopyAssignmentWorks 31: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 31: [ RUN ] RVecTest.MoveConstructorWorks 31: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 31: [ RUN ] RVecTest.MoveAssignmentWorks 31: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 31: [----------] 40 tests from RVecTest (5 ms total) 31: 31: [----------] Global test environment tear-down 31: [==========] 304 tests from 38 test suites ran. (111 ms total) 31: [ PASSED ] 304 tests. 31/87 Test #31: MathUnitTests ............................. Passed 0.16 sec test 32 Start 32: MdrunUtilityUnitTests 32: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrunutility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunUtilityUnitTests.xml" 32: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests 32: Test timeout computed to be: 30 32: [==========] Running 21 tests from 2 test suites. 32: [----------] Global test environment set-up. 32: [----------] 4 tests from MDModulesNotifierTest 32: [ RUN ] MDModulesNotifierTest.AddConsumer 32: [ OK ] MDModulesNotifierTest.AddConsumer (0 ms) 32: [ RUN ] MDModulesNotifierTest.AddConsumerWithPointerParameter 32: [ OK ] MDModulesNotifierTest.AddConsumerWithPointerParameter (0 ms) 32: [ RUN ] MDModulesNotifierTest.AddTwoDifferentConsumers 32: [ OK ] MDModulesNotifierTest.AddTwoDifferentConsumers (0 ms) 32: [ RUN ] MDModulesNotifierTest.AddConsumerOfTwoResources 32: [ OK ] MDModulesNotifierTest.AddConsumerOfTwoResources (0 ms) 32: [----------] 4 tests from MDModulesNotifierTest (0 ms total) 32: 32: [----------] 17 tests from ThreadAffinityTest 32: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 32: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 32: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 32: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 32: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 32: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms) 32: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 32: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 32: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 32: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) 32: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 32: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms) 32: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 32: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 32: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 32: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) 32: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 32: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 32: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 32: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms) 32: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 32: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) 32: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 32: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (0 ms) 32: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 32: NOTE: Affinity setting failed. 32: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) 32: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 32: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (7 ms) 32: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 32: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (7 ms) 32: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 32: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (15 ms) 32: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 32: NOTE: Affinity setting for 1/2 threads failed. 32: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (16 ms) 32: [----------] 17 tests from ThreadAffinityTest (48 ms total) 32: 32: [----------] Global test environment tear-down 32: [==========] 21 tests from 2 test suites ran. (48 ms total) 32: [ PASSED ] 21 tests. 32/87 Test #32: MdrunUtilityUnitTests ..................... Passed 0.08 sec test 33 Start 33: MdrunUtilityMpiUnitTests 33: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 33: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests 33: Test timeout computed to be: 30 33: [==========] Running 13 tests from 2 test suites. 33: [----------] Global test environment set-up. 33: [----------] 6 tests from ThreadAffinityMultiRankTest 33: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 33: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (114 ms) 33: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 33: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (108 ms) 33: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 33: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (148 ms) 33: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 33: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (19 ms) 33: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 33: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (5 ms) 33: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 33: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (74 ms) 33: [----------] 6 tests from ThreadAffinityMultiRankTest (470 ms total) 33: 33: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 33: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly 33: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly (83 ms) 33: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly 33: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly (123 ms) 33: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain 33: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain (24 ms) 33: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly 33: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly (67 ms) 33: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly 33: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly (109 ms) 33: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly 33: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly (94 ms) 33: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly 33: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly (4 ms) 33: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (512 ms total) 33: 33: [----------] Global test environment tear-down 33: [==========] 13 tests from 2 test suites ran. (983 ms total) 33: [ PASSED ] 13 tests. 33/87 Test #33: MdrunUtilityMpiUnitTests .................. Passed 1.01 sec test 34 Start 34: MDSpanTests 34: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdspan-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MDSpanTests.xml" 34: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdspan/tests 34: Test timeout computed to be: 30 34: [==========] Running 32 tests from 7 test suites. 34: [----------] Global test environment set-up. 34: [----------] 4 tests from BasicAccessorPolicy 34: [ RUN ] BasicAccessorPolicy.Decay 34: [ OK ] BasicAccessorPolicy.Decay (0 ms) 34: [ RUN ] BasicAccessorPolicy.Access 34: [ OK ] BasicAccessorPolicy.Access (0 ms) 34: [ RUN ] BasicAccessorPolicy.Offset 34: [ OK ] BasicAccessorPolicy.Offset (0 ms) 34: [ RUN ] BasicAccessorPolicy.CopyAccessor 34: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms) 34: [----------] 4 tests from BasicAccessorPolicy (0 ms total) 34: 34: [----------] 4 tests from ExtentsTest 34: [ RUN ] ExtentsTest.Construction 34: [ OK ] ExtentsTest.Construction (0 ms) 34: [ RUN ] ExtentsTest.PurelyStatic 34: [ OK ] ExtentsTest.PurelyStatic (0 ms) 34: [ RUN ] ExtentsTest.RankNought 34: [ OK ] ExtentsTest.RankNought (0 ms) 34: [ RUN ] ExtentsTest.Assignment 34: [ OK ] ExtentsTest.Assignment (0 ms) 34: [----------] 4 tests from ExtentsTest (0 ms total) 34: 34: [----------] 8 tests from MdSpanExtension 34: [ RUN ] MdSpanExtension.SlicingAllStatic 34: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms) 34: [ RUN ] MdSpanExtension.SlicingDynamic 34: [ OK ] MdSpanExtension.SlicingDynamic (0 ms) 34: [ RUN ] MdSpanExtension.SlicingAllStatic3D 34: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms) 34: [ RUN ] MdSpanExtension.SlicingEqualsView3D 34: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms) 34: [ RUN ] MdSpanExtension.additionWorks 34: [ OK ] MdSpanExtension.additionWorks (0 ms) 34: [ RUN ] MdSpanExtension.subtractionWorks 34: [ OK ] MdSpanExtension.subtractionWorks (0 ms) 34: [ RUN ] MdSpanExtension.multiplicationWorks 34: [ OK ] MdSpanExtension.multiplicationWorks (0 ms) 34: [ RUN ] MdSpanExtension.divisionWorks 34: [ OK ] MdSpanExtension.divisionWorks (0 ms) 34: [----------] 8 tests from MdSpanExtension (0 ms total) 34: 34: [----------] 3 tests from LayoutTests 34: [ RUN ] LayoutTests.LayoutRightConstruction 34: [ OK ] LayoutTests.LayoutRightConstruction (0 ms) 34: [ RUN ] LayoutTests.LayoutRightProperties 34: [ OK ] LayoutTests.LayoutRightProperties (0 ms) 34: [ RUN ] LayoutTests.LayoutRightOperator 34: [ OK ] LayoutTests.LayoutRightOperator (0 ms) 34: [----------] 3 tests from LayoutTests (0 ms total) 34: 34: [----------] 1 test from MdSpanTest 34: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly 34: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms) 34: [----------] 1 test from MdSpanTest (0 ms total) 34: 34: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 34: [ RUN ] MdSpanTest/0.Rank 34: [ OK ] MdSpanTest/0.Rank (0 ms) 34: [ RUN ] MdSpanTest/0.DynamicRank 34: [ OK ] MdSpanTest/0.DynamicRank (0 ms) 34: [ RUN ] MdSpanTest/0.Extents 34: [ OK ] MdSpanTest/0.Extents (0 ms) 34: [ RUN ] MdSpanTest/0.Strides 34: [ OK ] MdSpanTest/0.Strides (0 ms) 34: [ RUN ] MdSpanTest/0.Properties 34: [ OK ] MdSpanTest/0.Properties (0 ms) 34: [ RUN ] MdSpanTest/0.Operator 34: [ OK ] MdSpanTest/0.Operator (0 ms) 34: [----------] 6 tests from MdSpanTest/0 (0 ms total) 34: 34: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 34: [ RUN ] MdSpanTest/1.Rank 34: [ OK ] MdSpanTest/1.Rank (0 ms) 34: [ RUN ] MdSpanTest/1.DynamicRank 34: [ OK ] MdSpanTest/1.DynamicRank (0 ms) 34: [ RUN ] MdSpanTest/1.Extents 34: [ OK ] MdSpanTest/1.Extents (0 ms) 34: [ RUN ] MdSpanTest/1.Strides 34: [ OK ] MdSpanTest/1.Strides (0 ms) 34: [ RUN ] MdSpanTest/1.Properties 34: [ OK ] MdSpanTest/1.Properties (0 ms) 34: [ RUN ] MdSpanTest/1.Operator 34: [ OK ] MdSpanTest/1.Operator (0 ms) 34: [----------] 6 tests from MdSpanTest/1 (0 ms total) 34: 34: [----------] Global test environment tear-down 34: [==========] 32 tests from 7 test suites ran. (0 ms total) 34: [ PASSED ] 32 tests. 34/87 Test #34: MDSpanTests ............................... Passed 0.04 sec test 35 Start 35: MdtypesUnitTest 35: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdtypes-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdtypesUnitTest.xml" 35: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdtypes/tests 35: Test timeout computed to be: 30 35: [==========] Running 97 tests from 7 test suites. 35: [----------] Global test environment set-up. 35: [----------] 4 tests from ForeingLambdaTermsDhdl 35: [ RUN ] ForeingLambdaTermsDhdl.RateCheckWorks 35: [ OK ] ForeingLambdaTermsDhdl.RateCheckWorks (0 ms) 35: [ RUN ] ForeingLambdaTermsDhdl.AllLinear 35: [ OK ] ForeingLambdaTermsDhdl.AllLinear (0 ms) 35: [ RUN ] ForeingLambdaTermsDhdl.AllLinearNegative 35: [ OK ] ForeingLambdaTermsDhdl.AllLinearNegative (0 ms) 35: [ RUN ] ForeingLambdaTermsDhdl.SeparateVdwCoul 35: [ OK ] ForeingLambdaTermsDhdl.SeparateVdwCoul (0 ms) 35: [----------] 4 tests from ForeingLambdaTermsDhdl (0 ms total) 35: 35: [----------] 4 tests from ObservablesReducerTest 35: [ RUN ] ObservablesReducerTest.CanMoveAssign 35: [ OK ] ObservablesReducerTest.CanMoveAssign (0 ms) 35: [ RUN ] ObservablesReducerTest.CanMoveConstruct 35: [ OK ] ObservablesReducerTest.CanMoveConstruct (0 ms) 35: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers 35: [ OK ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers (0 ms) 35: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber 35: [ OK ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber (0 ms) 35: [----------] 4 tests from ObservablesReducerTest (0 ms total) 35: 35: [----------] 2 tests from CheckpointDataTest 35: [ RUN ] CheckpointDataTest.SingleDataTest 35: [ OK ] CheckpointDataTest.SingleDataTest (68 ms) 35: [ RUN ] CheckpointDataTest.MultiDataTest 35: [ OK ] CheckpointDataTest.MultiDataTest (403 ms) 35: [----------] 2 tests from CheckpointDataTest (472 ms total) 35: 35: [----------] 7 tests from ForceBuffers 35: [ RUN ] ForceBuffers.ConstructsUnpinned 35: [ OK ] ForceBuffers.ConstructsUnpinned (0 ms) 35: [ RUN ] ForceBuffers.ConstructsPinned 35: [ OK ] ForceBuffers.ConstructsPinned (0 ms) 35: [ RUN ] ForceBuffers.ConstructsEmpty 35: [ OK ] ForceBuffers.ConstructsEmpty (0 ms) 35: [ RUN ] ForceBuffers.ResizeWorks 35: [ OK ] ForceBuffers.ResizeWorks (0 ms) 35: [ RUN ] ForceBuffers.PaddingWorks 35: [ OK ] ForceBuffers.PaddingWorks (0 ms) 35: [ RUN ] ForceBuffers.CopyWorks 35: [ OK ] ForceBuffers.CopyWorks (0 ms) 35: [ RUN ] ForceBuffers.CopyDoesNotPin 35: [ OK ] ForceBuffers.CopyDoesNotPin (0 ms) 35: [----------] 7 tests from ForceBuffers (0 ms total) 35: 35: [----------] 5 tests from MultipleTimeStepping 35: [ RUN ] MultipleTimeStepping.ChecksNumLevels 35: [ OK ] MultipleTimeStepping.ChecksNumLevels (0 ms) 35: [ RUN ] MultipleTimeStepping.SelectsForceGroups 35: [ OK ] MultipleTimeStepping.SelectsForceGroups (0 ms) 35: [ RUN ] MultipleTimeStepping.ChecksStepFactor 35: [ OK ] MultipleTimeStepping.ChecksStepFactor (0 ms) 35: [ RUN ] MultipleTimeStepping.ChecksPmeIsAtLastLevel 35: [ OK ] MultipleTimeStepping.ChecksPmeIsAtLastLevel (0 ms) 35: [ RUN ] MultipleTimeStepping.ChecksIntegrator 35: [ OK ] MultipleTimeStepping.ChecksIntegrator (0 ms) 35: [----------] 5 tests from MultipleTimeStepping (0 ms total) 35: 35: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 (0 ms) 35: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest (0 ms total) 35: 35: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/0 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/0 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/1 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/1 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/2 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/2 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/3 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/3 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/4 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/4 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/5 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/5 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/6 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/6 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/7 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/7 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/8 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/8 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/9 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/9 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/10 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/10 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/11 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/11 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/12 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/12 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/13 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/13 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/14 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/14 (0 ms) 35: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest (0 ms total) 35: 35: [----------] Global test environment tear-down 35: [==========] 97 tests from 7 test suites ran. (477 ms total) 35: [ PASSED ] 97 tests. 35/87 Test #35: MdtypesUnitTest ........................... Passed 0.52 sec test 36 Start 36: OnlineHelpUnitTests 36: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/onlinehelp-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/OnlineHelpUnitTests.xml" 36: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/onlinehelp/tests 36: Test timeout computed to be: 30 36: [==========] Running 22 tests from 4 test suites. 36: [----------] Global test environment set-up. 36: [----------] 6 tests from TextTableFormatterTest 36: [ RUN ] TextTableFormatterTest.HandlesBasicCase 36: [ OK ] TextTableFormatterTest.HandlesBasicCase (2 ms) 36: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 36: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (3 ms) 36: [ RUN ] TextTableFormatterTest.HandlesIndentation 36: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) 36: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 36: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms) 36: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 36: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms) 36: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 36: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) 36: [----------] 6 tests from TextTableFormatterTest (8 ms total) 36: 36: [----------] 3 tests from HelpManagerTest 36: [ RUN ] HelpManagerTest.HandlesRootTopic 36: [ OK ] HelpManagerTest.HandlesRootTopic (1 ms) 36: [ RUN ] HelpManagerTest.HandlesSubTopics 36: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 36: [ RUN ] HelpManagerTest.HandlesInvalidTopics 36: [ OK ] HelpManagerTest.HandlesInvalidTopics (1 ms) 36: [----------] 3 tests from HelpManagerTest (3 ms total) 36: 36: [----------] 2 tests from HelpTopicFormattingTest 36: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 36: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (2 ms) 36: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 36: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) 36: [----------] 2 tests from HelpTopicFormattingTest (2 ms total) 36: 36: [----------] 11 tests from HelpWriterContextTest 36: [ RUN ] HelpWriterContextTest.FormatsParagraphs 36: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) 36: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 36: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) 36: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 36: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) 36: [ RUN ] HelpWriterContextTest.FormatsLiteralText 36: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms) 36: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 36: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) 36: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 36: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) 36: [ RUN ] HelpWriterContextTest.FormatsBulletList 36: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) 36: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 36: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) 36: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 36: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms) 36: [ RUN ] HelpWriterContextTest.FormatsGridTable 36: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms) 36: [ RUN ] HelpWriterContextTest.FormatsTitles 36: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms) 36: [----------] 11 tests from HelpWriterContextTest (7 ms total) 36: 36: [----------] Global test environment tear-down 36: [==========] 22 tests from 4 test suites ran. (22 ms total) 36: [ PASSED ] 22 tests. 36/87 Test #36: OnlineHelpUnitTests ....................... Passed 0.06 sec test 37 Start 37: OptionsUnitTests 37: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/options-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/OptionsUnitTests.xml" 37: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options/tests 37: Test timeout computed to be: 30 37: [==========] Running 111 tests from 18 test suites. 37: [----------] Global test environment set-up. 37: [----------] 5 tests from AbstractOptionStorageTest 37: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 37: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 37: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 37: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) 37: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 37: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 37: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 37: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (1 ms) 37: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 37: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 37: [----------] 5 tests from AbstractOptionStorageTest (2 ms total) 37: 37: [----------] 10 tests from FileNameOptionTest 37: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 37: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 37: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 37: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 37: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 37: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 37: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 37: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 37: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 37: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 37: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 37: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 37: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 37: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 37: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 37: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 37: [ RUN ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension 37: [ OK ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension (0 ms) 37: [ RUN ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue 37: [ OK ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue (0 ms) 37: [----------] 10 tests from FileNameOptionTest (0 ms total) 37: 37: [----------] 15 tests from FileNameOptionManagerTest 37: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 37: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 37: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 37: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 37: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 37: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) 37: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 37: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 37: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 37: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 37: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 37: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 37: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 37: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 37: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 37: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 37: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 37: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 37: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 37: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 37: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 37: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 37: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 37: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 37: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 37: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 37: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 37: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 37: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 37: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 37: [----------] 15 tests from FileNameOptionManagerTest (0 ms total) 37: 37: [----------] 1 test from OptionsTest 37: [ RUN ] OptionsTest.FailsOnNonsafeStorage 37: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 37: [----------] 1 test from OptionsTest (0 ms total) 37: 37: [----------] 9 tests from OptionsAssignerTest 37: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 37: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 37: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 37: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 37: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 37: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 37: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 37: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 37: [ RUN ] OptionsAssignerTest.HandlesMissingValue 37: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 37: [ RUN ] OptionsAssignerTest.HandlesExtraValue 37: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 37: [ RUN ] OptionsAssignerTest.HandlesGroups 37: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 37: [ RUN ] OptionsAssignerTest.HandlesSections 37: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 37: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 37: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 37: [----------] 9 tests from OptionsAssignerTest (0 ms total) 37: 37: [----------] 4 tests from OptionsAssignerBooleanTest 37: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 37: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 37: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 37: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 37: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 37: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 37: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 37: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 37: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 37: 37: [----------] 13 tests from OptionsAssignerIntegerTest 37: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 37: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 37: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 37: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 37: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 37: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 37: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 37: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 37: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 37: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 37: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 37: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 37: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 37: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 37: [----------] 13 tests from OptionsAssignerIntegerTest (0 ms total) 37: 37: [----------] 5 tests from OptionsAssignerDoubleTest 37: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 37: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 37: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 37: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 37: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 37: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 37: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 37: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 37: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 37: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 37: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) 37: 37: [----------] 9 tests from OptionsAssignerStringTest 37: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 37: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 37: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 37: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 37: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 37: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 37: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 37: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 37: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 37: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 37: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 37: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 37: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 37: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 37: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 37: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 37: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 37: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 37: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) 37: 37: [----------] 6 tests from OptionsAssignerEnumTest 37: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 37: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 37: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 37: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 37: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 37: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 37: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 37: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 37: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 37: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 37: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 37: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 37: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) 37: 37: [----------] 8 tests from RepeatingOptionSectionTest 37: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 37: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 37: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 37: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 37: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 37: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 37: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 37: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 37: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 37: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 37: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 37: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 37: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 37: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 37: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 37: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 37: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) 37: 37: [----------] 1 test from TimeUnitManagerTest 37: [ RUN ] TimeUnitManagerTest.BasicOperations 37: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 37: [----------] 1 test from TimeUnitManagerTest (0 ms total) 37: 37: [----------] 4 tests from TimeUnitBehaviorTest 37: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 37: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 37: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 37: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 37: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 37: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 37: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 37: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 37: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 37: 37: [----------] 2 tests from TreeValueSupportAssignTest 37: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 37: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 37: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 37: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 37: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) 37: 37: [----------] 1 test from TreeValueSupportAssignErrorTest 37: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 37: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 37: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 37: 37: [----------] 5 tests from TreeValueSupportCheckTest 37: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 37: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 37: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 37: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 37: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 37: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 37: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 37: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 37: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 37: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 37: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 37: 37: [----------] 6 tests from TreeValueSupportAdjustTest 37: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 37: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (12 ms) 37: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 37: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms) 37: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 37: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms) 37: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 37: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) 37: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 37: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) 37: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 37: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) 37: [----------] 6 tests from TreeValueSupportAdjustTest (15 ms total) 37: 37: [----------] 7 tests from TreeValueSupportTest 37: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 37: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms) 37: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 37: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms) 37: [ RUN ] TreeValueSupportTest.SupportsInt64Option 37: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms) 37: [ RUN ] TreeValueSupportTest.SupportsStringOption 37: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) 37: [ RUN ] TreeValueSupportTest.SupportsFloatOption 37: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) 37: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 37: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) 37: [ RUN ] TreeValueSupportTest.SupportsEnumOption 37: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) 37: [----------] 7 tests from TreeValueSupportTest (10 ms total) 37: 37: [----------] Global test environment tear-down 37: [==========] 111 tests from 18 test suites ran. (29 ms total) 37: [ PASSED ] 111 tests. 37/87 Test #37: OptionsUnitTests .......................... Passed 0.07 sec test 38 Start 38: PbcutilUnitTest 38: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/pbcutil-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/PbcutilUnitTest.xml" 38: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pbcutil/tests 38: Test timeout computed to be: 30 38: [==========] Running 37 tests from 5 test suites. 38: [----------] Global test environment set-up. 38: [----------] 1 test from ShiftTest 38: [ RUN ] ShiftTest.CoordinateShiftWorks 38: [ OK ] ShiftTest.CoordinateShiftWorks (0 ms) 38: [----------] 1 test from ShiftTest (0 ms total) 38: 38: [----------] 2 tests from MShift 38: [ RUN ] MShift.shiftsAndUnshifts 38: [ OK ] MShift.shiftsAndUnshifts (0 ms) 38: [ RUN ] MShift.shiftsAndUnshiftsSelf 38: [ OK ] MShift.shiftsAndUnshiftsSelf (0 ms) 38: [----------] 2 tests from MShift (0 ms total) 38: 38: [----------] 5 tests from PbcTest 38: [ RUN ] PbcTest.CalcShiftsWorks 38: [ OK ] PbcTest.CalcShiftsWorks (1 ms) 38: [ RUN ] PbcTest.PutAtomsInCubicBoxAlreadyInBox 38: [ OK ] PbcTest.PutAtomsInCubicBoxAlreadyInBox (0 ms) 38: [ RUN ] PbcTest.PutAtomsInCubicBoxFromOutsideBox 38: [ OK ] PbcTest.PutAtomsInCubicBoxFromOutsideBox (0 ms) 38: [ RUN ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox 38: [ OK ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox (0 ms) 38: [ RUN ] PbcTest.PutAtomsInBoxHandlesInf 38: [ OK ] PbcTest.PutAtomsInBoxHandlesInf (0 ms) 38: [----------] 5 tests from PbcTest (1 ms total) 38: 38: [----------] 2 tests from PbcEnumsTest 38: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect 38: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms) 38: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect 38: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms) 38: [----------] 2 tests from PbcEnumsTest (0 ms total) 38: 38: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 (2 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 (1 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 (1 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 (1 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 (0 ms) 38: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest (29 ms total) 38: 38: [----------] Global test environment tear-down 38: [==========] 37 tests from 5 test suites ran. (30 ms total) 38: [ PASSED ] 37 tests. 38/87 Test #38: PbcutilUnitTest ........................... Passed 0.06 sec test 39 Start 39: RandomUnitTests 39: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/random-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/RandomUnitTests.xml" 39: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/random/tests 39: Test timeout computed to be: 30 39: [==========] Running 44 tests from 10 test suites. 39: [----------] Global test environment set-up. 39: [----------] 4 tests from ExponentialDistributionTest 39: [ RUN ] ExponentialDistributionTest.Output 39: [ OK ] ExponentialDistributionTest.Output (0 ms) 39: [ RUN ] ExponentialDistributionTest.Logical 39: [ OK ] ExponentialDistributionTest.Logical (0 ms) 39: [ RUN ] ExponentialDistributionTest.Reset 39: [ OK ] ExponentialDistributionTest.Reset (0 ms) 39: [ RUN ] ExponentialDistributionTest.AltParam 39: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 39: [----------] 4 tests from ExponentialDistributionTest (0 ms total) 39: 39: [----------] 4 tests from GammaDistributionTest 39: [ RUN ] GammaDistributionTest.Output 39: [ OK ] GammaDistributionTest.Output (0 ms) 39: [ RUN ] GammaDistributionTest.Logical 39: [ OK ] GammaDistributionTest.Logical (0 ms) 39: [ RUN ] GammaDistributionTest.Reset 39: [ OK ] GammaDistributionTest.Reset (0 ms) 39: [ RUN ] GammaDistributionTest.AltParam 39: [ OK ] GammaDistributionTest.AltParam (0 ms) 39: [----------] 4 tests from GammaDistributionTest (0 ms total) 39: 39: [----------] 4 tests from NormalDistributionTest 39: [ RUN ] NormalDistributionTest.Output 39: [ OK ] NormalDistributionTest.Output (3 ms) 39: [ RUN ] NormalDistributionTest.Logical 39: [ OK ] NormalDistributionTest.Logical (0 ms) 39: [ RUN ] NormalDistributionTest.Reset 39: [ OK ] NormalDistributionTest.Reset (0 ms) 39: [ RUN ] NormalDistributionTest.AltParam 39: [ OK ] NormalDistributionTest.AltParam (0 ms) 39: [----------] 4 tests from NormalDistributionTest (3 ms total) 39: 39: [----------] 1 test from SeedTest 39: [ RUN ] SeedTest.makeRandomSeed 39: [ OK ] SeedTest.makeRandomSeed (0 ms) 39: [----------] 1 test from SeedTest (0 ms total) 39: 39: [----------] 6 tests from TabulatedNormalDistributionTest 39: [ RUN ] TabulatedNormalDistributionTest.Output14 39: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) 39: [ RUN ] TabulatedNormalDistributionTest.Output16 39: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms) 39: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 39: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (2 ms) 39: [ RUN ] TabulatedNormalDistributionTest.Logical 39: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 39: [ RUN ] TabulatedNormalDistributionTest.Reset 39: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 39: [ RUN ] TabulatedNormalDistributionTest.AltParam 39: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 39: [----------] 6 tests from TabulatedNormalDistributionTest (3 ms total) 39: 39: [----------] 1 test from TabulatedNormalDistributionTableTest 39: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 39: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (0 ms) 39: [----------] 1 test from TabulatedNormalDistributionTableTest (0 ms total) 39: 39: [----------] 6 tests from ThreeFry2x64Test 39: [ RUN ] ThreeFry2x64Test.Logical 39: [ OK ] ThreeFry2x64Test.Logical (0 ms) 39: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 39: [ OK ] ThreeFry2x64Test.InternalCounterSequence (3 ms) 39: [ RUN ] ThreeFry2x64Test.Reseed 39: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 39: [ RUN ] ThreeFry2x64Test.Discard 39: [ OK ] ThreeFry2x64Test.Discard (0 ms) 39: [ RUN ] ThreeFry2x64Test.InvalidCounter 39: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) 39: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 39: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 39: [----------] 6 tests from ThreeFry2x64Test (3 ms total) 39: 39: [----------] 4 tests from UniformIntDistributionTest 39: [ RUN ] UniformIntDistributionTest.Output 39: [ OK ] UniformIntDistributionTest.Output (1 ms) 39: [ RUN ] UniformIntDistributionTest.Logical 39: [ OK ] UniformIntDistributionTest.Logical (0 ms) 39: [ RUN ] UniformIntDistributionTest.Reset 39: [ OK ] UniformIntDistributionTest.Reset (0 ms) 39: [ RUN ] UniformIntDistributionTest.AltParam 39: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 39: [----------] 4 tests from UniformIntDistributionTest (1 ms total) 39: 39: [----------] 5 tests from UniformRealDistributionTest 39: [ RUN ] UniformRealDistributionTest.GenerateCanonical 39: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) 39: [ RUN ] UniformRealDistributionTest.Output 39: [ OK ] UniformRealDistributionTest.Output (0 ms) 39: [ RUN ] UniformRealDistributionTest.Logical 39: [ OK ] UniformRealDistributionTest.Logical (0 ms) 39: [ RUN ] UniformRealDistributionTest.Reset 39: [ OK ] UniformRealDistributionTest.Reset (0 ms) 39: [ RUN ] UniformRealDistributionTest.AltParam 39: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 39: [----------] 5 tests from UniformRealDistributionTest (2 ms total) 39: 39: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 39: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 39: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms) 39: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 39: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (1 ms) 39: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 39: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) 39: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 39: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 39: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 39: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) 39: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 39: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) 39: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 39: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 39: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 39: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) 39: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 39: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (3 ms) 39: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (16 ms total) 39: 39: [----------] Global test environment tear-down 39: [==========] 44 tests from 10 test suites ran. (34 ms total) 39: [ PASSED ] 44 tests. 39/87 Test #39: RandomUnitTests ........................... Passed 0.07 sec test 40 Start 40: RestraintTests 40: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/restraintpotential-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/RestraintTests.xml" 40: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/restraint/tests 40: Test timeout computed to be: 30 40: [==========] Running 1 test from 1 test suite. 40: [----------] Global test environment set-up. 40: [----------] 1 test from RestraintManager 40: [ RUN ] RestraintManager.restraintList 40: [ OK ] RestraintManager.restraintList (0 ms) 40: [----------] 1 test from RestraintManager (0 ms total) 40: 40: [----------] Global test environment tear-down 40: [==========] 1 test from 1 test suite ran. (0 ms total) 40: [ PASSED ] 1 test. 40/87 Test #40: RestraintTests ............................ Passed 0.03 sec test 41 Start 41: TableUnitTests 41: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/table-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/TableUnitTests.xml" 41: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tables/tests 41: Test timeout computed to be: 30 41: [==========] Running 20 tests from 2 test suites. 41: [----------] Global test environment set-up. 41: [----------] 10 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 41: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 41: [ OK ] SplineTableTest/0.HandlesIncorrectInput (0 ms) 41: [ RUN ] SplineTableTest/0.Sinc 41: [ OK ] SplineTableTest/0.Sinc (0 ms) 41: [ RUN ] SplineTableTest/0.LJ12 41: [ OK ] SplineTableTest/0.LJ12 (10 ms) 41: [ RUN ] SplineTableTest/0.PmeCorrection 41: [ OK ] SplineTableTest/0.PmeCorrection (0 ms) 41: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 41: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (0 ms) 41: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 41: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (0 ms) 41: [ RUN ] SplineTableTest/0.TwoFunctions 41: [ OK ] SplineTableTest/0.TwoFunctions (18 ms) 41: [ RUN ] SplineTableTest/0.ThreeFunctions 41: [ OK ] SplineTableTest/0.ThreeFunctions (22 ms) 41: [ RUN ] SplineTableTest/0.Simd 41: [ OK ] SplineTableTest/0.Simd (1 ms) 41: [ RUN ] SplineTableTest/0.SimdTwoFunctions 41: [ OK ] SplineTableTest/0.SimdTwoFunctions (17 ms) 41: [----------] 10 tests from SplineTableTest/0 (79 ms total) 41: 41: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 41: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 41: [ OK ] SplineTableTest/1.HandlesIncorrectInput (0 ms) 41: [ RUN ] SplineTableTest/1.Sinc 41: [ OK ] SplineTableTest/1.Sinc (0 ms) 41: [ RUN ] SplineTableTest/1.LJ12 41: [ OK ] SplineTableTest/1.LJ12 (27 ms) 41: [ RUN ] SplineTableTest/1.PmeCorrection 41: [ OK ] SplineTableTest/1.PmeCorrection (0 ms) 41: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 41: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (0 ms) 41: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 41: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (0 ms) 41: [ RUN ] SplineTableTest/1.TwoFunctions 41: [ OK ] SplineTableTest/1.TwoFunctions (64 ms) 41: [ RUN ] SplineTableTest/1.ThreeFunctions 41: [ OK ] SplineTableTest/1.ThreeFunctions (71 ms) 41: [ RUN ] SplineTableTest/1.Simd 41: [ OK ] SplineTableTest/1.Simd (7 ms) 41: [ RUN ] SplineTableTest/1.SimdTwoFunctions 41: [ OK ] SplineTableTest/1.SimdTwoFunctions (52 ms) 41: [----------] 10 tests from SplineTableTest/1 (239 ms total) 41: 41: [----------] Global test environment tear-down 41: [==========] 20 tests from 2 test suites ran. (320 ms total) 41: [ PASSED ] 20 tests. 41/87 Test #41: TableUnitTests ............................ Passed 0.36 sec test 42 Start 42: TaskAssignmentUnitTests 42: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/taskassignment-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/TaskAssignmentUnitTests.xml" 42: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/taskassignment/tests 42: Test timeout computed to be: 30 42: [==========] Running 3 tests from 2 test suites. 42: [----------] Global test environment set-up. 42: [----------] 2 tests from UserTaskAssignmentStringHandlingTest 42: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork 42: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (0 ms) 42: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid 42: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms) 42: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (0 ms total) 42: 42: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest 42: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow 42: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (0 ms) 42: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (0 ms total) 42: 42: [----------] Global test environment tear-down 42: [==========] 3 tests from 2 test suites ran. (0 ms total) 42: [ PASSED ] 3 tests. 42/87 Test #42: TaskAssignmentUnitTests ................... Passed 0.03 sec test 43 Start 43: GmxTimingTests 43: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/timing-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/GmxTimingTests.xml" 43: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/timing/tests 43: Test timeout computed to be: 30 43: [==========] Running 6 tests from 1 test suite. 43: [----------] Global test environment set-up. 43: [----------] 6 tests from TimingTest 43: [ RUN ] TimingTest.ElementCountingWorks 43: [ OK ] TimingTest.ElementCountingWorks (0 ms) 43: [ RUN ] TimingTest.ElementNoCountingWorks 43: [ OK ] TimingTest.ElementNoCountingWorks (0 ms) 43: [ RUN ] TimingTest.SubElementCountingWorks 43: [ OK ] TimingTest.SubElementCountingWorks (0 ms) 43: [ RUN ] TimingTest.SubElementNoCountingWorks 43: [ OK ] TimingTest.SubElementNoCountingWorks (0 ms) 43: [ RUN ] TimingTest.RunWallCycle 43: [ OK ] TimingTest.RunWallCycle (1 ms) 43: [ RUN ] TimingTest.RunWallCycleSub 43: [ OK ] TimingTest.RunWallCycleSub (0 ms) 43: [----------] 6 tests from TimingTest (1 ms total) 43: 43: [----------] Global test environment tear-down 43: [==========] 6 tests from 1 test suite ran. (1 ms total) 43: [ PASSED ] 6 tests. 43/87 Test #43: GmxTimingTests ............................ Passed 0.03 sec test 44 Start 44: TopologyTest 44: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/topology-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/TopologyTest.xml" 44: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/topology/tests 44: Test timeout computed to be: 30 44: [==========] Running 153 tests from 10 test suites. 44: [----------] Global test environment set-up. 44: [----------] 3 tests from PdbAtomEntryTest 44: [ RUN ] PdbAtomEntryTest.CanCreateBasicEntry 44: [ OK ] PdbAtomEntryTest.CanCreateBasicEntry (0 ms) 44: [ RUN ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac 44: [ OK ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac (0 ms) 44: [ RUN ] PdbAtomEntryTest.CanCreateFullEntry 44: [ OK ] PdbAtomEntryTest.CanCreateFullEntry (0 ms) 44: [----------] 3 tests from PdbAtomEntryTest (0 ms total) 44: 44: [----------] 3 tests from ExclusionBlockTest 44: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks 44: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms) 44: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka 44: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms) 44: [ RUN ] ExclusionBlockTest.MergeExclusions 44: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms) 44: [----------] 3 tests from ExclusionBlockTest (0 ms total) 44: 44: [----------] 6 tests from InteractionListTest 44: [ RUN ] InteractionListTest.EmptyWorks 44: [ OK ] InteractionListTest.EmptyWorks (0 ms) 44: [ RUN ] InteractionListTest.CanAddInteractionArray 44: [ OK ] InteractionListTest.CanAddInteractionArray (0 ms) 44: [ RUN ] InteractionListTest.CanAddInteractionArrayMultipleAtoms 44: [ OK ] InteractionListTest.CanAddInteractionArrayMultipleAtoms (0 ms) 44: [ RUN ] InteractionListTest.CanAddInteractionPointer 44: [ OK ] InteractionListTest.CanAddInteractionPointer (0 ms) 44: [ RUN ] InteractionListTest.CanAddListToOtherList 44: [ OK ] InteractionListTest.CanAddListToOtherList (0 ms) 44: [ RUN ] InteractionListTest.ClearingWorks 44: [ OK ] InteractionListTest.ClearingWorks (0 ms) 44: [----------] 6 tests from InteractionListTest (0 ms total) 44: 44: [----------] 3 tests from IndexTest 44: [ RUN ] IndexTest.AnalyseWorksDefaultGroups 44: 44: WARNING: Masses and atomic (Van der Waals) radii will be guessed 44: based on residue and atom names, since they could not be 44: definitively assigned from the information in your input 44: files. These guessed numbers might deviate from the mass 44: and radius of the atom type. Please check the output 44: files if necessary. Note, that this functionality may 44: be removed in a future GROMACS version. Please, consider 44: using another file format for your input. 44: 44: [ OK ] IndexTest.AnalyseWorksDefaultGroups (7 ms) 44: [ RUN ] IndexTest.WriteIndexWorks 44: 44: WARNING: Masses and atomic (Van der Waals) radii will be guessed 44: based on residue and atom names, since they could not be 44: definitively assigned from the information in your input 44: files. These guessed numbers might deviate from the mass 44: and radius of the atom type. Please check the output 44: files if necessary. Note, that this functionality may 44: be removed in a future GROMACS version. Please, consider 44: using another file format for your input. 44: 44: [ OK ] IndexTest.WriteIndexWorks (10 ms) 44: [ RUN ] IndexTest.WriteAndReadIndexWorks 44: 44: WARNING: Masses and atomic (Van der Waals) radii will be guessed 44: based on residue and atom names, since they could not be 44: definitively assigned from the information in your input 44: files. These guessed numbers might deviate from the mass 44: and radius of the atom type. Please check the output 44: files if necessary. Note, that this functionality may 44: be removed in a future GROMACS version. Please, consider 44: using another file format for your input. 44: 44: [ OK ] IndexTest.WriteAndReadIndexWorks (3 ms) 44: [----------] 3 tests from IndexTest (22 ms total) 44: 44: [----------] 4 tests from MtopTest 44: [ RUN ] MtopTest.RangeBasedLoop 44: [ OK ] MtopTest.RangeBasedLoop (0 ms) 44: [ RUN ] MtopTest.Operators 44: [ OK ] MtopTest.Operators (0 ms) 44: [ RUN ] MtopTest.CanFindResidueStartAndEndAtoms 44: [ OK ] MtopTest.CanFindResidueStartAndEndAtoms (0 ms) 44: [ RUN ] MtopTest.CanSortPerturbedInteractionsCorrectly 44: [ OK ] MtopTest.CanSortPerturbedInteractionsCorrectly (0 ms) 44: [----------] 4 tests from MtopTest (0 ms total) 44: 44: [----------] 2 tests from IListRangeTest 44: [ RUN ] IListRangeTest.RangeBasedLoopWorks 44: [ OK ] IListRangeTest.RangeBasedLoopWorks (0 ms) 44: [ RUN ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction 44: [ OK ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction (0 ms) 44: [----------] 2 tests from IListRangeTest (0 ms total) 44: 44: [----------] 13 tests from StringTableTest 44: [ RUN ] StringTableTest.AddSingleEntry 44: [ OK ] StringTableTest.AddSingleEntry (2 ms) 44: [ RUN ] StringTableTest.CanAccessWithAt 44: [ OK ] StringTableTest.CanAccessWithAt (0 ms) 44: [ RUN ] StringTableTest.CanAccessWithBracket 44: [ OK ] StringTableTest.CanAccessWithBracket (0 ms) 44: [ RUN ] StringTableTest.ThrowsOutOfRange 44: [ OK ] StringTableTest.ThrowsOutOfRange (1 ms) 44: [ RUN ] StringTableTest.StringCompareIsCorrect 44: [ OK ] StringTableTest.StringCompareIsCorrect (0 ms) 44: [ RUN ] StringTableTest.AddTwoDistinctEntries 44: [ OK ] StringTableTest.AddTwoDistinctEntries (0 ms) 44: [ RUN ] StringTableTest.TryToAddDuplicates 44: [ OK ] StringTableTest.TryToAddDuplicates (0 ms) 44: [ RUN ] StringTableTest.AddLargeNumberOfEntries 44: [ OK ] StringTableTest.AddLargeNumberOfEntries (0 ms) 44: [ RUN ] StringTableTest.NoDuplicatesInLargeTable 44: [ OK ] StringTableTest.NoDuplicatesInLargeTable (0 ms) 44: [ RUN ] StringTableTest.CanWriteToBuffer 44: [ OK ] StringTableTest.CanWriteToBuffer (1 ms) 44: [ RUN ] StringTableTest.Roundtrip 44: [ OK ] StringTableTest.Roundtrip (0 ms) 44: [ RUN ] StringTableTest.RoundtripWithCorrectStringIndices 44: [ OK ] StringTableTest.RoundtripWithCorrectStringIndices (0 ms) 44: [ RUN ] StringTableTest.CanCopyToLegacyTable 44: [ OK ] StringTableTest.CanCopyToLegacyTable (0 ms) 44: [----------] 13 tests from StringTableTest (17 ms total) 44: 44: [----------] 6 tests from LegacySymtabTest 44: [ RUN ] LegacySymtabTest.EmptyOnOpen 44: [ OK ] LegacySymtabTest.EmptyOnOpen (0 ms) 44: [ RUN ] LegacySymtabTest.AddSingleEntry 44: [ OK ] LegacySymtabTest.AddSingleEntry (0 ms) 44: [ RUN ] LegacySymtabTest.AddTwoDistinctEntries 44: [ OK ] LegacySymtabTest.AddTwoDistinctEntries (0 ms) 44: [ RUN ] LegacySymtabTest.TryToAddDuplicates 44: [ OK ] LegacySymtabTest.TryToAddDuplicates (0 ms) 44: [ RUN ] LegacySymtabTest.AddLargeNumberOfEntries 44: [ OK ] LegacySymtabTest.AddLargeNumberOfEntries (0 ms) 44: [ RUN ] LegacySymtabTest.NoDuplicatesInLargeTable 44: [ OK ] LegacySymtabTest.NoDuplicatesInLargeTable (0 ms) 44: [----------] 6 tests from LegacySymtabTest (4 ms total) 44: 44: [----------] 5 tests from TopSortTest 44: [ RUN ] TopSortTest.WorksOnEmptyIdef 44: [ OK ] TopSortTest.WorksOnEmptyIdef (0 ms) 44: [ RUN ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction 44: [ OK ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction (0 ms) 44: [ RUN ] TopSortTest.WorksOnIdefWithPerturbedInteractions 44: [ OK ] TopSortTest.WorksOnIdefWithPerturbedInteractions (0 ms) 44: [ RUN ] TopSortTest.SortsIdefWithPerturbedInteractions 44: [ OK ] TopSortTest.SortsIdefWithPerturbedInteractions (0 ms) 44: [ RUN ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions 44: [ OK ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions (0 ms) 44: [----------] 5 tests from TopSortTest (0 ms total) 44: 44: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 (2 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 (1 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 (1 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 (3 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 (2 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 (4 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 (3 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 (1 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 (5 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 (2 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 (1 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 (1 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 (1 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 (2 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 (6 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 (1 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 (1 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 (1 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 (1 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 (1 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 (3 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 (1 ms) 44: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest (140 ms total) 44: 44: [----------] Global test environment tear-down 44: [==========] 153 tests from 10 test suites ran. (190 ms total) 44: [ PASSED ] 153 tests. 44: 44: YOU HAVE 1 DISABLED TEST 44: 44/87 Test #44: TopologyTest .............................. Passed 0.23 sec test 45 Start 45: PullTest 45: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/pull-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/PullTest.xml" 45: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pulling/tests 45: Test timeout computed to be: 30 45: [==========] Running 10 tests from 1 test suite. 45: [----------] Global test environment set-up. 45: [----------] 10 tests from PullTest 45: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 45: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) 45: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 45: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 45: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 45: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 45: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 45: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 45: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 45: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 45: [ RUN ] PullTest.TransformationCoordSimple 45: [ OK ] PullTest.TransformationCoordSimple (1 ms) 45: [ RUN ] PullTest.TransformationCoordAdvanced 45: [ OK ] PullTest.TransformationCoordAdvanced (0 ms) 45: [ RUN ] PullTest.TransformationCoordTime 45: [ OK ] PullTest.TransformationCoordTime (0 ms) 45: [ RUN ] PullTest.TransformationCoordTimeNotAllowed 45: [ OK ] PullTest.TransformationCoordTimeNotAllowed (0 ms) 45: [ RUN ] PullTest.TransformationCoordDummyExpression 45: [ OK ] PullTest.TransformationCoordDummyExpression (0 ms) 45: [----------] 10 tests from PullTest (6 ms total) 45: 45: [----------] Global test environment tear-down 45: [==========] 10 tests from 1 test suite ran. (6 ms total) 45: [ PASSED ] 10 tests. 45/87 Test #45: PullTest .................................. Passed 0.04 sec test 46 Start 46: SimdUnitTests 46: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/simd-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/SimdUnitTests.xml" 46: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/simd/tests 46: Test timeout computed to be: 30 46: [==========] Running 247 tests from 19 test suites. 46: [----------] Global test environment set-up. 46: [----------] 6 tests from SimdBootstrapTest 46: [ RUN ] SimdBootstrapTest.loadStore 46: [ OK ] SimdBootstrapTest.loadStore (0 ms) 46: [ RUN ] SimdBootstrapTest.loadU 46: [ OK ] SimdBootstrapTest.loadU (0 ms) 46: [ RUN ] SimdBootstrapTest.storeU 46: [ OK ] SimdBootstrapTest.storeU (0 ms) 46: [ RUN ] SimdBootstrapTest.loadStoreI 46: [ OK ] SimdBootstrapTest.loadStoreI (0 ms) 46: [ RUN ] SimdBootstrapTest.loadUI 46: [ OK ] SimdBootstrapTest.loadUI (0 ms) 46: [ RUN ] SimdBootstrapTest.storeUI 46: [ OK ] SimdBootstrapTest.storeUI (0 ms) 46: [----------] 6 tests from SimdBootstrapTest (0 ms total) 46: 46: [----------] 41 tests from SimdScalarTest 46: [ RUN ] SimdScalarTest.load 46: [ OK ] SimdScalarTest.load (0 ms) 46: [ RUN ] SimdScalarTest.loadU 46: [ OK ] SimdScalarTest.loadU (0 ms) 46: [ RUN ] SimdScalarTest.store 46: [ OK ] SimdScalarTest.store (0 ms) 46: [ RUN ] SimdScalarTest.storeU 46: [ OK ] SimdScalarTest.storeU (0 ms) 46: [ RUN ] SimdScalarTest.setZero 46: [ OK ] SimdScalarTest.setZero (0 ms) 46: [ RUN ] SimdScalarTest.andNot 46: [ OK ] SimdScalarTest.andNot (0 ms) 46: [ RUN ] SimdScalarTest.fma 46: [ OK ] SimdScalarTest.fma (0 ms) 46: [ RUN ] SimdScalarTest.fms 46: [ OK ] SimdScalarTest.fms (0 ms) 46: [ RUN ] SimdScalarTest.fnma 46: [ OK ] SimdScalarTest.fnma (0 ms) 46: [ RUN ] SimdScalarTest.fnms 46: [ OK ] SimdScalarTest.fnms (0 ms) 46: [ RUN ] SimdScalarTest.maskAdd 46: [ OK ] SimdScalarTest.maskAdd (0 ms) 46: [ RUN ] SimdScalarTest.maskzMul 46: [ OK ] SimdScalarTest.maskzMul (0 ms) 46: [ RUN ] SimdScalarTest.maskzFma 46: [ OK ] SimdScalarTest.maskzFma (0 ms) 46: [ RUN ] SimdScalarTest.abs 46: [ OK ] SimdScalarTest.abs (0 ms) 46: [ RUN ] SimdScalarTest.max 46: [ OK ] SimdScalarTest.max (0 ms) 46: [ RUN ] SimdScalarTest.min 46: [ OK ] SimdScalarTest.min (0 ms) 46: [ RUN ] SimdScalarTest.round 46: [ OK ] SimdScalarTest.round (0 ms) 46: [ RUN ] SimdScalarTest.trunc 46: [ OK ] SimdScalarTest.trunc (0 ms) 46: [ RUN ] SimdScalarTest.reduce 46: [ OK ] SimdScalarTest.reduce (0 ms) 46: [ RUN ] SimdScalarTest.testBits 46: [ OK ] SimdScalarTest.testBits (0 ms) 46: [ RUN ] SimdScalarTest.anyTrue 46: [ OK ] SimdScalarTest.anyTrue (0 ms) 46: [ RUN ] SimdScalarTest.selectByMask 46: [ OK ] SimdScalarTest.selectByMask (0 ms) 46: [ RUN ] SimdScalarTest.selectByNotMask 46: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 46: [ RUN ] SimdScalarTest.blend 46: [ OK ] SimdScalarTest.blend (0 ms) 46: [ RUN ] SimdScalarTest.cvtR2I 46: [ OK ] SimdScalarTest.cvtR2I (0 ms) 46: [ RUN ] SimdScalarTest.cvttR2I 46: [ OK ] SimdScalarTest.cvttR2I (0 ms) 46: [ RUN ] SimdScalarTest.cvtI2R 46: [ OK ] SimdScalarTest.cvtI2R (0 ms) 46: [ RUN ] SimdScalarTest.cvtF2D 46: [ OK ] SimdScalarTest.cvtF2D (0 ms) 46: [ RUN ] SimdScalarTest.cvtD2D 46: [ OK ] SimdScalarTest.cvtD2D (0 ms) 46: [ RUN ] SimdScalarTest.loadI 46: [ OK ] SimdScalarTest.loadI (0 ms) 46: [ RUN ] SimdScalarTest.loadUI 46: [ OK ] SimdScalarTest.loadUI (0 ms) 46: [ RUN ] SimdScalarTest.storeI 46: [ OK ] SimdScalarTest.storeI (0 ms) 46: [ RUN ] SimdScalarTest.storeUI 46: [ OK ] SimdScalarTest.storeUI (0 ms) 46: [ RUN ] SimdScalarTest.andNotI 46: [ OK ] SimdScalarTest.andNotI (0 ms) 46: [ RUN ] SimdScalarTest.testBitsI 46: [ OK ] SimdScalarTest.testBitsI (0 ms) 46: [ RUN ] SimdScalarTest.selectByMaskI 46: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 46: [ RUN ] SimdScalarTest.selectByNotMaskI 46: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 46: [ RUN ] SimdScalarTest.blendI 46: [ OK ] SimdScalarTest.blendI (0 ms) 46: [ RUN ] SimdScalarTest.cvtB2IB 46: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 46: [ RUN ] SimdScalarTest.cvtIB2B 46: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 46: [ RUN ] SimdScalarTest.expandScalarsToTriplets 46: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 46: [----------] 41 tests from SimdScalarTest (5 ms total) 46: 46: [----------] 8 tests from SimdScalarUtilTest 46: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 46: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 46: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 46: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 46: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 46: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 46: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 46: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 46: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 46: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 46: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 46: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 46: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 46: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 46: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 46: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 46: [----------] 8 tests from SimdScalarUtilTest (0 ms total) 46: 46: [----------] 37 tests from SimdScalarMathTest 46: [ RUN ] SimdScalarMathTest.copysign 46: [ OK ] SimdScalarMathTest.copysign (0 ms) 46: [ RUN ] SimdScalarMathTest.invsqrtPair 46: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 46: [ RUN ] SimdScalarMathTest.inv 46: [ OK ] SimdScalarMathTest.inv (0 ms) 46: [ RUN ] SimdScalarMathTest.maskzInvsqrt 46: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 46: [ RUN ] SimdScalarMathTest.log 46: [ OK ] SimdScalarMathTest.log (0 ms) 46: [ RUN ] SimdScalarMathTest.exp2 46: [ OK ] SimdScalarMathTest.exp2 (0 ms) 46: [ RUN ] SimdScalarMathTest.exp 46: [ OK ] SimdScalarMathTest.exp (0 ms) 46: [ RUN ] SimdScalarMathTest.erf 46: [ OK ] SimdScalarMathTest.erf (0 ms) 46: [ RUN ] SimdScalarMathTest.erfc 46: [ OK ] SimdScalarMathTest.erfc (0 ms) 46: [ RUN ] SimdScalarMathTest.sincos 46: [ OK ] SimdScalarMathTest.sincos (0 ms) 46: [ RUN ] SimdScalarMathTest.sin 46: [ OK ] SimdScalarMathTest.sin (0 ms) 46: [ RUN ] SimdScalarMathTest.cos 46: [ OK ] SimdScalarMathTest.cos (0 ms) 46: [ RUN ] SimdScalarMathTest.tan 46: [ OK ] SimdScalarMathTest.tan (0 ms) 46: [ RUN ] SimdScalarMathTest.asin 46: [ OK ] SimdScalarMathTest.asin (0 ms) 46: [ RUN ] SimdScalarMathTest.acos 46: [ OK ] SimdScalarMathTest.acos (0 ms) 46: [ RUN ] SimdScalarMathTest.atan 46: [ OK ] SimdScalarMathTest.atan (0 ms) 46: [ RUN ] SimdScalarMathTest.atan2 46: [ OK ] SimdScalarMathTest.atan2 (0 ms) 46: [ RUN ] SimdScalarMathTest.pmeForceCorrection 46: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 46: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 46: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 46: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 46: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.invSingleAccuracy 46: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 46: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.logSingleAccuracy 46: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 46: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.expSingleAccuracy 46: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 46: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 46: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 46: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 46: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 46: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 46: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 46: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 46: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 46: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 46: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 46: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 46: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 46: [----------] 37 tests from SimdScalarMathTest (0 ms total) 46: 46: [----------] 1 test from SimdTest 46: [ RUN ] SimdTest.GmxAligned 46: [ OK ] SimdTest.GmxAligned (0 ms) 46: [----------] 1 test from SimdTest (0 ms total) 46: 46: [----------] 42 tests from SimdFloatingpointTest 46: [ RUN ] SimdFloatingpointTest.setZero 46: [ OK ] SimdFloatingpointTest.setZero (0 ms) 46: [ RUN ] SimdFloatingpointTest.set 46: [ OK ] SimdFloatingpointTest.set (0 ms) 46: [ RUN ] SimdFloatingpointTest.add 46: [ OK ] SimdFloatingpointTest.add (0 ms) 46: [ RUN ] SimdFloatingpointTest.maskAdd 46: [ OK ] SimdFloatingpointTest.maskAdd (0 ms) 46: [ RUN ] SimdFloatingpointTest.sub 46: [ OK ] SimdFloatingpointTest.sub (0 ms) 46: [ RUN ] SimdFloatingpointTest.mul 46: [ OK ] SimdFloatingpointTest.mul (0 ms) 46: [ RUN ] SimdFloatingpointTest.maskzMul 46: [ OK ] SimdFloatingpointTest.maskzMul (0 ms) 46: [ RUN ] SimdFloatingpointTest.fma 46: [ OK ] SimdFloatingpointTest.fma (0 ms) 46: [ RUN ] SimdFloatingpointTest.maskzFma 46: [ OK ] SimdFloatingpointTest.maskzFma (0 ms) 46: [ RUN ] SimdFloatingpointTest.fms 46: [ OK ] SimdFloatingpointTest.fms (0 ms) 46: [ RUN ] SimdFloatingpointTest.fnma 46: [ OK ] SimdFloatingpointTest.fnma (0 ms) 46: [ RUN ] SimdFloatingpointTest.fnms 46: [ OK ] SimdFloatingpointTest.fnms (0 ms) 46: [ RUN ] SimdFloatingpointTest.abs 46: [ OK ] SimdFloatingpointTest.abs (0 ms) 46: [ RUN ] SimdFloatingpointTest.neg 46: [ OK ] SimdFloatingpointTest.neg (0 ms) 46: [ RUN ] SimdFloatingpointTest.and 46: [ OK ] SimdFloatingpointTest.and (0 ms) 46: [ RUN ] SimdFloatingpointTest.or 46: [ OK ] SimdFloatingpointTest.or (0 ms) 46: [ RUN ] SimdFloatingpointTest.xor 46: [ OK ] SimdFloatingpointTest.xor (0 ms) 46: [ RUN ] SimdFloatingpointTest.andNot 46: [ OK ] SimdFloatingpointTest.andNot (0 ms) 46: [ RUN ] SimdFloatingpointTest.max 46: [ OK ] SimdFloatingpointTest.max (0 ms) 46: [ RUN ] SimdFloatingpointTest.min 46: [ OK ] SimdFloatingpointTest.min (0 ms) 46: [ RUN ] SimdFloatingpointTest.round 46: [ OK ] SimdFloatingpointTest.round (0 ms) 46: [ RUN ] SimdFloatingpointTest.roundMode 46: [ OK ] SimdFloatingpointTest.roundMode (0 ms) 46: [ RUN ] SimdFloatingpointTest.trunc 46: [ OK ] SimdFloatingpointTest.trunc (0 ms) 46: [ RUN ] SimdFloatingpointTest.frexp 46: [ OK ] SimdFloatingpointTest.frexp (0 ms) 46: [ RUN ] SimdFloatingpointTest.ldexp 46: [ OK ] SimdFloatingpointTest.ldexp (0 ms) 46: [ RUN ] SimdFloatingpointTest.rsqrt 46: [ OK ] SimdFloatingpointTest.rsqrt (0 ms) 46: [ RUN ] SimdFloatingpointTest.maskzRsqrt 46: [ OK ] SimdFloatingpointTest.maskzRsqrt (0 ms) 46: [ RUN ] SimdFloatingpointTest.rcp 46: [ OK ] SimdFloatingpointTest.rcp (0 ms) 46: [ RUN ] SimdFloatingpointTest.maskzRcp 46: [ OK ] SimdFloatingpointTest.maskzRcp (0 ms) 46: [ RUN ] SimdFloatingpointTest.cmpEqAndSelectByMask 46: [ OK ] SimdFloatingpointTest.cmpEqAndSelectByMask (0 ms) 46: [ RUN ] SimdFloatingpointTest.selectByNotMask 46: [ OK ] SimdFloatingpointTest.selectByNotMask (0 ms) 46: [ RUN ] SimdFloatingpointTest.cmpNe 46: [ OK ] SimdFloatingpointTest.cmpNe (0 ms) 46: [ RUN ] SimdFloatingpointTest.cmpLe 46: [ OK ] SimdFloatingpointTest.cmpLe (0 ms) 46: [ RUN ] SimdFloatingpointTest.cmpLt 46: [ OK ] SimdFloatingpointTest.cmpLt (0 ms) 46: [ RUN ] SimdFloatingpointTest.testBits 46: [ OK ] SimdFloatingpointTest.testBits (0 ms) 46: [ RUN ] SimdFloatingpointTest.andB 46: [ OK ] SimdFloatingpointTest.andB (0 ms) 46: [ RUN ] SimdFloatingpointTest.orB 46: [ OK ] SimdFloatingpointTest.orB (0 ms) 46: [ RUN ] SimdFloatingpointTest.anyTrueB 46: [ OK ] SimdFloatingpointTest.anyTrueB (0 ms) 46: [ RUN ] SimdFloatingpointTest.blend 46: [ OK ] SimdFloatingpointTest.blend (0 ms) 46: [ RUN ] SimdFloatingpointTest.reduce 46: [ OK ] SimdFloatingpointTest.reduce (0 ms) 46: [ RUN ] SimdFloatingpointTest.cvtFloat2Double 46: [ OK ] SimdFloatingpointTest.cvtFloat2Double (0 ms) 46: [ RUN ] SimdFloatingpointTest.cvtDouble2Float 46: [ OK ] SimdFloatingpointTest.cvtDouble2Float (0 ms) 46: [----------] 42 tests from SimdFloatingpointTest (0 ms total) 46: 46: [----------] 13 tests from SimdFloatingpointUtilTest 46: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose4 46: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose4 (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose2 46: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose2 (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 46: [ OK ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.transposeScatterStoreU3 46: [ OK ] SimdFloatingpointUtilTest.transposeScatterStoreU3 (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3 46: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3 (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping 46: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3 46: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3 (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping 46: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.expandScalarsToTriplets 46: [ OK ] SimdFloatingpointUtilTest.expandScalarsToTriplets (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 46: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 46: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 46: [ OK ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.reduceIncr4Sum 46: [ OK ] SimdFloatingpointUtilTest.reduceIncr4Sum (0 ms) 46: [----------] 13 tests from SimdFloatingpointUtilTest (1 ms total) 46: 46: [----------] 23 tests from SimdIntegerTest 46: [ RUN ] SimdIntegerTest.setZero 46: [ OK ] SimdIntegerTest.setZero (0 ms) 46: [ RUN ] SimdIntegerTest.set 46: [ OK ] SimdIntegerTest.set (0 ms) 46: [ RUN ] SimdIntegerTest.add 46: [ OK ] SimdIntegerTest.add (0 ms) 46: [ RUN ] SimdIntegerTest.sub 46: [ OK ] SimdIntegerTest.sub (0 ms) 46: [ RUN ] SimdIntegerTest.mul 46: [ OK ] SimdIntegerTest.mul (0 ms) 46: [ RUN ] SimdIntegerTest.and 46: [ OK ] SimdIntegerTest.and (0 ms) 46: [ RUN ] SimdIntegerTest.andNot 46: [ OK ] SimdIntegerTest.andNot (0 ms) 46: [ RUN ] SimdIntegerTest.or 46: [ OK ] SimdIntegerTest.or (0 ms) 46: [ RUN ] SimdIntegerTest.xor 46: [ OK ] SimdIntegerTest.xor (0 ms) 46: [ RUN ] SimdIntegerTest.extract 46: [ OK ] SimdIntegerTest.extract (0 ms) 46: [ RUN ] SimdIntegerTest.cvtR2I 46: [ OK ] SimdIntegerTest.cvtR2I (0 ms) 46: [ RUN ] SimdIntegerTest.cvttR2I 46: [ OK ] SimdIntegerTest.cvttR2I (0 ms) 46: [ RUN ] SimdIntegerTest.cvtI2R 46: [ OK ] SimdIntegerTest.cvtI2R (0 ms) 46: [ RUN ] SimdIntegerTest.cmpEqAndSelectMask 46: [ OK ] SimdIntegerTest.cmpEqAndSelectMask (0 ms) 46: [ RUN ] SimdIntegerTest.cmpEqAndSelectNotMask 46: [ OK ] SimdIntegerTest.cmpEqAndSelectNotMask (0 ms) 46: [ RUN ] SimdIntegerTest.cmpLt 46: [ OK ] SimdIntegerTest.cmpLt (0 ms) 46: [ RUN ] SimdIntegerTest.testBits 46: [ OK ] SimdIntegerTest.testBits (0 ms) 46: [ RUN ] SimdIntegerTest.andB 46: [ OK ] SimdIntegerTest.andB (0 ms) 46: [ RUN ] SimdIntegerTest.orB 46: [ OK ] SimdIntegerTest.orB (0 ms) 46: [ RUN ] SimdIntegerTest.anyTrue 46: [ OK ] SimdIntegerTest.anyTrue (0 ms) 46: [ RUN ] SimdIntegerTest.blend 46: [ OK ] SimdIntegerTest.blend (0 ms) 46: [ RUN ] SimdIntegerTest.cvtB2IB 46: [ OK ] SimdIntegerTest.cvtB2IB (0 ms) 46: [ RUN ] SimdIntegerTest.cvtIB2B 46: [ OK ] SimdIntegerTest.cvtIB2B (0 ms) 46: [----------] 23 tests from SimdIntegerTest (0 ms total) 46: 46: [----------] 56 tests from SimdMathTest 46: [ RUN ] SimdMathTest.generateTestPointsDouble 46: [ OK ] SimdMathTest.generateTestPointsDouble (6 ms) 46: [ RUN ] SimdMathTest.copysign 46: [ OK ] SimdMathTest.copysign (0 ms) 46: [ RUN ] SimdMathTest.invsqrt 46: [ OK ] SimdMathTest.invsqrt (0 ms) 46: [ RUN ] SimdMathTest.maskzInvsqrt 46: [ OK ] SimdMathTest.maskzInvsqrt (0 ms) 46: [ RUN ] SimdMathTest.invsqrtPair 46: [ OK ] SimdMathTest.invsqrtPair (0 ms) 46: [ RUN ] SimdMathTest.sqrt 46: [ OK ] SimdMathTest.sqrt (0 ms) 46: [ RUN ] SimdMathTest.sqrtUnsafe 46: [ OK ] SimdMathTest.sqrtUnsafe (0 ms) 46: [ RUN ] SimdMathTest.inv 46: [ OK ] SimdMathTest.inv (0 ms) 46: [ RUN ] SimdMathTest.maskzInv 46: [ OK ] SimdMathTest.maskzInv (0 ms) 46: [ RUN ] SimdMathTest.cbrt 46: [ OK ] SimdMathTest.cbrt (0 ms) 46: [ RUN ] SimdMathTest.invcbrt 46: [ OK ] SimdMathTest.invcbrt (0 ms) 46: [ RUN ] SimdMathTest.log2 46: [ OK ] SimdMathTest.log2 (0 ms) 46: [ RUN ] SimdMathTest.log 46: [ OK ] SimdMathTest.log (4 ms) 46: [ RUN ] SimdMathTest.exp2 46: [ OK ] SimdMathTest.exp2 (1 ms) 46: [ RUN ] SimdMathTest.exp2Unsafe 46: [ OK ] SimdMathTest.exp2Unsafe (0 ms) 46: [ RUN ] SimdMathTest.exp 46: [ OK ] SimdMathTest.exp (1 ms) 46: [ RUN ] SimdMathTest.expUnsafe 46: [ OK ] SimdMathTest.expUnsafe (0 ms) 46: [ RUN ] SimdMathTest.pow 46: [ OK ] SimdMathTest.pow (0 ms) 46: [ RUN ] SimdMathTest.powUnsafe 46: [ OK ] SimdMathTest.powUnsafe (0 ms) 46: [ RUN ] SimdMathTest.erf 46: [ OK ] SimdMathTest.erf (0 ms) 46: [ RUN ] SimdMathTest.erfc 46: [ OK ] SimdMathTest.erfc (0 ms) 46: [ RUN ] SimdMathTest.sin 46: [ OK ] SimdMathTest.sin (0 ms) 46: [ RUN ] SimdMathTest.cos 46: [ OK ] SimdMathTest.cos (0 ms) 46: [ RUN ] SimdMathTest.tan 46: [ OK ] SimdMathTest.tan (1 ms) 46: [ RUN ] SimdMathTest.asin 46: [ OK ] SimdMathTest.asin (0 ms) 46: [ RUN ] SimdMathTest.acos 46: [ OK ] SimdMathTest.acos (0 ms) 46: [ RUN ] SimdMathTest.atan 46: [ OK ] SimdMathTest.atan (0 ms) 46: [ RUN ] SimdMathTest.atan2 46: [ OK ] SimdMathTest.atan2 (0 ms) 46: [ RUN ] SimdMathTest.pmeForceCorrection 46: [ OK ] SimdMathTest.pmeForceCorrection (0 ms) 46: [ RUN ] SimdMathTest.pmePotentialCorrection 46: [ OK ] SimdMathTest.pmePotentialCorrection (0 ms) 46: [ RUN ] SimdMathTest.invsqrtSingleAccuracy 46: [ OK ] SimdMathTest.invsqrtSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.invsqrtPairSingleAccuracy 46: [ OK ] SimdMathTest.invsqrtPairSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.sqrtSingleAccuracy 46: [ OK ] SimdMathTest.sqrtSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.sqrtSingleAccuracyUnsafe 46: [ OK ] SimdMathTest.sqrtSingleAccuracyUnsafe (0 ms) 46: [ RUN ] SimdMathTest.invSingleAccuracy 46: [ OK ] SimdMathTest.invSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.cbrtSingleAccuracy 46: [ OK ] SimdMathTest.cbrtSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.invcbrtSingleAccuracy 46: [ OK ] SimdMathTest.invcbrtSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.log2SingleAccuracy 46: [ OK ] SimdMathTest.log2SingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.logSingleAccuracy 46: [ OK ] SimdMathTest.logSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.exp2SingleAccuracy 46: [ OK ] SimdMathTest.exp2SingleAccuracy (1 ms) 46: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe 46: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (0 ms) 46: [ RUN ] SimdMathTest.expSingleAccuracy 46: [ OK ] SimdMathTest.expSingleAccuracy (1 ms) 46: [ RUN ] SimdMathTest.expSingleAccuracyUnsafe 46: [ OK ] SimdMathTest.expSingleAccuracyUnsafe (0 ms) 46: [ RUN ] SimdMathTest.powSingleAccuracy 46: [ OK ] SimdMathTest.powSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.powSingleAccuracyUnsafe 46: [ OK ] SimdMathTest.powSingleAccuracyUnsafe (0 ms) 46: [ RUN ] SimdMathTest.erfSingleAccuracy 46: [ OK ] SimdMathTest.erfSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.erfcSingleAccuracy 46: [ OK ] SimdMathTest.erfcSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.sinSingleAccuracy 46: [ OK ] SimdMathTest.sinSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.cosSingleAccuracy 46: [ OK ] SimdMathTest.cosSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.tanSingleAccuracy 46: [ OK ] SimdMathTest.tanSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.asinSingleAccuracy 46: [ OK ] SimdMathTest.asinSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.acosSingleAccuracy 46: [ OK ] SimdMathTest.acosSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.atanSingleAccuracy 46: [ OK ] SimdMathTest.atanSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.atan2SingleAccuracy 46: [ OK ] SimdMathTest.atan2SingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.pmeForceCorrectionSingleAccuracy 46: [ OK ] SimdMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy 46: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 46: [----------] 56 tests from SimdMathTest (38 ms total) 46: 46: [----------] 1 test from EmptyArrayRefTest 46: [ RUN ] EmptyArrayRefTest.IsEmpty 46: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 46: [----------] 1 test from EmptyArrayRefTest (0 ms total) 46: 46: [----------] 3 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 46: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 46: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 46: [ RUN ] ArrayRefTest/0.ConstructFromArrayRefWorks 46: [ OK ] ArrayRefTest/0.ConstructFromArrayRefWorks (0 ms) 46: [ RUN ] ArrayRefTest/0.ConstructFromArrayWorks 46: [ OK ] ArrayRefTest/0.ConstructFromArrayWorks (0 ms) 46: [----------] 3 tests from ArrayRefTest/0 (0 ms total) 46: 46: [----------] 3 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 46: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 46: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 46: [ RUN ] ArrayRefTest/1.ConstructFromArrayRefWorks 46: [ OK ] ArrayRefTest/1.ConstructFromArrayRefWorks (0 ms) 46: [ RUN ] ArrayRefTest/1.ConstructFromArrayWorks 46: [ OK ] ArrayRefTest/1.ConstructFromArrayWorks (0 ms) 46: [----------] 3 tests from ArrayRefTest/1 (0 ms total) 46: 46: [----------] 3 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 46: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 46: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 46: [ RUN ] ArrayRefTest/2.ConstructFromArrayRefWorks 46: [ OK ] ArrayRefTest/2.ConstructFromArrayRefWorks (0 ms) 46: [ RUN ] ArrayRefTest/2.ConstructFromArrayWorks 46: [ OK ] ArrayRefTest/2.ConstructFromArrayWorks (0 ms) 46: [----------] 3 tests from ArrayRefTest/2 (0 ms total) 46: 46: [----------] 3 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 46: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 46: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 46: [ RUN ] ArrayRefTest/3.ConstructFromArrayRefWorks 46: [ OK ] ArrayRefTest/3.ConstructFromArrayRefWorks (0 ms) 46: [ RUN ] ArrayRefTest/3.ConstructFromArrayWorks 46: [ OK ] ArrayRefTest/3.ConstructFromArrayWorks (0 ms) 46: [----------] 3 tests from ArrayRefTest/3 (0 ms total) 46: 46: [----------] 1 test from ArrayRefReadWriteTest/0, where TypeParam = gmx::ArrayRef 46: [ RUN ] ArrayRefReadWriteTest/0.Assignment 46: [ OK ] ArrayRefReadWriteTest/0.Assignment (0 ms) 46: [----------] 1 test from ArrayRefReadWriteTest/0 (0 ms total) 46: 46: [----------] 1 test from ArrayRefReadWriteTest/1, where TypeParam = gmx::ArrayRef 46: [ RUN ] ArrayRefReadWriteTest/1.Assignment 46: [ OK ] ArrayRefReadWriteTest/1.Assignment (0 ms) 46: [----------] 1 test from ArrayRefReadWriteTest/1 (0 ms total) 46: 46: [----------] 1 test from ArrayRefArithmeticTest/0, where TypeParam = gmx::ArrayRef 46: [ RUN ] ArrayRefArithmeticTest/0.Basic 46: [ OK ] ArrayRefArithmeticTest/0.Basic (0 ms) 46: [----------] 1 test from ArrayRefArithmeticTest/0 (0 ms total) 46: 46: [----------] 1 test from ArrayRefArithmeticTest/1, where TypeParam = gmx::ArrayRef 46: [ RUN ] ArrayRefArithmeticTest/1.Basic 46: [ OK ] ArrayRefArithmeticTest/1.Basic (0 ms) 46: [----------] 1 test from ArrayRefArithmeticTest/1 (0 ms total) 46: 46: [----------] 3 tests from SimdVectorOperationsTest 46: [ RUN ] SimdVectorOperationsTest.iprod 46: [ OK ] SimdVectorOperationsTest.iprod (0 ms) 46: [ RUN ] SimdVectorOperationsTest.norm2 46: [ OK ] SimdVectorOperationsTest.norm2 (0 ms) 46: [ RUN ] SimdVectorOperationsTest.cprod 46: [ OK ] SimdVectorOperationsTest.cprod (0 ms) 46: [----------] 3 tests from SimdVectorOperationsTest (0 ms total) 46: 46: [----------] Global test environment tear-down 46: [==========] 247 tests from 19 test suites ran. (49 ms total) 46: [ PASSED ] 247 tests. 46/87 Test #46: SimdUnitTests ............................. Passed 0.08 sec test 47 Start 47: CompatibilityHelpersTests 47: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/compat-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/CompatibilityHelpersTests.xml" 47: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/compat/tests 47: Test timeout computed to be: 30 47: [==========] Running 9 tests from 6 test suites. 47: [----------] Global test environment set-up. 47: [----------] 4 tests from TemplateMPTest 47: [ RUN ] TemplateMPTest.MpWithIndexInt 47: [ OK ] TemplateMPTest.MpWithIndexInt (0 ms) 47: [ RUN ] TemplateMPTest.MpWithIndexIntBad 47: [ OK ] TemplateMPTest.MpWithIndexIntBad (0 ms) 47: [ RUN ] TemplateMPTest.MpWithIndexBool 47: [ OK ] TemplateMPTest.MpWithIndexBool (0 ms) 47: [ RUN ] TemplateMPTest.MpWithIndexEnum 47: [ OK ] TemplateMPTest.MpWithIndexEnum (0 ms) 47: [----------] 4 tests from TemplateMPTest (0 ms total) 47: 47: [----------] 1 test from NotNullConstruction 47: [ RUN ] NotNullConstruction.Works 47: [ OK ] NotNullConstruction.Works (0 ms) 47: [----------] 1 test from NotNullConstruction (0 ms total) 47: 47: [----------] 1 test from NotNullCasting 47: [ RUN ] NotNullCasting.Works 47: [ OK ] NotNullCasting.Works (0 ms) 47: [----------] 1 test from NotNullCasting (0 ms total) 47: 47: [----------] 1 test from NotNullAssignment 47: [ RUN ] NotNullAssignment.Works 47: [ OK ] NotNullAssignment.Works (0 ms) 47: [----------] 1 test from NotNullAssignment (0 ms total) 47: 47: [----------] 1 test from MakeNotNull 47: [ RUN ] MakeNotNull.Works 47: [ OK ] MakeNotNull.Works (0 ms) 47: [----------] 1 test from MakeNotNull (0 ms total) 47: 47: [----------] 1 test from NotNull 47: [ RUN ] NotNull.WorksInContainers 47: [ OK ] NotNull.WorksInContainers (0 ms) 47: [----------] 1 test from NotNull (0 ms total) 47: 47: [----------] Global test environment tear-down 47: [==========] 9 tests from 6 test suites ran. (0 ms total) 47: [ PASSED ] 9 tests. 47/87 Test #47: CompatibilityHelpersTests ................. Passed 0.03 sec test 48 Start 48: GmxAnaTest 48: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/gmxana-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/GmxAnaTest.xml" 48: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxana/tests 48: Test timeout computed to be: 600 48: [==========] Running 31 tests from 4 test suites. 48: [----------] Global test environment set-up. 48: [----------] 7 tests from Entropy 48: [ RUN ] Entropy.Schlitter_300_NoLinear 48: [ OK ] Entropy.Schlitter_300_NoLinear (1 ms) 48: [ RUN ] Entropy.Schlitter_300_Linear 48: [ OK ] Entropy.Schlitter_300_Linear (0 ms) 48: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear 48: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms) 48: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear 48: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms) 48: [ RUN ] Entropy.QuasiHarmonic_200_Linear 48: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms) 48: [ RUN ] Entropy.EntropyCompare_200_Linear 48: [ OK ] Entropy.EntropyCompare_200_Linear (0 ms) 48: [ RUN ] Entropy.EntropyCompare_300_Linear 48: [ OK ] Entropy.EntropyCompare_300_Linear (0 ms) 48: [----------] 7 tests from Entropy (5 ms total) 48: 48: [----------] 2 tests from GmxChiTest 48: [ RUN ] GmxChiTest.gmxchiWorksWithAll 48: Analyzing from residue 1 to residue 11 48: 10 residues with dihedrals found 48: 46 dihedrals found 48: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 48: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 48: j after resetting (nr. active dihedrals) = 46 48: Printing phiLYS1.xvg Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing phiGLU7.xvg Printing phiLEU8.xvg Printing phiALA9.xvg Printing phiALA10.xvg Printing psiLYS1.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing psiGLU7.xvg Printing psiLEU8.xvg Printing psiALA9.xvg Printing psiALA10.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing omegaGLU7.xvg Printing omegaLEU8.xvg Printing omegaALA9.xvg Printing omegaALA10.xvg Printing chi1LYS1.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi1GLU7.xvg Printing chi1LEU8.xvg Printing chi2LYS1.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi2GLU7.xvg Printing chi2LEU8.xvg Printing chi3LYS1.xvg Printing chi3ARG5.xvg Printing chi3GLU7.xvg Printing chi4LYS1.xvg Printing chi4ARG5.xvg 48: Now calculating transitions... 48: Total number of transitions: 0 48: Now printing out transitions and OPs... 48: Now printing out rotamer occupancies... 48: Now calculating Chi product trajectories... 48: Printing chiproductLYS1.xvg and histo-chiprodLYS1.xvg Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg Printing chiproductGLU7.xvg and histo-chiprodGLU7.xvg Printing chiproductLEU8.xvg and histo-chiprodLEU8.xvg 48: [ OK ] GmxChiTest.gmxchiWorksWithAll (882 ms) 48: [ RUN ] GmxChiTest.gmxchiWorksWithr0AndrN 48: Analyzing from residue 2 to residue 6 48: 5 residues with dihedrals found 48: 23 dihedrals found 48: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 48: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 48: j after resetting (nr. active dihedrals) = 23 48: Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi3ARG5.xvg Printing chi4ARG5.xvg 48: Now calculating transitions... 48: Total number of transitions: 0 48: Now printing out transitions and OPs... 48: Now printing out rotamer occupancies... 48: Now calculating Chi product trajectories... 48: Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg 48: [ OK ] GmxChiTest.gmxchiWorksWithr0AndrN (347 ms) 48: [----------] 2 tests from GmxChiTest (1341 ms total) 48: 48: [----------] 10 tests from MindistTest 48: [ RUN ] MindistTest.mindistWorksWithSingleAtoms 48: Group 0 ( atom1) has 1 elements 48: Group 1 ( atom2) has 1 elements 48: Group 2 ( atom3) has 1 elements 48: Group 3 ( atoms12) has 2 elements 48: Group 4 ( atoms23) has 2 elements 48: Group 5 ( atoms123) has 3 elements 48: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: Selected 0: 'atom1' 48: Selected 1: 'atom2' 48: [ OK ] MindistTest.mindistWorksWithSingleAtoms (30 ms) 48: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms 48: Group 0 ( atom1) has 1 elements 48: Group 1 ( atom2) has 1 elements 48: Group 2 ( atom3) has 1 elements 48: Group 3 ( atoms12) has 2 elements 48: Group 4 ( atoms23) has 2 elements 48: Group 5 ( atoms123) has 3 elements 48: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: Selected 2: 'atom3' 48: Selected 3: 'atoms12' 48: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (1 ms) 48: [ RUN ] MindistTest.mindistDoesNotPickUpContacts 48: Group 0 ( atom1) has 1 elements 48: Group 1 ( atom2) has 1 elements 48: Group 2 ( atom3) has 1 elements 48: Group 3 ( atoms12) has 2 elements 48: Group 4 ( atoms23) has 2 elements 48: Group 5 ( atoms123) has 3 elements 48: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: Selected 0: 'atom1' 48: Selected 1: 'atom2' 48: [ OK ] MindistTest.mindistDoesNotPickUpContacts (6 ms) 48: [ RUN ] MindistTest.mindistPicksUpContacts 48: Group 0 ( atom1) has 1 elements 48: Group 1 ( atom2) has 1 elements 48: Group 2 ( atom3) has 1 elements 48: Group 3 ( atoms12) has 2 elements 48: Group 4 ( atoms23) has 2 elements 48: Group 5 ( atoms123) has 3 elements 48: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: Selected 0: 'atom1' 48: Selected 1: 'atom2' 48: [ OK ] MindistTest.mindistPicksUpContacts (3 ms) 48: [ RUN ] MindistTest.ngWorks 48: Group 0 ( atom1) has 1 elements 48: Group 1 ( atom2) has 1 elements 48: Group 2 ( atom3) has 1 elements 48: Group 3 ( atoms12) has 2 elements 48: Group 4 ( atoms23) has 2 elements 48: Group 5 ( atoms123) has 3 elements 48: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: Selected 0: 'atom1' 48: Selected 1: 'atom2' 48: Selected 2: 'atom3' 48: [ OK ] MindistTest.ngWorks (1 ms) 48: [ RUN ] MindistTest.groupWorks 48: Group 0 ( atom1) has 1 elements 48: Group 1 ( atom2) has 1 elements 48: Group 2 ( atom3) has 1 elements 48: Group 3 ( atoms12) has 2 elements 48: Group 4 ( atoms23) has 2 elements 48: Group 5 ( atoms123) has 3 elements 48: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: Selected 3: 'atoms12' 48: Selected 2: 'atom3' 48: [ OK ] MindistTest.groupWorks (1 ms) 48: [ RUN ] MindistTest.maxDistWorks 48: Group 0 ( atom1) has 1 elements 48: Group 1 ( atom2) has 1 elements 48: Group 2 ( atom3) has 1 elements 48: Group 3 ( atoms12) has 2 elements 48: Group 4 ( atoms23) has 2 elements 48: Group 5 ( atoms123) has 3 elements 48: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: Selected 2: 'atom3' 48: Selected 3: 'atoms12' 48: [ OK ] MindistTest.maxDistWorks (1 ms) 48: [ RUN ] MindistTest.noPbcWorks 48: Group 0 ( atom1) has 1 elements 48: Group 1 ( atom2) has 1 elements 48: Group 2 ( atom3) has 1 elements 48: Group 3 ( atoms12) has 2 elements 48: Group 4 ( atoms23) has 2 elements 48: Group 5 ( atoms123) has 3 elements 48: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: Selected 0: 'atom1' 48: Selected 1: 'atom2' 48: [ OK ] MindistTest.noPbcWorks (12 ms) 48: [ RUN ] MindistTest.resPerTimeWorks 48: Group 0 ( atom1) has 1 elements 48: Group 1 ( atom2) has 1 elements 48: Group 2 ( atom3) has 1 elements 48: Group 3 ( atoms12) has 2 elements 48: Group 4 ( atoms23) has 2 elements 48: Group 5 ( atoms123) has 3 elements 48: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: Selected 3: 'atoms12' 48: Selected 2: 'atom3' 48: [ OK ] MindistTest.resPerTimeWorks (1 ms) 48: [ RUN ] MindistTest.matrixWorks 48: Group 0 ( atom1) has 1 elements 48: Group 1 ( atom2) has 1 elements 48: Group 2 ( atom3) has 1 elements 48: Group 3 ( atoms12) has 2 elements 48: Group 4 ( atoms23) has 2 elements 48: Group 5 ( atoms123) has 3 elements 48: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: Selected 5: 'atoms123' 48: Special case: making distance matrix between all atoms in group atoms123 48: [ OK ] MindistTest.matrixWorks (2 ms) 48: [----------] 10 tests from MindistTest (64 ms total) 48: 48: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: trr version: GMX_trn_file (single precision) 48: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (4 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (2 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 48: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (7 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 48: Reading frame 1 time 1.000 Last frame 1 time 1.000 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (2 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (3 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (10 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frame 0 time 0.000 48: WARNING: If there are molecules in the input trajectory file 48: that are broken across periodic boundaries, they 48: cannot be made whole (or treated as whole) without 48: you providing a run input file. 48: 48: Reading frame 1 time 1.000 Last frame 1 time 1.000 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 (6 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frame 0 time 0.000 48: WARNING: If there are molecules in the input trajectory file 48: that are broken across periodic boundaries, they 48: cannot be made whole (or treated as whole) without 48: you providing a run input file. 48: 48: Reading frame 1 time 1.000 Last frame 1 time 1.000 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 (7 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 48: Reading frame 0 time 0.000 48: WARNING: If there are molecules in the input trajectory file 48: that are broken across periodic boundaries, they 48: cannot be made whole (or treated as whole) without 48: you providing a run input file. 48: 48: Reading frame 1 time 1.000 Last frame 1 time 1.000 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 (3 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 48: WARNING: If there are molecules in the input trajectory file 48: that are broken across periodic boundaries, they 48: cannot be made whole (or treated as whole) without 48: you providing a run input file. 48: 48: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 48: Reading frame 1 time 1.000 Last frame 1 time 1.000 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 (8 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frame 0 time 0.000 48: WARNING: If there are molecules in the input trajectory file 48: that are broken across periodic boundaries, they 48: cannot be made whole (or treated as whole) without 48: you providing a run input file. 48: 48: Reading frame 1 time 1.000 Last frame 1 time 1.000 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 (3 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frame 0 time 0.000 48: WARNING: If there are molecules in the input trajectory file 48: that are broken across periodic boundaries, they 48: cannot be made whole (or treated as whole) without 48: you providing a run input file. 48: 48: Reading frame 1 time 1.000 Last frame 1 time 1.000 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 (5 ms) 48: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj (67 ms total) 48: 48: [----------] Global test environment tear-down 48: [==========] 31 tests from 4 test suites ran. (1479 ms total) 48: [ PASSED ] 31 tests. 48/87 Test #48: GmxAnaTest ................................ Passed 1.54 sec test 49 Start 49: GmxPreprocessTests 49: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/gmxpreprocess-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/GmxPreprocessTests.xml" 49: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests 49: Test timeout computed to be: 1920 49: [==========] Running 93 tests from 12 test suites. 49: [----------] Global test environment set-up. 49: [----------] 4 tests from GenconfTest 49: [ RUN ] GenconfTest.nbox_Works 49: [ OK ] GenconfTest.nbox_Works (6 ms) 49: [ RUN ] GenconfTest.nbox_norenumber_Works 49: [ OK ] GenconfTest.nbox_norenumber_Works (1 ms) 49: [ RUN ] GenconfTest.nbox_dist_Works 49: [ OK ] GenconfTest.nbox_dist_Works (1 ms) 49: [ RUN ] GenconfTest.nbox_rot_Works 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: [ OK ] GenconfTest.nbox_rot_Works (1 ms) 49: [----------] 4 tests from GenconfTest (11 ms total) 49: 49: [----------] 2 tests from GenionTest 49: [ RUN ] GenionTest.HighConcentrationIonPlacement 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 49: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 49: buffer. The cluster pair list does have a buffering effect, but choosing 49: a larger rlist might be necessary for good energy conservation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 49: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 49: < 0 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: Generating 1-4 interactions: fudge = 0.5 49: Number of degrees of freedom in T-Coupling group rest is 1308.00 49: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 NOTEs 49: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 49: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 49: Group 0 ( System) has 653 elements 49: Group 1 ( Water) has 648 elements 49: Group 2 ( SOL) has 648 elements 49: Group 3 ( non-Water) has 5 elements 49: Group 4 ( Other) has 5 elements 49: Group 5 ( METH) has 5 elements 49: Select a group: Number of (3-atomic) solvent molecules: 216 49: Using random seed 1997. 49: Replacing solvent molecule 56 (atom 168) with NA 49: Replacing solvent molecule 120 (atom 360) with NA 49: Replacing solvent molecule 182 (atom 546) with NA 49: Replacing solvent molecule 71 (atom 213) with NA 49: Replacing solvent molecule 189 (atom 567) with CL 49: Replacing solvent molecule 54 (atom 162) with CL 49: Replacing solvent molecule 155 (atom 465) with CL 49: Replacing solvent molecule 99 (atom 297) with CL 49: 49: Setting the LD random seed to -12648483 49: 49: Generated 331705 of the 331705 non-bonded parameter combinations 49: 49: Generated 331705 of the 331705 1-4 parameter combinations 49: 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: 49: Excluding 3 bonded neighbours molecule type 'methane' 49: Analysing residue names: 49: There are: 216 Water residues 49: There are: 1 Other residues 49: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 49: 49: This run will generate roughly 0 Mb of data 49: Will try to add 4 NA ions and 4 CL ions. 49: Select a continuous group of solvent molecules 49: Selected 1: 'Water' 49: [ OK ] GenionTest.HighConcentrationIonPlacement (854 ms) 49: [ RUN ] GenionTest.NoIonPlacement 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 49: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 49: buffer. The cluster pair list does have a buffering effect, but choosing 49: a larger rlist might be necessary for good energy conservation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 49: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 49: < 0 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: Generating 1-4 interactions: fudge = 0.5 49: Number of degrees of freedom in T-Coupling group rest is 1308.00 49: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 NOTEs 49: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 49: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 49: No ions to add, will just copy input configuration. 49: Setting the LD random seed to -269174435 49: 49: Generated 331705 of the 331705 non-bonded parameter combinations 49: 49: Generated 331705 of the 331705 1-4 parameter combinations 49: 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: 49: Excluding 3 bonded neighbours molecule type 'methane' 49: Analysing residue names: 49: There are: 216 Water residues 49: There are: 1 Other residues 49: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 49: 49: This run will generate roughly 0 Mb of data 49: [ OK ] GenionTest.NoIonPlacement (632 ms) 49: [----------] 2 tests from GenionTest (1486 ms total) 49: 49: [----------] 1 test from GenRestrTest 49: [ RUN ] GenRestrTest.SimpleRestraintsGenerated 49: 49: Reading structure file 49: Group 0 ( System) has 156 elements 49: Group 1 ( Protein) has 156 elements 49: Group 2 ( Protein-H) has 75 elements 49: Group 3 ( C-alpha) has 10 elements 49: Group 4 ( Backbone) has 30 elements 49: Group 5 ( MainChain) has 40 elements 49: Group 6 ( MainChain+Cb) has 49 elements 49: Group 7 ( MainChain+H) has 52 elements 49: Group 8 ( SideChain) has 104 elements 49: Group 9 ( SideChain-H) has 35 elements 49: Select a group: Select group to position restrain 49: Selected 3: 'C-alpha' 49: [ OK ] GenRestrTest.SimpleRestraintsGenerated (2 ms) 49: [----------] 1 test from GenRestrTest (3 ms total) 49: 49: [----------] 9 tests from PreprocessingAtomTypesTest 49: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate 49: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms) 49: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid 49: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms) 49: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks 49: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms) 49: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks 49: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms) 49: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry 49: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms) 49: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound 49: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms) 49: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound 49: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms) 49: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber 49: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms) 49: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber 49: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms) 49: [----------] 9 tests from PreprocessingAtomTypesTest (1 ms total) 49: 49: [----------] 10 tests from PreprocessingBondAtomTypeTest 49: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate 49: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms) 49: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid 49: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms) 49: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks 49: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms) 49: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks 49: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms) 49: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry 49: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms) 49: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType 49: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms) 49: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound 49: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms) 49: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound 49: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms) 49: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber 49: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms) 49: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber 49: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms) 49: [----------] 10 tests from PreprocessingBondAtomTypeTest (1 ms total) 49: 49: [----------] 1 test from GromppDirectiveTest 49: [ RUN ] GromppDirectiveTest.edgeCaseAtomTypeNames 49: Ignoring obsolete mdp entry 'title' 49: Generating 1-4 interactions: fudge = 0.5 49: 49: NOTE 1 [file directives.top, line 44]: 49: In moleculetype 'A' 2 atoms are not bound by a potential or constraint to 49: any other atom in the same moleculetype. Although technically this might 49: not cause issues in a simulation, this often means that the user forgot 49: to add a bond/potential/constraint or put multiple molecules in the same 49: moleculetype definition by mistake. Run with -v to get information for 49: each atom. 49: 49: Number of degrees of freedom in T-Coupling group rest is 9.00 49: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.mdp]: 49: NVE simulation: will use the initial temperature of 300.000 K for 49: determining the Verlet buffer size 49: 49: 49: There were 2 NOTEs 49: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 49: Setting the LD random seed to -50364417 49: 49: Generated 10 of the 10 non-bonded parameter combinations 49: 49: Generated 10 of the 10 1-4 parameter combinations 49: 49: Excluding 0 bonded neighbours molecule type 'A' 49: 49: Setting gen_seed to -134907017 49: 49: Velocities were taken from a Maxwell distribution at 300 K 49: Analysing residue names: 49: There are: 1 Other residues 49: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 49: 49: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 49: 49: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 49: 49: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 49: 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: 49: This run will generate roughly 0 Mb of data 49: [ OK ] GromppDirectiveTest.edgeCaseAtomTypeNames (9 ms) 49: [----------] 1 test from GromppDirectiveTest (9 ms total) 49: 49: [----------] 5 tests from InsertMoleculesTest 49: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration 49: Reading solute configuration 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Using random seed 1997 49: Try 1 success (now 8 atoms)! 49: 49: Added 1 molecules (out of 1 requested) 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro 49: 49: Output configuration contains 8 atoms in 4 residues 49: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (7 ms) 49: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Using random seed 1997 49: Try 1 success (now 2 atoms)! 49: Try 2 success (now 4 atoms)! 49: Try 3 success (now 6 atoms)! 49: Try 4 success (now 8 atoms)! 49: Try 5 success (now 10 atoms)! 49: 49: Added 5 molecules (out of 5 requested) 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro 49: 49: Output configuration contains 10 atoms in 10 residues 49: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (3 ms) 49: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox 49: Reading solute configuration 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Using random seed 1997 49: Try 1 success (now 8 atoms)! 49: Try 2 success (now 10 atoms)! 49: 49: Added 2 molecules (out of 2 requested) 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro 49: 49: Output configuration contains 10 atoms in 4 residues 49: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (3 ms) 49: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement 49: Reading solute configuration 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Using random seed 1997 49: Try 1 success (now 650 atoms)! 49: Try 2 success (now 652 atoms)! 49: Try 3 success (now 654 atoms)! 49: Try 4 success (now 656 atoms)! 49: 49: Added 4 molecules (out of 4 requested) 49: Replaced 8 residues (24 atoms) 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro 49: 49: Output configuration contains 632 atoms in 212 residues 49: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (10 ms) 49: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Using random seed 1997 49: Read 4 positions from file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat 49: 49: Try 1 success (now 2 atoms)! 49: Try 2 success (now 4 atoms)! 49: Try 3 Try 4 Try 5 Try 6 Try 7 Try 8 Try 9 Try 10 Try 11 Try 12 skipped position (0.990, 2.010, 3.000) 49: Try 13 success (now 6 atoms)! 49: 49: Added 3 molecules (out of 4 requested) 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro 49: 49: Output configuration contains 6 atoms in 3 residues 49: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (7 ms) 49: [----------] 5 tests from InsertMoleculesTest (32 ms total) 49: 49: [----------] 3 tests from MassRepartitioning 49: [ RUN ] MassRepartitioning.ValidCaseWorks 49: The smallest mass in the system is 2, setting the minimum mass to 6 49: [ OK ] MassRepartitioning.ValidCaseWorks (0 ms) 49: [ RUN ] MassRepartitioning.UnboundGivesWarning 49: 49: WARNING 1 [file unknown]: 49: The are 1 atoms that have a mass below the mass repartitioning limit but 49: are not bound. These masses cannot be repartitioned. 49: 49: The smallest mass in the system is 2, setting the minimum mass to 6 49: [ OK ] MassRepartitioning.UnboundGivesWarning (0 ms) 49: [ RUN ] MassRepartitioning.LightPartnerGivesError 49: 49: ERROR 1 [file unknown]: 49: Light atoms are bound to at least one atom that has a too low mass for 49: repartioning 49: 49: The smallest mass in the system is 2, setting the minimum mass to 6 49: [ OK ] MassRepartitioning.LightPartnerGivesError (0 ms) 49: [----------] 3 tests from MassRepartitioning (6 ms total) 49: 49: [----------] 35 tests from GetIrTest 49: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines 49: Ignoring obsolete mdp entry 'title' 49: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps' 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (8 ms) 49: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals 49: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (19 ms) 49: [ RUN ] GetIrTest.AcceptsKeyWithoutValue 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.AcceptsKeyWithoutValue (9 ms) 49: [ RUN ] GetIrTest.RejectsValueWithoutKey 49: [ OK ] GetIrTest.RejectsValueWithoutKey (18 ms) 49: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue 49: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (12 ms) 49: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (3 ms) 49: [ RUN ] GetIrTest.AcceptsEmptyLines 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.AcceptsEmptyLines (3 ms) 49: [ RUN ] GetIrTest.MtsCheckNstcalcenergy 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 49: With MTS, nstcalcenergy = 5 should be a multiple of mts-factor = 2 49: 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.MtsCheckNstcalcenergy (6 ms) 49: [ RUN ] GetIrTest.MtsCheckNstenergy 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 49: With MTS, nstenergy = 5 should be a multiple of mts-factor = 2 49: 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (5) 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.MtsCheckNstenergy (0 ms) 49: [ RUN ] GetIrTest.MtsCheckNstpcouple 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 49: Pressure coupling incorrect number of values (I need exactly 1) 49: 49: 49: ERROR 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 49: Pressure coupling incorrect number of values (I need exactly 1) 49: 49: 49: ERROR 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 49: With multiple time stepping, nstpcouple should be a multiple of 49: mts-factor 49: 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: 49: ERROR 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 49: The Berendsen barostat does not generate any strictly correct ensemble, 49: and should not be used for new production simulations (in our opinion). 49: We recommend using the C-rescale barostat instead. 49: 49: 49: ERROR 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 49: compressibility must be > 0 when using pressure coupling Berendsen 49: 49: 49: [ OK ] GetIrTest.MtsCheckNstpcouple (0 ms) 49: [ RUN ] GetIrTest.MtsCheckNstdhdl 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 49: With MTS, nstdhdl = 5 should be a multiple of mts-factor = 2 49: 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstdhdl (5) 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: 49: ERROR 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 49: Lambda state must be set, either with init-lambda-state or with 49: init-lambda 49: 49: [ OK ] GetIrTest.MtsCheckNstdhdl (0 ms) 49: [ RUN ] GetIrTest.MtsCheckSDNotSupported 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 49: Multiple time stepping is only supported with integrator md 49: 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.MtsCheckSDNotSupported (1 ms) 49: [ RUN ] GetIrTest.AcceptsElectricField 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.AcceptsElectricField (7 ms) 49: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (8 ms) 49: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (2 ms) 49: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys 49: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (6 ms) 49: [ RUN ] GetIrTest.AcceptsImplicitSolventNo 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.AcceptsImplicitSolventNo (9 ms) 49: [ RUN ] GetIrTest.RejectsImplicitSolventYes 49: [ OK ] GetIrTest.RejectsImplicitSolventYes (12 ms) 49: [ RUN ] GetIrTest.AcceptsMimic 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.AcceptsMimic (11 ms) 49: [ RUN ] GetIrTest.AcceptsTransformationCoord 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp, line 11]: 49: pull-coord2 has a non-zero force constant and is also referenced in 49: pull-coord1-expression. Make sure that this is intended. In most use 49: cases, the pull coordinates referenced by a transformation coordinate 49: should have their force constant set to zero. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.AcceptsTransformationCoord (3 ms) 49: [ RUN ] GetIrTest.InvalidTransformationCoordWithConstraint 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp, line 7]: 49: pull-coord1 cannot have type 'constraint' and geometry 'transformation' 49: 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.InvalidTransformationCoordWithConstraint (4 ms) 49: [ RUN ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp, line 10]: 49: pull-coord2 can not use pull-coord1 in the transformation since this is a 49: constraint 49: 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression (7 ms) 49: [ RUN ] GetIrTest.InvalidTransformationCoordDxValue 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp, line 7]: 49: pull-coord1-dx cannot be set to zero for pull coordinate of geometry 49: 'transformation' 49: 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.InvalidTransformationCoordDxValue (1 ms) 49: [ RUN ] GetIrTest.MissingTransformationCoordExpression 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp, line 5]: 49: pull-coord1-expression not set for pull coordinate of geometry 49: 'transformation' 49: 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.MissingTransformationCoordExpression (1 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep 49: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep (0 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta 49: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta (3 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep 49: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep (1 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta 49: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta (0 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_input.mdp]: 49: With init-lambda = 0 and delta_lambda = 1e-05 and no explicit input, 49: coul-lambdas and vdw-lambdas will be greater than 1 after step 100000 of 49: in total 100001 steps. This is not compatible with using soft-core 49: potentials. 49: 49: 49: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch (1 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta_input.mdp]: 49: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 49: won't change anymore after step 100000 until the end of the simulation 49: after 100001 steps. 49: 49: 49: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta (1 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta_input.mdp]: 49: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 49: won't change anymore after step 100000 until the end of the simulation 49: after 100001 steps. 49: 49: 49: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta (6 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_input.mdp]: 49: With init-lambda-state = 0 and delta_lambda = 1e-05, the lambda 49: components won't change anymore after step 100000 until the end of the 49: simulation after 100001 steps. 49: 49: 49: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch (0 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta_input.mdp]: 49: With init-lambda-state = 2 and delta_lambda = -1e-05, the lambda 49: components won't change anymore after step 100000 until the end of the 49: simulation after 100001 steps. 49: 49: 49: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta (1 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep 49: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep (0 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta 49: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta (2 ms) 49: [----------] 35 tests from GetIrTest (193 ms total) 49: 49: [----------] 6 tests from SolvateTest 49: [ RUN ] SolvateTest.cs_box_Works 49: Reading solvent configuration 49: 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Generating solvent configuration 49: Will generate new solvent configuration of 1x1x1 boxes 49: Solvent box contains 270 atoms in 90 residues 49: Removed 129 solvent atoms due to solvent-solvent overlap 49: Sorting configuration 49: Found 1 molecule type: 49: SOL ( 3 atoms): 47 residues 49: Generated solvent containing 141 atoms in 47 residues 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro 49: 49: Output configuration contains 141 atoms in 47 residues 49: Volume : 1.331 (nm^3) 49: Density : 1056.36 (g/l) 49: Number of solvent molecules: 47 49: 49: [ OK ] SolvateTest.cs_box_Works (11 ms) 49: [ RUN ] SolvateTest.cs_cp_Works 49: Reading solute configuration 49: Reading solvent configuration 49: 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Generating solvent configuration 49: Will generate new solvent configuration of 2x2x2 boxes 49: Solvent box contains 3660 atoms in 1220 residues 49: Removed 987 solvent atoms due to solvent-solvent overlap 49: Removed 15 solvent atoms due to solute-solvent overlap 49: Sorting configuration 49: Found 1 molecule type: 49: SOL ( 3 atoms): 886 residues 49: Generated solvent containing 2658 atoms in 886 residues 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro 49: 49: Output configuration contains 2664 atoms in 888 residues 49: Volume : 27.2709 (nm^3) 49: Density : 974.777 (g/l) 49: Number of solvent molecules: 886 49: 49: [ OK ] SolvateTest.cs_cp_Works (22 ms) 49: [ RUN ] SolvateTest.cs_cp_p_Works 49: Reading solute configuration 49: Reading solvent configuration 49: 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Generating solvent configuration 49: Will generate new solvent configuration of 2x2x2 boxes 49: Solvent box contains 3660 atoms in 1220 residues 49: Removed 987 solvent atoms due to solvent-solvent overlap 49: Removed 15 solvent atoms due to solute-solvent overlap 49: Sorting configuration 49: Found 1 molecule type: 49: SOL ( 3 atoms): 886 residues 49: Generated solvent containing 2658 atoms in 886 residues 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro 49: 49: Output configuration contains 2664 atoms in 888 residues 49: Volume : 27.2709 (nm^3) 49: Density : 974.777 (g/l) 49: Number of solvent molecules: 886 49: 49: Processing topology 49: Adding line for 886 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top) 49: [ OK ] SolvateTest.cs_cp_p_Works (29 ms) 49: [ RUN ] SolvateTest.shell_Works 49: Reading solute configuration 49: Reading solvent configuration 49: 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Generating solvent configuration 49: Will generate new solvent configuration of 2x2x2 boxes 49: Solvent box contains 3660 atoms in 1220 residues 49: Removed 987 solvent atoms due to solvent-solvent overlap 49: Removed 1902 solvent atoms more than 1.000000 nm from solute. 49: Removed 15 solvent atoms due to solute-solvent overlap 49: Sorting configuration 49: Found 1 molecule type: 49: SOL ( 3 atoms): 252 residues 49: Generated solvent containing 756 atoms in 252 residues 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro 49: 49: Output configuration contains 762 atoms in 254 residues 49: Volume : 27.2709 (nm^3) 49: Density : 279.3 (g/l) 49: Number of solvent molecules: 252 49: 49: [ OK ] SolvateTest.shell_Works (16 ms) 49: [ RUN ] SolvateTest.update_Topology_Works 49: Reading solute configuration 49: Reading solvent configuration 49: 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Generating solvent configuration 49: Will generate new solvent configuration of 3x3x3 boxes 49: Solvent box contains 14952 atoms in 4984 residues 49: Removed 2787 solvent atoms due to solvent-solvent overlap 49: Removed 30 solvent atoms due to solute-solvent overlap 49: Sorting configuration 49: Found 2 different molecule types: 49: HOH ( 3 atoms): 1876 residues 49: SOL ( 3 atoms): 2169 residues 49: Generated solvent containing 0 atoms in 0 residues 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro 49: 49: Output configuration contains 12141 atoms in 4047 residues 49: Volume : 125 (nm^3) 49: Density : 968.963 (g/l) 49: Number of solvent molecules: 4045 49: 49: Processing topology 49: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 49: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 49: [ OK ] SolvateTest.update_Topology_Works (54 ms) 49: [ RUN ] SolvateTest.cs_pdb_big_box_Works 49: Reading solvent configuration 49: 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Generating solvent configuration 49: Will generate new solvent configuration of 2x2x2 boxes 49: Solvent box contains 1218 atoms in 406 residues 49: Removed 555 solvent atoms due to solvent-solvent overlap 49: Sorting configuration 49: Found 1 molecule type: 49: SOL ( 3 atoms): 221 residues 49: Generated solvent containing 663 atoms in 221 residues 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_pdb_big_box_Works_out.gro 49: 49: Output configuration contains 663 atoms in 221 residues 49: Volume : 8 (nm^3) 49: Density : 826.409 (g/l) 49: Number of solvent molecules: 221 49: 49: [ OK ] SolvateTest.cs_pdb_big_box_Works (15 ms) 49: [----------] 6 tests from SolvateTest (150 ms total) 49: 49: [----------] 1 test from TopDirTests 49: [ RUN ] TopDirTests.NamesArrayHasCorrectSize 49: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms) 49: [----------] 1 test from TopDirTests (0 ms total) 49: 49: [----------] 16 tests from CorrectVelocity/MaxwellTest 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/0 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/0 (1 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/1 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/1 (3 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/2 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/2 (1 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/3 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/3 (1 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/4 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/4 (1 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/5 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/5 (2 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/6 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/6 (1 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/7 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/7 (2 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/8 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/8 (0 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/9 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/9 (2 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/10 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/10 (0 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/11 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/11 (2 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/12 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/12 (0 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/13 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/13 (2 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/14 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/14 (0 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/15 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/15 (6 ms) 49: [----------] 16 tests from CorrectVelocity/MaxwellTest (49 ms total) 49: 49: [----------] Global test environment tear-down 49: [==========] 93 tests from 12 test suites ran. (1946 ms total) 49: [ PASSED ] 93 tests. 49/87 Test #49: GmxPreprocessTests ........................ Passed 2.00 sec test 50 Start 50: Pdb2gmx1Test 50: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/pdb2gmx1-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/Pdb2gmx1Test.xml" 50: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests 50: Test timeout computed to be: 1920 50: [==========] Running 30 tests from 1 test suite. 50: [----------] Global test environment set-up. 50: [----------] 30 tests from Oplsaa/Pdb2gmxTest 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 25 donors and 23 acceptors were found. 50: There are 41 hydrogen bonds 50: Will use HISE for residue 8 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS3 HIS8 50: SG9 NE251 50: HIS8 NE251 1.055 50: MET12 SD83 0.763 0.990 50: Before cleaning: 653 pairs 50: Before cleaning: 663 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 50: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 128 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (128 atoms, 16 residues) 50: 50: Identified residue ALA2 as a starting terminus. 50: 50: Identified residue SER17 as a ending terminus. 50: Start terminus ALA-2: NH3+ 50: End terminus SER-17: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 252 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 254, now 254 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 663 dihedrals, 51 impropers, 457 angles 50: 650 pairs, 254 bonds and 0 virtual sites 50: 50: Total mass 1846.112 a.m.u. 50: 50: Total charge 0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 50: 50: The Oplsaa force field and the tip3p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (48 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 30 donors and 22 acceptors were found. 50: There are 36 hydrogen bonds 50: Will use HISE for residue 29 50: Will use HISE for residue 32 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS27 HIS29 50: SG90 NE2111 50: HIS29 NE2111 0.987 50: HIS32 NE2135 1.590 1.155 50: Before cleaning: 748 pairs 50: Before cleaning: 778 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 50: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 149 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (149 atoms, 16 residues) 50: 50: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue THR18 as a starting terminus. 50: 50: Identified residue PHE33 as a ending terminus. 50: Start terminus THR-18: NH3+ 50: End terminus PHE-33: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 281 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 290, now 290 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 778 dihedrals, 72 impropers, 516 angles 50: 736 pairs, 290 bonds and 0 virtual sites 50: 50: Total mass 2088.357 a.m.u. 50: 50: Total charge 1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 50: 50: The Oplsaa force field and the tip3p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (36 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 22 acceptors were found. 50: There are 26 hydrogen bonds 50: Will use HISE for residue 45 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS45 50: NE295 50: MET46 SD102 1.078 50: Before cleaning: 676 pairs 50: Before cleaning: 696 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 50: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 132 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (132 atoms, 16 residues) 50: 50: Identified residue ALA34 as a starting terminus. 50: 50: Identified residue ALA49 as a ending terminus. 50: Start terminus ALA-34: NH3+ 50: End terminus ALA-49: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 255 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 261, now 261 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 696 dihedrals, 56 impropers, 472 angles 50: 667 pairs, 261 bonds and 0 virtual sites 50: 50: Total mass 1861.128 a.m.u. 50: 50: Total charge -1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 50: 50: The Oplsaa force field and the tip3p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (50 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 21 acceptors were found. 50: There are 30 hydrogen bonds 50: Will use HISE for residue 60 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS60 50: NE285 50: CYS62 SG98 0.803 50: Before cleaning: 603 pairs 50: Before cleaning: 618 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 50: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 117 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (117 atoms, 16 residues) 50: 50: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue LYS50 as a starting terminus. 50: 50: Identified residue PRO65 as a ending terminus. 50: Start terminus LYS-50: NH3+ 50: End terminus PRO-65: PRO-COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 228 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 232, now 232 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 618 dihedrals, 48 impropers, 419 angles 50: 597 pairs, 232 bonds and 0 virtual sites 50: 50: Total mass 1662.883 a.m.u. 50: 50: Total charge 0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 50: 50: The Oplsaa force field and the tip3p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (28 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 89 donors and 98 acceptors were found. 50: There are 129 hydrogen bonds 50: Will use HISE for residue 31 50: Will use HISE for residue 51 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS25 HIS31 HIS51 50: SG14 NE264 NE2226 50: HIS31 NE264 1.921 50: HIS51 NE2226 1.498 2.650 50: CYS80 SG477 0.207 1.984 1.570 50: Linking CYS-25 SG-14 and CYS-80 SG-477... 50: Before cleaning: 2499 pairs 50: Before cleaning: 2524 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 50: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 50: 50: chain #res #atoms 50: 50: 1 'A' 58 488 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 'A' (488 atoms, 58 residues) 50: 50: Identified residue ASN24 as a starting terminus. 50: 50: Identified residue ARG81 as a ending terminus. 50: Start terminus ASN-24: NH3+ 50: End terminus ARG-81: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 58 residues with 936 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 951, now 951 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 2524 dihedrals, 208 impropers, 1704 angles 50: 2469 pairs, 951 bonds and 0 virtual sites 50: 50: Total mass 6908.578 a.m.u. 50: 50: Total charge -6.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 50: 50: The Oplsaa force field and the tip3p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (136 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 25 donors and 23 acceptors were found. 50: There are 41 hydrogen bonds 50: Will use HISE for residue 8 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS3 HIS8 50: SG9 NE251 50: HIS8 NE251 1.055 50: MET12 SD83 0.763 0.990 50: Marked 124 virtual sites 50: Added 16 dummy masses 50: Added 26 new constraints 50: Before cleaning: 653 pairs 50: Before cleaning: 663 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 50: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 128 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (128 atoms, 16 residues) 50: 50: Identified residue ALA2 as a starting terminus. 50: 50: Identified residue SER17 as a ending terminus. 50: Start terminus ALA-2: NH3+ 50: End terminus SER-17: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 252 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 254, now 254 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 663 dihedrals, 51 impropers, 457 angles 50: 650 pairs, 254 bonds and 130 virtual sites 50: 50: Total mass 1846.112 a.m.u. 50: 50: Total charge 0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 50: 50: The Oplsaa force field and the tip3p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (40 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 30 donors and 22 acceptors were found. 50: There are 36 hydrogen bonds 50: Will use HISE for residue 29 50: Will use HISE for residue 32 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS27 HIS29 50: SG90 NE2111 50: HIS29 NE2111 0.987 50: HIS32 NE2135 1.590 1.155 50: Marked 132 virtual sites 50: Added 10 dummy masses 50: Added 19 new constraints 50: Before cleaning: 748 pairs 50: Before cleaning: 778 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 50: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 149 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (149 atoms, 16 residues) 50: 50: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue THR18 as a starting terminus. 50: 50: Identified residue PHE33 as a ending terminus. 50: Start terminus THR-18: NH3+ 50: End terminus PHE-33: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 281 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 290, now 290 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 778 dihedrals, 72 impropers, 516 angles 50: 736 pairs, 290 bonds and 133 virtual sites 50: 50: Total mass 2088.357 a.m.u. 50: 50: Total charge 1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 50: 50: The Oplsaa force field and the tip3p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (47 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 22 acceptors were found. 50: There are 26 hydrogen bonds 50: Will use HISE for residue 45 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS45 50: NE295 50: MET46 SD102 1.078 50: Marked 123 virtual sites 50: Added 22 dummy masses 50: Added 35 new constraints 50: Before cleaning: 676 pairs 50: Before cleaning: 696 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 50: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 132 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (132 atoms, 16 residues) 50: 50: Identified residue ALA34 as a starting terminus. 50: 50: Identified residue ALA49 as a ending terminus. 50: Start terminus ALA-34: NH3+ 50: End terminus ALA-49: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 255 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 261, now 261 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 696 dihedrals, 56 impropers, 472 angles 50: 667 pairs, 261 bonds and 132 virtual sites 50: 50: Total mass 1861.128 a.m.u. 50: 50: Total charge -1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 50: 50: The Oplsaa force field and the tip3p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (46 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 21 acceptors were found. 50: There are 30 hydrogen bonds 50: Will use HISE for residue 60 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS60 50: NE285 50: CYS62 SG98 0.803 50: Marked 111 virtual sites 50: Added 18 dummy masses 50: Added 31 new constraints 50: Before cleaning: 603 pairs 50: Before cleaning: 618 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 50: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 117 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (117 atoms, 16 residues) 50: 50: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue LYS50 as a starting terminus. 50: 50: Identified residue PRO65 as a ending terminus. 50: Start terminus LYS-50: NH3+ 50: End terminus PRO-65: PRO-COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 228 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 232, now 232 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 618 dihedrals, 48 impropers, 419 angles 50: 597 pairs, 232 bonds and 116 virtual sites 50: 50: Total mass 1662.883 a.m.u. 50: 50: Total charge 0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 50: 50: The Oplsaa force field and the tip3p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (49 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 89 donors and 98 acceptors were found. 50: There are 129 hydrogen bonds 50: Will use HISE for residue 31 50: Will use HISE for residue 51 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS25 HIS31 HIS51 50: SG14 NE264 NE2226 50: HIS31 NE264 1.921 50: HIS51 NE2226 1.498 2.650 50: CYS80 SG477 0.207 1.984 1.570 50: Linking CYS-25 SG-14 and CYS-80 SG-477... 50: Marked 447 virtual sites 50: Added 58 dummy masses 50: Added 101 new constraints 50: Before cleaning: 2499 pairs 50: Before cleaning: 2524 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 50: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 50: 50: chain #res #atoms 50: 50: 1 'A' 58 488 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 'A' (488 atoms, 58 residues) 50: 50: Identified residue ASN24 as a starting terminus. 50: 50: Identified residue ARG81 as a ending terminus. 50: Start terminus ASN-24: NH3+ 50: End terminus ARG-81: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 58 residues with 936 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 951, now 951 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 2524 dihedrals, 208 impropers, 1704 angles 50: 2469 pairs, 951 bonds and 462 virtual sites 50: 50: Total mass 6908.578 a.m.u. 50: 50: Total charge -6.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 50: 50: The Oplsaa force field and the tip3p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (86 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 25 donors and 23 acceptors were found. 50: There are 41 hydrogen bonds 50: Will use HISE for residue 8 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS3 HIS8 50: SG9 NE251 50: HIS8 NE251 1.055 50: MET12 SD83 0.763 0.990 50: Before cleaning: 653 pairs 50: Before cleaning: 663 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 50: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 128 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (128 atoms, 16 residues) 50: 50: Identified residue ALA2 as a starting terminus. 50: 50: Identified residue SER17 as a ending terminus. 50: Start terminus ALA-2: NH3+ 50: End terminus SER-17: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 252 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 254, now 254 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 663 dihedrals, 51 impropers, 457 angles 50: 650 pairs, 254 bonds and 0 virtual sites 50: 50: Total mass 1846.112 a.m.u. 50: 50: Total charge 0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 50: 50: The Oplsaa force field and the tip4p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (30 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 30 donors and 22 acceptors were found. 50: There are 36 hydrogen bonds 50: Will use HISE for residue 29 50: Will use HISE for residue 32 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS27 HIS29 50: SG90 NE2111 50: HIS29 NE2111 0.987 50: HIS32 NE2135 1.590 1.155 50: Before cleaning: 748 pairs 50: Before cleaning: 778 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 50: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 149 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (149 atoms, 16 residues) 50: 50: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue THR18 as a starting terminus. 50: 50: Identified residue PHE33 as a ending terminus. 50: Start terminus THR-18: NH3+ 50: End terminus PHE-33: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 281 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 290, now 290 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 778 dihedrals, 72 impropers, 516 angles 50: 736 pairs, 290 bonds and 0 virtual sites 50: 50: Total mass 2088.357 a.m.u. 50: 50: Total charge 1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 50: 50: The Oplsaa force field and the tip4p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (35 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 22 acceptors were found. 50: There are 26 hydrogen bonds 50: Will use HISE for residue 45 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS45 50: NE295 50: MET46 SD102 1.078 50: Before cleaning: 676 pairs 50: Before cleaning: 696 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 50: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 132 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (132 atoms, 16 residues) 50: 50: Identified residue ALA34 as a starting terminus. 50: 50: Identified residue ALA49 as a ending terminus. 50: Start terminus ALA-34: NH3+ 50: End terminus ALA-49: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 255 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 261, now 261 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 696 dihedrals, 56 impropers, 472 angles 50: 667 pairs, 261 bonds and 0 virtual sites 50: 50: Total mass 1861.128 a.m.u. 50: 50: Total charge -1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 50: 50: The Oplsaa force field and the tip4p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (111 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 21 acceptors were found. 50: There are 30 hydrogen bonds 50: Will use HISE for residue 60 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS60 50: NE285 50: CYS62 SG98 0.803 50: Before cleaning: 603 pairs 50: Before cleaning: 618 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 50: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 117 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (117 atoms, 16 residues) 50: 50: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue LYS50 as a starting terminus. 50: 50: Identified residue PRO65 as a ending terminus. 50: Start terminus LYS-50: NH3+ 50: End terminus PRO-65: PRO-COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 228 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 232, now 232 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 618 dihedrals, 48 impropers, 419 angles 50: 597 pairs, 232 bonds and 0 virtual sites 50: 50: Total mass 1662.883 a.m.u. 50: 50: Total charge 0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 50: 50: The Oplsaa force field and the tip4p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (28 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 89 donors and 98 acceptors were found. 50: There are 129 hydrogen bonds 50: Will use HISE for residue 31 50: Will use HISE for residue 51 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS25 HIS31 HIS51 50: SG14 NE264 NE2226 50: HIS31 NE264 1.921 50: HIS51 NE2226 1.498 2.650 50: CYS80 SG477 0.207 1.984 1.570 50: Linking CYS-25 SG-14 and CYS-80 SG-477... 50: Before cleaning: 2499 pairs 50: Before cleaning: 2524 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 50: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 50: 50: chain #res #atoms 50: 50: 1 'A' 58 488 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 'A' (488 atoms, 58 residues) 50: 50: Identified residue ASN24 as a starting terminus. 50: 50: Identified residue ARG81 as a ending terminus. 50: Start terminus ASN-24: NH3+ 50: End terminus ARG-81: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 58 residues with 936 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 951, now 951 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 2524 dihedrals, 208 impropers, 1704 angles 50: 2469 pairs, 951 bonds and 0 virtual sites 50: 50: Total mass 6908.578 a.m.u. 50: 50: Total charge -6.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 50: 50: The Oplsaa force field and the tip4p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (80 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 25 donors and 23 acceptors were found. 50: There are 41 hydrogen bonds 50: Will use HISE for residue 8 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS3 HIS8 50: SG9 NE251 50: HIS8 NE251 1.055 50: MET12 SD83 0.763 0.990 50: Marked 124 virtual sites 50: Added 16 dummy masses 50: Added 26 new constraints 50: Before cleaning: 653 pairs 50: Before cleaning: 663 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 50: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 128 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (128 atoms, 16 residues) 50: 50: Identified residue ALA2 as a starting terminus. 50: 50: Identified residue SER17 as a ending terminus. 50: Start terminus ALA-2: NH3+ 50: End terminus SER-17: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 252 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 254, now 254 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 663 dihedrals, 51 impropers, 457 angles 50: 650 pairs, 254 bonds and 130 virtual sites 50: 50: Total mass 1846.112 a.m.u. 50: 50: Total charge 0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 50: 50: The Oplsaa force field and the tip4p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (35 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 30 donors and 22 acceptors were found. 50: There are 36 hydrogen bonds 50: Will use HISE for residue 29 50: Will use HISE for residue 32 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS27 HIS29 50: SG90 NE2111 50: HIS29 NE2111 0.987 50: HIS32 NE2135 1.590 1.155 50: Marked 132 virtual sites 50: Added 10 dummy masses 50: Added 19 new constraints 50: Before cleaning: 748 pairs 50: Before cleaning: 778 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 50: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 149 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (149 atoms, 16 residues) 50: 50: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue THR18 as a starting terminus. 50: 50: Identified residue PHE33 as a ending terminus. 50: Start terminus THR-18: NH3+ 50: End terminus PHE-33: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 281 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 290, now 290 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 778 dihedrals, 72 impropers, 516 angles 50: 736 pairs, 290 bonds and 133 virtual sites 50: 50: Total mass 2088.357 a.m.u. 50: 50: Total charge 1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 50: 50: The Oplsaa force field and the tip4p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (36 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 22 acceptors were found. 50: There are 26 hydrogen bonds 50: Will use HISE for residue 45 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS45 50: NE295 50: MET46 SD102 1.078 50: Marked 123 virtual sites 50: Added 22 dummy masses 50: Added 35 new constraints 50: Before cleaning: 676 pairs 50: Before cleaning: 696 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 50: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 132 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (132 atoms, 16 residues) 50: 50: Identified residue ALA34 as a starting terminus. 50: 50: Identified residue ALA49 as a ending terminus. 50: Start terminus ALA-34: NH3+ 50: End terminus ALA-49: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 255 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 261, now 261 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 696 dihedrals, 56 impropers, 472 angles 50: 667 pairs, 261 bonds and 132 virtual sites 50: 50: Total mass 1861.128 a.m.u. 50: 50: Total charge -1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 50: 50: The Oplsaa force field and the tip4p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (52 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 21 acceptors were found. 50: There are 30 hydrogen bonds 50: Will use HISE for residue 60 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS60 50: NE285 50: CYS62 SG98 0.803 50: Marked 111 virtual sites 50: Added 18 dummy masses 50: Added 31 new constraints 50: Before cleaning: 603 pairs 50: Before cleaning: 618 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 50: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 117 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (117 atoms, 16 residues) 50: 50: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue LYS50 as a starting terminus. 50: 50: Identified residue PRO65 as a ending terminus. 50: Start terminus LYS-50: NH3+ 50: End terminus PRO-65: PRO-COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 228 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 232, now 232 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 618 dihedrals, 48 impropers, 419 angles 50: 597 pairs, 232 bonds and 116 virtual sites 50: 50: Total mass 1662.883 a.m.u. 50: 50: Total charge 0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 50: 50: The Oplsaa force field and the tip4p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (30 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 89 donors and 98 acceptors were found. 50: There are 129 hydrogen bonds 50: Will use HISE for residue 31 50: Will use HISE for residue 51 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS25 HIS31 HIS51 50: SG14 NE264 NE2226 50: HIS31 NE264 1.921 50: HIS51 NE2226 1.498 2.650 50: CYS80 SG477 0.207 1.984 1.570 50: Linking CYS-25 SG-14 and CYS-80 SG-477... 50: Marked 447 virtual sites 50: Added 58 dummy masses 50: Added 101 new constraints 50: Before cleaning: 2499 pairs 50: Before cleaning: 2524 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 50: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 50: 50: chain #res #atoms 50: 50: 1 'A' 58 488 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 'A' (488 atoms, 58 residues) 50: 50: Identified residue ASN24 as a starting terminus. 50: 50: Identified residue ARG81 as a ending terminus. 50: Start terminus ASN-24: NH3+ 50: End terminus ARG-81: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 58 residues with 936 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 951, now 951 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 2524 dihedrals, 208 impropers, 1704 angles 50: 2469 pairs, 951 bonds and 462 virtual sites 50: 50: Total mass 6908.578 a.m.u. 50: 50: Total charge -6.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 50: 50: The Oplsaa force field and the tip4p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (123 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 25 donors and 23 acceptors were found. 50: There are 41 hydrogen bonds 50: Will use HISE for residue 8 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS3 HIS8 50: SG9 NE251 50: HIS8 NE251 1.055 50: MET12 SD83 0.763 0.990 50: Before cleaning: 653 pairs 50: Before cleaning: 663 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 50: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 128 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (128 atoms, 16 residues) 50: 50: Identified residue ALA2 as a starting terminus. 50: 50: Identified residue SER17 as a ending terminus. 50: Start terminus ALA-2: NH3+ 50: End terminus SER-17: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 252 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 254, now 254 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 663 dihedrals, 51 impropers, 457 angles 50: 650 pairs, 254 bonds and 0 virtual sites 50: 50: Total mass 1846.112 a.m.u. 50: 50: Total charge 0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 50: 50: The Oplsaa force field and the tip5p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (36 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 30 donors and 22 acceptors were found. 50: There are 36 hydrogen bonds 50: Will use HISE for residue 29 50: Will use HISE for residue 32 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS27 HIS29 50: SG90 NE2111 50: HIS29 NE2111 0.987 50: HIS32 NE2135 1.590 1.155 50: Before cleaning: 748 pairs 50: Before cleaning: 778 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 50: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 149 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (149 atoms, 16 residues) 50: 50: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue THR18 as a starting terminus. 50: 50: Identified residue PHE33 as a ending terminus. 50: Start terminus THR-18: NH3+ 50: End terminus PHE-33: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 281 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 290, now 290 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 778 dihedrals, 72 impropers, 516 angles 50: 736 pairs, 290 bonds and 0 virtual sites 50: 50: Total mass 2088.357 a.m.u. 50: 50: Total charge 1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 50: 50: The Oplsaa force field and the tip5p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (50 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 22 acceptors were found. 50: There are 26 hydrogen bonds 50: Will use HISE for residue 45 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS45 50: NE295 50: MET46 SD102 1.078 50: Before cleaning: 676 pairs 50: Before cleaning: 696 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 50: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 132 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (132 atoms, 16 residues) 50: 50: Identified residue ALA34 as a starting terminus. 50: 50: Identified residue ALA49 as a ending terminus. 50: Start terminus ALA-34: NH3+ 50: End terminus ALA-49: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 255 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 261, now 261 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 696 dihedrals, 56 impropers, 472 angles 50: 667 pairs, 261 bonds and 0 virtual sites 50: 50: Total mass 1861.128 a.m.u. 50: 50: Total charge -1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 50: 50: The Oplsaa force field and the tip5p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (31 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 21 acceptors were found. 50: There are 30 hydrogen bonds 50: Will use HISE for residue 60 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS60 50: NE285 50: CYS62 SG98 0.803 50: Before cleaning: 603 pairs 50: Before cleaning: 618 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 50: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 117 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (117 atoms, 16 residues) 50: 50: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue LYS50 as a starting terminus. 50: 50: Identified residue PRO65 as a ending terminus. 50: Start terminus LYS-50: NH3+ 50: End terminus PRO-65: PRO-COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 228 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 232, now 232 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 618 dihedrals, 48 impropers, 419 angles 50: 597 pairs, 232 bonds and 0 virtual sites 50: 50: Total mass 1662.883 a.m.u. 50: 50: Total charge 0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 50: 50: The Oplsaa force field and the tip5p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (25 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 89 donors and 98 acceptors were found. 50: There are 129 hydrogen bonds 50: Will use HISE for residue 31 50: Will use HISE for residue 51 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS25 HIS31 HIS51 50: SG14 NE264 NE2226 50: HIS31 NE264 1.921 50: HIS51 NE2226 1.498 2.650 50: CYS80 SG477 0.207 1.984 1.570 50: Linking CYS-25 SG-14 and CYS-80 SG-477... 50: Before cleaning: 2499 pairs 50: Before cleaning: 2524 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 50: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 50: 50: chain #res #atoms 50: 50: 1 'A' 58 488 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 'A' (488 atoms, 58 residues) 50: 50: Identified residue ASN24 as a starting terminus. 50: 50: Identified residue ARG81 as a ending terminus. 50: Start terminus ASN-24: NH3+ 50: End terminus ARG-81: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 58 residues with 936 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 951, now 951 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 2524 dihedrals, 208 impropers, 1704 angles 50: 2469 pairs, 951 bonds and 0 virtual sites 50: 50: Total mass 6908.578 a.m.u. 50: 50: Total charge -6.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 50: 50: The Oplsaa force field and the tip5p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (79 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 25 donors and 23 acceptors were found. 50: There are 41 hydrogen bonds 50: Will use HISE for residue 8 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS3 HIS8 50: SG9 NE251 50: HIS8 NE251 1.055 50: MET12 SD83 0.763 0.990 50: Marked 124 virtual sites 50: Added 16 dummy masses 50: Added 26 new constraints 50: Before cleaning: 653 pairs 50: Before cleaning: 663 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 50: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 128 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (128 atoms, 16 residues) 50: 50: Identified residue ALA2 as a starting terminus. 50: 50: Identified residue SER17 as a ending terminus. 50: Start terminus ALA-2: NH3+ 50: End terminus SER-17: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 252 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 254, now 254 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 663 dihedrals, 51 impropers, 457 angles 50: 650 pairs, 254 bonds and 130 virtual sites 50: 50: Total mass 1846.112 a.m.u. 50: 50: Total charge 0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 50: 50: The Oplsaa force field and the tip5p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (34 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 30 donors and 22 acceptors were found. 50: There are 36 hydrogen bonds 50: Will use HISE for residue 29 50: Will use HISE for residue 32 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS27 HIS29 50: SG90 NE2111 50: HIS29 NE2111 0.987 50: HIS32 NE2135 1.590 1.155 50: Marked 132 virtual sites 50: Added 10 dummy masses 50: Added 19 new constraints 50: Before cleaning: 748 pairs 50: Before cleaning: 778 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 50: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 149 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (149 atoms, 16 residues) 50: 50: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue THR18 as a starting terminus. 50: 50: Identified residue PHE33 as a ending terminus. 50: Start terminus THR-18: NH3+ 50: End terminus PHE-33: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 281 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 290, now 290 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 778 dihedrals, 72 impropers, 516 angles 50: 736 pairs, 290 bonds and 133 virtual sites 50: 50: Total mass 2088.357 a.m.u. 50: 50: Total charge 1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 50: 50: The Oplsaa force field and the tip5p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (46 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 22 acceptors were found. 50: There are 26 hydrogen bonds 50: Will use HISE for residue 45 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS45 50: NE295 50: MET46 SD102 1.078 50: Marked 123 virtual sites 50: Added 22 dummy masses 50: Added 35 new constraints 50: Before cleaning: 676 pairs 50: Before cleaning: 696 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 50: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 132 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (132 atoms, 16 residues) 50: 50: Identified residue ALA34 as a starting terminus. 50: 50: Identified residue ALA49 as a ending terminus. 50: Start terminus ALA-34: NH3+ 50: End terminus ALA-49: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 255 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 261, now 261 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 696 dihedrals, 56 impropers, 472 angles 50: 667 pairs, 261 bonds and 132 virtual sites 50: 50: Total mass 1861.128 a.m.u. 50: 50: Total charge -1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 50: 50: The Oplsaa force field and the tip5p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (64 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 21 acceptors were found. 50: There are 30 hydrogen bonds 50: Will use HISE for residue 60 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS60 50: NE285 50: CYS62 SG98 0.803 50: Marked 111 virtual sites 50: Added 18 dummy masses 50: Added 31 new constraints 50: Before cleaning: 603 pairs 50: Before cleaning: 618 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 50: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 117 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (117 atoms, 16 residues) 50: 50: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue LYS50 as a starting terminus. 50: 50: Identified residue PRO65 as a ending terminus. 50: Start terminus LYS-50: NH3+ 50: End terminus PRO-65: PRO-COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 228 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 232, now 232 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 618 dihedrals, 48 impropers, 419 angles 50: 597 pairs, 232 bonds and 116 virtual sites 50: 50: Total mass 1662.883 a.m.u. 50: 50: Total charge 0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 50: 50: The Oplsaa force field and the tip5p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (86 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 89 donors and 98 acceptors were found. 50: There are 129 hydrogen bonds 50: Will use HISE for residue 31 50: Will use HISE for residue 51 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS25 HIS31 HIS51 50: SG14 NE264 NE2226 50: HIS31 NE264 1.921 50: HIS51 NE2226 1.498 2.650 50: CYS80 SG477 0.207 1.984 1.570 50: Linking CYS-25 SG-14 and CYS-80 SG-477... 50: Marked 447 virtual sites 50: Added 58 dummy masses 50: Added 101 new constraints 50: Before cleaning: 2499 pairs 50: Before cleaning: 2524 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 50: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 50: 50: chain #res #atoms 50: 50: 1 'A' 58 488 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 'A' (488 atoms, 58 residues) 50: 50: Identified residue ASN24 as a starting terminus. 50: 50: Identified residue ARG81 as a ending terminus. 50: Start terminus ASN-24: NH3+ 50: End terminus ARG-81: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 58 residues with 936 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 951, now 951 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 2524 dihedrals, 208 impropers, 1704 angles 50: 2469 pairs, 951 bonds and 462 virtual sites 50: 50: Total mass 6908.578 a.m.u. 50: 50: Total charge -6.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 50: 50: The Oplsaa force field and the tip5p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (101 ms) 50: [----------] 30 tests from Oplsaa/Pdb2gmxTest (1847 ms total) 50: 50: [----------] Global test environment tear-down 50: [==========] 30 tests from 1 test suite ran. (1847 ms total) 50: [ PASSED ] 30 tests. 50/87 Test #50: Pdb2gmx1Test .............................. Passed 1.89 sec test 51 Start 51: Pdb2gmx2Test 51: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/pdb2gmx2-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/Pdb2gmx2Test.xml" 51: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests 51: Test timeout computed to be: 1920 51: [==========] Running 40 tests from 2 test suites. 51: [----------] Global test environment set-up. 51: [----------] 20 tests from G43a1/Pdb2gmxTest 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 25 donors and 23 acceptors were found. 51: There are 41 hydrogen bonds 51: Will use HISE for residue 8 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS3 HIS8 51: SG9 NE251 51: HIS8 NE251 1.055 51: MET12 SD83 0.763 0.990 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 267 pairs 51: Before cleaning: 305 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 51: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 128 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (128 atoms, 16 residues) 51: 51: Identified residue ALA2 as a starting terminus. 51: 51: Identified residue SER17 as a ending terminus. 51: Start terminus ALA-2: NH3+ 51: End terminus SER-17: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 165 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 172, now 167 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 90 dihedrals, 77 impropers, 241 angles 51: 267 pairs, 167 bonds and 0 virtual sites 51: 51: Total mass 1846.116 a.m.u. 51: 51: Total charge 0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 51: 51: The Gromos43a1 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (61 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 30 donors and 22 acceptors were found. 51: There are 36 hydrogen bonds 51: Will use HISE for residue 29 51: Will use HISE for residue 32 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS27 HIS29 51: SG90 NE2111 51: HIS29 NE2111 0.987 51: HIS32 NE2135 1.590 1.155 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 273 pairs 51: Before cleaning: 429 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 51: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 149 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (149 atoms, 16 residues) 51: 51: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue THR18 as a starting terminus. 51: 51: Identified residue PHE33 as a ending terminus. 51: Start terminus THR-18: NH3+ 51: End terminus PHE-33: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 202 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 216, now 211 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 93 dihedrals, 134 impropers, 316 angles 51: 273 pairs, 211 bonds and 0 virtual sites 51: 51: Total mass 2088.361 a.m.u. 51: 51: Total charge 1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 51: 51: The Gromos43a1 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (37 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 22 acceptors were found. 51: There are 26 hydrogen bonds 51: Will use HISE for residue 45 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS45 51: NE295 51: MET46 SD102 1.078 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 242 pairs 51: Before cleaning: 349 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 51: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 132 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (132 atoms, 16 residues) 51: 51: Identified residue ALA34 as a starting terminus. 51: 51: Identified residue ALA49 as a ending terminus. 51: Start terminus ALA-34: NH3+ 51: End terminus ALA-49: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 168 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 179, now 174 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 81 dihedrals, 102 impropers, 260 angles 51: 242 pairs, 174 bonds and 0 virtual sites 51: 51: Total mass 1861.132 a.m.u. 51: 51: Total charge -1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 51: 51: The Gromos43a1 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (33 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 21 acceptors were found. 51: There are 30 hydrogen bonds 51: Will use HISE for residue 60 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS60 51: NE285 51: CYS62 SG98 0.803 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 232 pairs 51: Before cleaning: 299 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 51: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 117 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (117 atoms, 16 residues) 51: 51: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue LYS50 as a starting terminus. 51: 51: Identified residue PRO65 as a ending terminus. 51: Start terminus LYS-50: NH3+ 51: End terminus PRO-65: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 150 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 159, now 154 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 78 dihedrals, 80 impropers, 227 angles 51: 232 pairs, 154 bonds and 0 virtual sites 51: 51: Total mass 1662.887 a.m.u. 51: 51: Total charge 0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 51: 51: The Gromos43a1 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (36 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 89 donors and 98 acceptors were found. 51: There are 129 hydrogen bonds 51: Will use HISE for residue 31 51: Will use HISE for residue 51 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS25 HIS31 HIS51 51: SG14 NE264 NE2226 51: HIS31 NE264 1.921 51: HIS51 NE2226 1.498 2.650 51: CYS80 SG477 0.207 1.984 1.570 51: Linking CYS-25 SG-14 and CYS-80 SG-477... 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 972 pairs 51: Before cleaning: 1256 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 51: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 51: 51: chain #res #atoms 51: 51: 1 'A' 58 488 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 'A' (488 atoms, 58 residues) 51: 51: Identified residue ASN24 as a starting terminus. 51: 51: Identified residue ARG81 as a ending terminus. 51: Start terminus ASN-24: NH3+ 51: End terminus ARG-81: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 58 residues with 635 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 655, now 650 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 321 dihedrals, 350 impropers, 955 angles 51: 972 pairs, 650 bonds and 0 virtual sites 51: 51: Total mass 6908.582 a.m.u. 51: 51: Total charge -6.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 51: 51: The Gromos43a1 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (71 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 25 donors and 23 acceptors were found. 51: There are 41 hydrogen bonds 51: Will use HISE for residue 8 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS3 HIS8 51: SG9 NE251 51: HIS8 NE251 1.055 51: MET12 SD83 0.763 0.990 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 37 virtual sites 51: Added 4 dummy masses 51: Added 8 new constraints 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 267 pairs 51: Before cleaning: 305 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 51: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 128 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (128 atoms, 16 residues) 51: 51: Identified residue ALA2 as a starting terminus. 51: 51: Identified residue SER17 as a ending terminus. 51: Start terminus ALA-2: NH3+ 51: End terminus SER-17: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 165 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 172, now 167 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 90 dihedrals, 77 impropers, 241 angles 51: 267 pairs, 167 bonds and 37 virtual sites 51: 51: Total mass 1846.116 a.m.u. 51: 51: Total charge 0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 51: 51: The Gromos43a1 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (35 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 30 donors and 22 acceptors were found. 51: There are 36 hydrogen bonds 51: Will use HISE for residue 29 51: Will use HISE for residue 32 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS27 HIS29 51: SG90 NE2111 51: HIS29 NE2111 0.987 51: HIS32 NE2135 1.590 1.155 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 53 virtual sites 51: Added 4 dummy masses 51: Added 10 new constraints 51: 51: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 273 pairs 51: Before cleaning: 429 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 51: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 149 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (149 atoms, 16 residues) 51: 51: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue THR18 as a starting terminus. 51: 51: Identified residue PHE33 as a ending terminus. 51: Start terminus THR-18: NH3+ 51: End terminus PHE-33: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 202 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 216, now 211 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 93 dihedrals, 134 impropers, 316 angles 51: 273 pairs, 211 bonds and 51 virtual sites 51: 51: Total mass 2088.361 a.m.u. 51: 51: Total charge 1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 51: 51: The Gromos43a1 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (42 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 22 acceptors were found. 51: There are 26 hydrogen bonds 51: Will use HISE for residue 45 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS45 51: NE295 51: MET46 SD102 1.078 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 36 virtual sites 51: Added 4 dummy masses 51: Added 8 new constraints 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 242 pairs 51: Before cleaning: 349 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 51: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 132 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (132 atoms, 16 residues) 51: 51: Identified residue ALA34 as a starting terminus. 51: 51: Identified residue ALA49 as a ending terminus. 51: Start terminus ALA-34: NH3+ 51: End terminus ALA-49: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 168 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 179, now 174 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 81 dihedrals, 102 impropers, 260 angles 51: 242 pairs, 174 bonds and 36 virtual sites 51: 51: Total mass 1861.132 a.m.u. 51: 51: Total charge -1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 51: 51: The Gromos43a1 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (32 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 21 acceptors were found. 51: There are 30 hydrogen bonds 51: Will use HISE for residue 60 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS60 51: NE285 51: CYS62 SG98 0.803 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 33 virtual sites 51: Added 4 dummy masses 51: Added 10 new constraints 51: 51: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 232 pairs 51: Before cleaning: 299 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 51: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 117 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (117 atoms, 16 residues) 51: 51: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue LYS50 as a starting terminus. 51: 51: Identified residue PRO65 as a ending terminus. 51: Start terminus LYS-50: NH3+ 51: End terminus PRO-65: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 150 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 159, now 154 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 78 dihedrals, 80 impropers, 227 angles 51: 232 pairs, 154 bonds and 31 virtual sites 51: 51: Total mass 1662.887 a.m.u. 51: 51: Total charge 0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 51: 51: The Gromos43a1 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (39 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 89 donors and 98 acceptors were found. 51: There are 129 hydrogen bonds 51: Will use HISE for residue 31 51: Will use HISE for residue 51 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS25 HIS31 HIS51 51: SG14 NE264 NE2226 51: HIS31 NE264 1.921 51: HIS51 NE2226 1.498 2.650 51: CYS80 SG477 0.207 1.984 1.570 51: Linking CYS-25 SG-14 and CYS-80 SG-477... 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 146 virtual sites 51: Added 10 dummy masses 51: Added 29 new constraints 51: 51: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 972 pairs 51: Before cleaning: 1256 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 51: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 51: 51: chain #res #atoms 51: 51: 1 'A' 58 488 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 'A' (488 atoms, 58 residues) 51: 51: Identified residue ASN24 as a starting terminus. 51: 51: Identified residue ARG81 as a ending terminus. 51: Start terminus ASN-24: NH3+ 51: End terminus ARG-81: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 58 residues with 635 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 655, now 650 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 321 dihedrals, 350 impropers, 955 angles 51: 972 pairs, 650 bonds and 137 virtual sites 51: 51: Total mass 6908.582 a.m.u. 51: 51: Total charge -6.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 51: 51: The Gromos43a1 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (66 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 25 donors and 23 acceptors were found. 51: There are 41 hydrogen bonds 51: Will use HISE for residue 8 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS3 HIS8 51: SG9 NE251 51: HIS8 NE251 1.055 51: MET12 SD83 0.763 0.990 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 267 pairs 51: Before cleaning: 305 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 51: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 128 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (128 atoms, 16 residues) 51: 51: Identified residue ALA2 as a starting terminus. 51: 51: Identified residue SER17 as a ending terminus. 51: Start terminus ALA-2: NH3+ 51: End terminus SER-17: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 165 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 172, now 167 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 90 dihedrals, 77 impropers, 241 angles 51: 267 pairs, 167 bonds and 0 virtual sites 51: 51: Total mass 1846.116 a.m.u. 51: 51: Total charge 0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 51: 51: The Gromos43a1 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (28 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 30 donors and 22 acceptors were found. 51: There are 36 hydrogen bonds 51: Will use HISE for residue 29 51: Will use HISE for residue 32 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS27 HIS29 51: SG90 NE2111 51: HIS29 NE2111 0.987 51: HIS32 NE2135 1.590 1.155 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 273 pairs 51: Before cleaning: 429 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 51: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 149 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (149 atoms, 16 residues) 51: 51: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue THR18 as a starting terminus. 51: 51: Identified residue PHE33 as a ending terminus. 51: Start terminus THR-18: NH3+ 51: End terminus PHE-33: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 202 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 216, now 211 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 93 dihedrals, 134 impropers, 316 angles 51: 273 pairs, 211 bonds and 0 virtual sites 51: 51: Total mass 2088.361 a.m.u. 51: 51: Total charge 1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 51: 51: The Gromos43a1 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (36 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 22 acceptors were found. 51: There are 26 hydrogen bonds 51: Will use HISE for residue 45 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS45 51: NE295 51: MET46 SD102 1.078 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 242 pairs 51: Before cleaning: 349 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 51: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 132 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (132 atoms, 16 residues) 51: 51: Identified residue ALA34 as a starting terminus. 51: 51: Identified residue ALA49 as a ending terminus. 51: Start terminus ALA-34: NH3+ 51: End terminus ALA-49: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 168 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 179, now 174 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 81 dihedrals, 102 impropers, 260 angles 51: 242 pairs, 174 bonds and 0 virtual sites 51: 51: Total mass 1861.132 a.m.u. 51: 51: Total charge -1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 51: 51: The Gromos43a1 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (38 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 21 acceptors were found. 51: There are 30 hydrogen bonds 51: Will use HISE for residue 60 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS60 51: NE285 51: CYS62 SG98 0.803 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 232 pairs 51: Before cleaning: 299 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 51: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 117 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (117 atoms, 16 residues) 51: 51: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue LYS50 as a starting terminus. 51: 51: Identified residue PRO65 as a ending terminus. 51: Start terminus LYS-50: NH3+ 51: End terminus PRO-65: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 150 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 159, now 154 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 78 dihedrals, 80 impropers, 227 angles 51: 232 pairs, 154 bonds and 0 virtual sites 51: 51: Total mass 1662.887 a.m.u. 51: 51: Total charge 0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 51: 51: The Gromos43a1 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (46 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 89 donors and 98 acceptors were found. 51: There are 129 hydrogen bonds 51: Will use HISE for residue 31 51: Will use HISE for residue 51 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS25 HIS31 HIS51 51: SG14 NE264 NE2226 51: HIS31 NE264 1.921 51: HIS51 NE2226 1.498 2.650 51: CYS80 SG477 0.207 1.984 1.570 51: Linking CYS-25 SG-14 and CYS-80 SG-477... 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 972 pairs 51: Before cleaning: 1256 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 51: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 51: 51: chain #res #atoms 51: 51: 1 'A' 58 488 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 'A' (488 atoms, 58 residues) 51: 51: Identified residue ASN24 as a starting terminus. 51: 51: Identified residue ARG81 as a ending terminus. 51: Start terminus ASN-24: NH3+ 51: End terminus ARG-81: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 58 residues with 635 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 655, now 650 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 321 dihedrals, 350 impropers, 955 angles 51: 972 pairs, 650 bonds and 0 virtual sites 51: 51: Total mass 6908.582 a.m.u. 51: 51: Total charge -6.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 51: 51: The Gromos43a1 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (57 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 25 donors and 23 acceptors were found. 51: There are 41 hydrogen bonds 51: Will use HISE for residue 8 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS3 HIS8 51: SG9 NE251 51: HIS8 NE251 1.055 51: MET12 SD83 0.763 0.990 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 37 virtual sites 51: Added 4 dummy masses 51: Added 8 new constraints 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 267 pairs 51: Before cleaning: 305 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 51: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 128 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (128 atoms, 16 residues) 51: 51: Identified residue ALA2 as a starting terminus. 51: 51: Identified residue SER17 as a ending terminus. 51: Start terminus ALA-2: NH3+ 51: End terminus SER-17: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 165 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 172, now 167 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 90 dihedrals, 77 impropers, 241 angles 51: 267 pairs, 167 bonds and 37 virtual sites 51: 51: Total mass 1846.116 a.m.u. 51: 51: Total charge 0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 51: 51: The Gromos43a1 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (34 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 30 donors and 22 acceptors were found. 51: There are 36 hydrogen bonds 51: Will use HISE for residue 29 51: Will use HISE for residue 32 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS27 HIS29 51: SG90 NE2111 51: HIS29 NE2111 0.987 51: HIS32 NE2135 1.590 1.155 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 53 virtual sites 51: Added 4 dummy masses 51: Added 10 new constraints 51: 51: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 273 pairs 51: Before cleaning: 429 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 51: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 149 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (149 atoms, 16 residues) 51: 51: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue THR18 as a starting terminus. 51: 51: Identified residue PHE33 as a ending terminus. 51: Start terminus THR-18: NH3+ 51: End terminus PHE-33: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 202 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 216, now 211 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 93 dihedrals, 134 impropers, 316 angles 51: 273 pairs, 211 bonds and 51 virtual sites 51: 51: Total mass 2088.361 a.m.u. 51: 51: Total charge 1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 51: 51: The Gromos43a1 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (51 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 22 acceptors were found. 51: There are 26 hydrogen bonds 51: Will use HISE for residue 45 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS45 51: NE295 51: MET46 SD102 1.078 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 36 virtual sites 51: Added 4 dummy masses 51: Added 8 new constraints 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 242 pairs 51: Before cleaning: 349 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 51: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 132 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (132 atoms, 16 residues) 51: 51: Identified residue ALA34 as a starting terminus. 51: 51: Identified residue ALA49 as a ending terminus. 51: Start terminus ALA-34: NH3+ 51: End terminus ALA-49: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 168 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 179, now 174 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 81 dihedrals, 102 impropers, 260 angles 51: 242 pairs, 174 bonds and 36 virtual sites 51: 51: Total mass 1861.132 a.m.u. 51: 51: Total charge -1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 51: 51: The Gromos43a1 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (49 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 21 acceptors were found. 51: There are 30 hydrogen bonds 51: Will use HISE for residue 60 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS60 51: NE285 51: CYS62 SG98 0.803 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 33 virtual sites 51: Added 4 dummy masses 51: Added 10 new constraints 51: 51: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 232 pairs 51: Before cleaning: 299 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 51: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 117 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (117 atoms, 16 residues) 51: 51: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue LYS50 as a starting terminus. 51: 51: Identified residue PRO65 as a ending terminus. 51: Start terminus LYS-50: NH3+ 51: End terminus PRO-65: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 150 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 159, now 154 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 78 dihedrals, 80 impropers, 227 angles 51: 232 pairs, 154 bonds and 31 virtual sites 51: 51: Total mass 1662.887 a.m.u. 51: 51: Total charge 0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 51: 51: The Gromos43a1 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (32 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 89 donors and 98 acceptors were found. 51: There are 129 hydrogen bonds 51: Will use HISE for residue 31 51: Will use HISE for residue 51 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS25 HIS31 HIS51 51: SG14 NE264 NE2226 51: HIS31 NE264 1.921 51: HIS51 NE2226 1.498 2.650 51: CYS80 SG477 0.207 1.984 1.570 51: Linking CYS-25 SG-14 and CYS-80 SG-477... 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 146 virtual sites 51: Added 10 dummy masses 51: Added 29 new constraints 51: 51: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 972 pairs 51: Before cleaning: 1256 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 51: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 51: 51: chain #res #atoms 51: 51: 1 'A' 58 488 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 'A' (488 atoms, 58 residues) 51: 51: Identified residue ASN24 as a starting terminus. 51: 51: Identified residue ARG81 as a ending terminus. 51: Start terminus ASN-24: NH3+ 51: End terminus ARG-81: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 58 residues with 635 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 655, now 650 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 321 dihedrals, 350 impropers, 955 angles 51: 972 pairs, 650 bonds and 137 virtual sites 51: 51: Total mass 6908.582 a.m.u. 51: 51: Total charge -6.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 51: 51: The Gromos43a1 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (65 ms) 51: [----------] 20 tests from G43a1/Pdb2gmxTest (943 ms total) 51: 51: [----------] 20 tests from G53a6/Pdb2gmxTest 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 25 donors and 23 acceptors were found. 51: There are 41 hydrogen bonds 51: Will use HISE for residue 8 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS3 HIS8 51: SG9 NE251 51: HIS8 NE251 1.055 51: MET12 SD83 0.763 0.990 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 267 pairs 51: Before cleaning: 312 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 51: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 128 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (128 atoms, 16 residues) 51: 51: Identified residue ALA2 as a starting terminus. 51: 51: Identified residue SER17 as a ending terminus. 51: Start terminus ALA-2: NH3+ 51: End terminus SER-17: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 167 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 174, now 169 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 90 dihedrals, 79 impropers, 245 angles 51: 267 pairs, 169 bonds and 0 virtual sites 51: 51: Total mass 1846.116 a.m.u. 51: 51: Total charge 0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 51: 51: The Gromos53a6 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (52 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 30 donors and 22 acceptors were found. 51: There are 36 hydrogen bonds 51: Will use HISE for residue 29 51: Will use HISE for residue 32 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS27 HIS29 51: SG90 NE2111 51: HIS29 NE2111 0.987 51: HIS32 NE2135 1.590 1.155 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 273 pairs 51: Before cleaning: 443 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 51: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 149 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (149 atoms, 16 residues) 51: 51: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue THR18 as a starting terminus. 51: 51: Identified residue PHE33 as a ending terminus. 51: Start terminus THR-18: NH3+ 51: End terminus PHE-33: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 206 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 220, now 215 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 93 dihedrals, 138 impropers, 324 angles 51: 273 pairs, 215 bonds and 0 virtual sites 51: 51: Total mass 2088.361 a.m.u. 51: 51: Total charge 1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 51: 51: The Gromos53a6 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (45 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 22 acceptors were found. 51: There are 26 hydrogen bonds 51: Will use HISE for residue 45 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS45 51: NE295 51: MET46 SD102 1.078 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 242 pairs 51: Before cleaning: 356 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 51: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 132 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (132 atoms, 16 residues) 51: 51: Identified residue ALA34 as a starting terminus. 51: 51: Identified residue ALA49 as a ending terminus. 51: Start terminus ALA-34: NH3+ 51: End terminus ALA-49: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 170 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 181, now 176 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 81 dihedrals, 104 impropers, 264 angles 51: 242 pairs, 176 bonds and 0 virtual sites 51: 51: Total mass 1861.132 a.m.u. 51: 51: Total charge -1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 51: 51: The Gromos53a6 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (39 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 21 acceptors were found. 51: There are 30 hydrogen bonds 51: Will use HISE for residue 60 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS60 51: NE285 51: CYS62 SG98 0.803 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 232 pairs 51: Before cleaning: 306 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 51: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 117 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (117 atoms, 16 residues) 51: 51: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue LYS50 as a starting terminus. 51: 51: Identified residue PRO65 as a ending terminus. 51: Start terminus LYS-50: NH3+ 51: End terminus PRO-65: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 152 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 161, now 156 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 78 dihedrals, 82 impropers, 231 angles 51: 232 pairs, 156 bonds and 0 virtual sites 51: 51: Total mass 1662.887 a.m.u. 51: 51: Total charge -0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 51: 51: The Gromos53a6 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (25 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 89 donors and 98 acceptors were found. 51: There are 129 hydrogen bonds 51: Will use HISE for residue 31 51: Will use HISE for residue 51 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS25 HIS31 HIS51 51: SG14 NE264 NE2226 51: HIS31 NE264 1.921 51: HIS51 NE2226 1.498 2.650 51: CYS80 SG477 0.207 1.984 1.570 51: Linking CYS-25 SG-14 and CYS-80 SG-477... 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 972 pairs 51: Before cleaning: 1270 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 51: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 51: 51: chain #res #atoms 51: 51: 1 'A' 58 488 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 'A' (488 atoms, 58 residues) 51: 51: Identified residue ASN24 as a starting terminus. 51: 51: Identified residue ARG81 as a ending terminus. 51: Start terminus ASN-24: NH3+ 51: End terminus ARG-81: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 58 residues with 639 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 659, now 654 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 321 dihedrals, 354 impropers, 963 angles 51: 972 pairs, 654 bonds and 0 virtual sites 51: 51: Total mass 6908.582 a.m.u. 51: 51: Total charge -6.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 51: 51: The Gromos53a6 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (82 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 25 donors and 23 acceptors were found. 51: There are 41 hydrogen bonds 51: Will use HISE for residue 8 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS3 HIS8 51: SG9 NE251 51: HIS8 NE251 1.055 51: MET12 SD83 0.763 0.990 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 39 virtual sites 51: Added 4 dummy masses 51: Added 8 new constraints 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 267 pairs 51: Before cleaning: 312 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 51: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 128 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (128 atoms, 16 residues) 51: 51: Identified residue ALA2 as a starting terminus. 51: 51: Identified residue SER17 as a ending terminus. 51: Start terminus ALA-2: NH3+ 51: End terminus SER-17: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 167 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 174, now 169 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 90 dihedrals, 79 impropers, 245 angles 51: 267 pairs, 169 bonds and 39 virtual sites 51: 51: Total mass 1846.116 a.m.u. 51: 51: Total charge 0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 51: 51: The Gromos53a6 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (43 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 30 donors and 22 acceptors were found. 51: There are 36 hydrogen bonds 51: Will use HISE for residue 29 51: Will use HISE for residue 32 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS27 HIS29 51: SG90 NE2111 51: HIS29 NE2111 0.987 51: HIS32 NE2135 1.590 1.155 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 57 virtual sites 51: Added 4 dummy masses 51: Added 10 new constraints 51: 51: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 273 pairs 51: Before cleaning: 443 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 51: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 149 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (149 atoms, 16 residues) 51: 51: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue THR18 as a starting terminus. 51: 51: Identified residue PHE33 as a ending terminus. 51: Start terminus THR-18: NH3+ 51: End terminus PHE-33: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 206 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 220, now 215 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 93 dihedrals, 138 impropers, 324 angles 51: 273 pairs, 215 bonds and 55 virtual sites 51: 51: Total mass 2088.361 a.m.u. 51: 51: Total charge 1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 51: 51: The Gromos53a6 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (61 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 22 acceptors were found. 51: There are 26 hydrogen bonds 51: Will use HISE for residue 45 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS45 51: NE295 51: MET46 SD102 1.078 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 38 virtual sites 51: Added 4 dummy masses 51: Added 8 new constraints 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 242 pairs 51: Before cleaning: 356 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 51: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 132 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (132 atoms, 16 residues) 51: 51: Identified residue ALA34 as a starting terminus. 51: 51: Identified residue ALA49 as a ending terminus. 51: Start terminus ALA-34: NH3+ 51: End terminus ALA-49: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 170 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 181, now 176 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 81 dihedrals, 104 impropers, 264 angles 51: 242 pairs, 176 bonds and 38 virtual sites 51: 51: Total mass 1861.132 a.m.u. 51: 51: Total charge -1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 51: 51: The Gromos53a6 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (33 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 21 acceptors were found. 51: There are 30 hydrogen bonds 51: Will use HISE for residue 60 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS60 51: NE285 51: CYS62 SG98 0.803 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 35 virtual sites 51: Added 4 dummy masses 51: Added 10 new constraints 51: 51: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 232 pairs 51: Before cleaning: 306 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 51: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 117 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (117 atoms, 16 residues) 51: 51: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue LYS50 as a starting terminus. 51: 51: Identified residue PRO65 as a ending terminus. 51: Start terminus LYS-50: NH3+ 51: End terminus PRO-65: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 152 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 161, now 156 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 78 dihedrals, 82 impropers, 231 angles 51: 232 pairs, 156 bonds and 33 virtual sites 51: 51: Total mass 1662.887 a.m.u. 51: 51: Total charge -0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 51: 51: The Gromos53a6 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (28 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 89 donors and 98 acceptors were found. 51: There are 129 hydrogen bonds 51: Will use HISE for residue 31 51: Will use HISE for residue 51 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS25 HIS31 HIS51 51: SG14 NE264 NE2226 51: HIS31 NE264 1.921 51: HIS51 NE2226 1.498 2.650 51: CYS80 SG477 0.207 1.984 1.570 51: Linking CYS-25 SG-14 and CYS-80 SG-477... 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 150 virtual sites 51: Added 10 dummy masses 51: Added 29 new constraints 51: 51: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 972 pairs 51: Before cleaning: 1270 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 51: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 51: 51: chain #res #atoms 51: 51: 1 'A' 58 488 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 'A' (488 atoms, 58 residues) 51: 51: Identified residue ASN24 as a starting terminus. 51: 51: Identified residue ARG81 as a ending terminus. 51: Start terminus ASN-24: NH3+ 51: End terminus ARG-81: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 58 residues with 639 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 659, now 654 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 321 dihedrals, 354 impropers, 963 angles 51: 972 pairs, 654 bonds and 141 virtual sites 51: 51: Total mass 6908.582 a.m.u. 51: 51: Total charge -6.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 51: 51: The Gromos53a6 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (65 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 25 donors and 23 acceptors were found. 51: There are 41 hydrogen bonds 51: Will use HISE for residue 8 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS3 HIS8 51: SG9 NE251 51: HIS8 NE251 1.055 51: MET12 SD83 0.763 0.990 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 267 pairs 51: Before cleaning: 312 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 51: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 128 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (128 atoms, 16 residues) 51: 51: Identified residue ALA2 as a starting terminus. 51: 51: Identified residue SER17 as a ending terminus. 51: Start terminus ALA-2: NH3+ 51: End terminus SER-17: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 167 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 174, now 169 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 90 dihedrals, 79 impropers, 245 angles 51: 267 pairs, 169 bonds and 0 virtual sites 51: 51: Total mass 1846.116 a.m.u. 51: 51: Total charge 0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 51: 51: The Gromos53a6 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (71 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 30 donors and 22 acceptors were found. 51: There are 36 hydrogen bonds 51: Will use HISE for residue 29 51: Will use HISE for residue 32 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS27 HIS29 51: SG90 NE2111 51: HIS29 NE2111 0.987 51: HIS32 NE2135 1.590 1.155 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 273 pairs 51: Before cleaning: 443 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 51: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 149 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (149 atoms, 16 residues) 51: 51: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue THR18 as a starting terminus. 51: 51: Identified residue PHE33 as a ending terminus. 51: Start terminus THR-18: NH3+ 51: End terminus PHE-33: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 206 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 220, now 215 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 93 dihedrals, 138 impropers, 324 angles 51: 273 pairs, 215 bonds and 0 virtual sites 51: 51: Total mass 2088.361 a.m.u. 51: 51: Total charge 1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 51: 51: The Gromos53a6 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (120 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 22 acceptors were found. 51: There are 26 hydrogen bonds 51: Will use HISE for residue 45 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS45 51: NE295 51: MET46 SD102 1.078 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 242 pairs 51: Before cleaning: 356 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 51: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 132 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (132 atoms, 16 residues) 51: 51: Identified residue ALA34 as a starting terminus. 51: 51: Identified residue ALA49 as a ending terminus. 51: Start terminus ALA-34: NH3+ 51: End terminus ALA-49: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 170 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 181, now 176 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 81 dihedrals, 104 impropers, 264 angles 51: 242 pairs, 176 bonds and 0 virtual sites 51: 51: Total mass 1861.132 a.m.u. 51: 51: Total charge -1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 51: 51: The Gromos53a6 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (52 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 21 acceptors were found. 51: There are 30 hydrogen bonds 51: Will use HISE for residue 60 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS60 51: NE285 51: CYS62 SG98 0.803 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 232 pairs 51: Before cleaning: 306 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 51: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 117 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (117 atoms, 16 residues) 51: 51: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue LYS50 as a starting terminus. 51: 51: Identified residue PRO65 as a ending terminus. 51: Start terminus LYS-50: NH3+ 51: End terminus PRO-65: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 152 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 161, now 156 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 78 dihedrals, 82 impropers, 231 angles 51: 232 pairs, 156 bonds and 0 virtual sites 51: 51: Total mass 1662.887 a.m.u. 51: 51: Total charge -0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 51: 51: The Gromos53a6 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (146 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 89 donors and 98 acceptors were found. 51: There are 129 hydrogen bonds 51: Will use HISE for residue 31 51: Will use HISE for residue 51 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS25 HIS31 HIS51 51: SG14 NE264 NE2226 51: HIS31 NE264 1.921 51: HIS51 NE2226 1.498 2.650 51: CYS80 SG477 0.207 1.984 1.570 51: Linking CYS-25 SG-14 and CYS-80 SG-477... 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 972 pairs 51: Before cleaning: 1270 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 51: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 51: 51: chain #res #atoms 51: 51: 1 'A' 58 488 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 'A' (488 atoms, 58 residues) 51: 51: Identified residue ASN24 as a starting terminus. 51: 51: Identified residue ARG81 as a ending terminus. 51: Start terminus ASN-24: NH3+ 51: End terminus ARG-81: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 58 residues with 639 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 659, now 654 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 321 dihedrals, 354 impropers, 963 angles 51: 972 pairs, 654 bonds and 0 virtual sites 51: 51: Total mass 6908.582 a.m.u. 51: 51: Total charge -6.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 51: 51: The Gromos53a6 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (109 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 25 donors and 23 acceptors were found. 51: There are 41 hydrogen bonds 51: Will use HISE for residue 8 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS3 HIS8 51: SG9 NE251 51: HIS8 NE251 1.055 51: MET12 SD83 0.763 0.990 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 39 virtual sites 51: Added 4 dummy masses 51: Added 8 new constraints 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 267 pairs 51: Before cleaning: 312 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 51: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 128 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (128 atoms, 16 residues) 51: 51: Identified residue ALA2 as a starting terminus. 51: 51: Identified residue SER17 as a ending terminus. 51: Start terminus ALA-2: NH3+ 51: End terminus SER-17: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 167 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 174, now 169 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 90 dihedrals, 79 impropers, 245 angles 51: 267 pairs, 169 bonds and 39 virtual sites 51: 51: Total mass 1846.116 a.m.u. 51: 51: Total charge 0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 51: 51: The Gromos53a6 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (68 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 30 donors and 22 acceptors were found. 51: There are 36 hydrogen bonds 51: Will use HISE for residue 29 51: Will use HISE for residue 32 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS27 HIS29 51: SG90 NE2111 51: HIS29 NE2111 0.987 51: HIS32 NE2135 1.590 1.155 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 57 virtual sites 51: Added 4 dummy masses 51: Added 10 new constraints 51: 51: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 273 pairs 51: Before cleaning: 443 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 51: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 149 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (149 atoms, 16 residues) 51: 51: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue THR18 as a starting terminus. 51: 51: Identified residue PHE33 as a ending terminus. 51: Start terminus THR-18: NH3+ 51: End terminus PHE-33: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 206 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 220, now 215 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 93 dihedrals, 138 impropers, 324 angles 51: 273 pairs, 215 bonds and 55 virtual sites 51: 51: Total mass 2088.361 a.m.u. 51: 51: Total charge 1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 51: 51: The Gromos53a6 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (103 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 22 acceptors were found. 51: There are 26 hydrogen bonds 51: Will use HISE for residue 45 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS45 51: NE295 51: MET46 SD102 1.078 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 38 virtual sites 51: Added 4 dummy masses 51: Added 8 new constraints 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 242 pairs 51: Before cleaning: 356 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 51: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 132 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (132 atoms, 16 residues) 51: 51: Identified residue ALA34 as a starting terminus. 51: 51: Identified residue ALA49 as a ending terminus. 51: Start terminus ALA-34: NH3+ 51: End terminus ALA-49: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 170 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 181, now 176 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 81 dihedrals, 104 impropers, 264 angles 51: 242 pairs, 176 bonds and 38 virtual sites 51: 51: Total mass 1861.132 a.m.u. 51: 51: Total charge -1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 51: 51: The Gromos53a6 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (87 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 21 acceptors were found. 51: There are 30 hydrogen bonds 51: Will use HISE for residue 60 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS60 51: NE285 51: CYS62 SG98 0.803 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 35 virtual sites 51: Added 4 dummy masses 51: Added 10 new constraints 51: 51: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 232 pairs 51: Before cleaning: 306 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 51: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 117 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (117 atoms, 16 residues) 51: 51: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue LYS50 as a starting terminus. 51: 51: Identified residue PRO65 as a ending terminus. 51: Start terminus LYS-50: NH3+ 51: End terminus PRO-65: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 152 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 161, now 156 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 78 dihedrals, 82 impropers, 231 angles 51: 232 pairs, 156 bonds and 33 virtual sites 51: 51: Total mass 1662.887 a.m.u. 51: 51: Total charge -0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 51: 51: The Gromos53a6 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (48 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 89 donors and 98 acceptors were found. 51: There are 129 hydrogen bonds 51: Will use HISE for residue 31 51: Will use HISE for residue 51 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS25 HIS31 HIS51 51: SG14 NE264 NE2226 51: HIS31 NE264 1.921 51: HIS51 NE2226 1.498 2.650 51: CYS80 SG477 0.207 1.984 1.570 51: Linking CYS-25 SG-14 and CYS-80 SG-477... 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 150 virtual sites 51: Added 10 dummy masses 51: Added 29 new constraints 51: 51: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 972 pairs 51: Before cleaning: 1270 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 51: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 51: 51: chain #res #atoms 51: 51: 1 'A' 58 488 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 'A' (488 atoms, 58 residues) 51: 51: Identified residue ASN24 as a starting terminus. 51: 51: Identified residue ARG81 as a ending terminus. 51: Start terminus ASN-24: NH3+ 51: End terminus ARG-81: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 58 residues with 639 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 659, now 654 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 321 dihedrals, 354 impropers, 963 angles 51: 972 pairs, 654 bonds and 141 virtual sites 51: 51: Total mass 6908.582 a.m.u. 51: 51: Total charge -6.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 51: 51: The Gromos53a6 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (115 ms) 51: [----------] 20 tests from G53a6/Pdb2gmxTest (1414 ms total) 51: 51: [----------] Global test environment tear-down 51: [==========] 40 tests from 2 test suites ran. (2358 ms total) 51: [ PASSED ] 40 tests. 51/87 Test #51: Pdb2gmx2Test .............................. Passed 2.39 sec test 52 Start 52: Pdb2gmx3Test 52: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/pdb2gmx3-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/Pdb2gmx3Test.xml" 52: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests 52: Test timeout computed to be: 1920 52: [==========] Running 39 tests from 6 test suites. 52: [----------] Global test environment set-up. 52: [----------] 10 tests from Amber/Pdb2gmxTest 52: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Before cleaning: 653 pairs 52: Before cleaning: 691 dihedrals 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 255, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 691 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 0 virtual sites 52: 52: Total mass 1846.132 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Amber99sb-ildn force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (108 ms) 52: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Before cleaning: 748 pairs 52: Before cleaning: 788 dihedrals 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 291, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 788 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 0 virtual sites 52: 52: Total mass 2088.366 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Amber99sb-ildn force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (53 ms) 52: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Before cleaning: 676 pairs 52: Before cleaning: 727 dihedrals 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 262, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 727 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 0 virtual sites 52: 52: Total mass 1861.124 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Amber99sb-ildn force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (49 ms) 52: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Before cleaning: 603 pairs 52: Before cleaning: 634 dihedrals 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 233, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 634 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 0 virtual sites 52: 52: Total mass 1662.888 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Amber99sb-ildn force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (66 ms) 52: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Before cleaning: 2499 pairs 52: Before cleaning: 2631 dihedrals 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 952, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2631 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 0 virtual sites 52: 52: Total mass 6908.576 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Amber99sb-ildn force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (62 ms) 52: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Marked 124 virtual sites 52: Added 16 dummy masses 52: Added 26 new constraints 52: Before cleaning: 653 pairs 52: Before cleaning: 691 dihedrals 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 255, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 691 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 130 virtual sites 52: 52: Total mass 1846.132 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Amber99sb-ildn force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (49 ms) 52: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Marked 132 virtual sites 52: Added 10 dummy masses 52: Added 19 new constraints 52: Before cleaning: 748 pairs 52: Before cleaning: 788 dihedrals 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 291, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 788 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 133 virtual sites 52: 52: Total mass 2088.366 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Amber99sb-ildn force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (42 ms) 52: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Marked 123 virtual sites 52: Added 22 dummy masses 52: Added 35 new constraints 52: Before cleaning: 676 pairs 52: Before cleaning: 727 dihedrals 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 262, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 727 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 132 virtual sites 52: 52: Total mass 1861.124 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Amber99sb-ildn force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (47 ms) 52: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Marked 111 virtual sites 52: Added 18 dummy masses 52: Added 31 new constraints 52: Before cleaning: 603 pairs 52: Before cleaning: 634 dihedrals 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 233, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 634 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 116 virtual sites 52: 52: Total mass 1662.888 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Amber99sb-ildn force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (40 ms) 52: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Marked 447 virtual sites 52: Added 58 dummy masses 52: Added 101 new constraints 52: Before cleaning: 2499 pairs 52: Before cleaning: 2631 dihedrals 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 952, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2631 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 462 virtual sites 52: 52: Total mass 6908.576 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Amber99sb-ildn force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (109 ms) 52: [----------] 10 tests from Amber/Pdb2gmxTest (641 ms total) 52: 52: [----------] 1 test from AmberTip4p/Pdb2gmxTest 52: [ RUN ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/tip4p.pdb... 52: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 2 4 (only water) 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 (4 atoms, 2 residues) 52: 52: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 2 residues with 8 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 4, now 4 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 0 dihedrals, 0 impropers, 2 angles 52: 0 pairs, 4 bonds and 0 virtual sites 52: 52: Total mass 36.032 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/tip4p.pdb. 52: 52: The Amber99sb-ildn force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (32 ms) 52: [----------] 1 test from AmberTip4p/Pdb2gmxTest (35 ms total) 52: 52: [----------] 12 tests from Charmm/Pdb2gmxTest 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 14 cmap torsion pairs 52: 52: There are 663 dihedrals, 48 impropers, 457 angles 52: 650 pairs, 254 bonds and 0 virtual sites 52: 52: Total mass 1846.115 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (66 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 14 cmap torsion pairs 52: 52: There are 778 dihedrals, 49 impropers, 516 angles 52: 736 pairs, 290 bonds and 0 virtual sites 52: 52: Total mass 2088.361 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (53 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 14 cmap torsion pairs 52: 52: There are 696 dihedrals, 39 impropers, 472 angles 52: 667 pairs, 261 bonds and 0 virtual sites 52: 52: Total mass 1861.130 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (34 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 14 cmap torsion pairs 52: 52: There are 618 dihedrals, 38 impropers, 419 angles 52: 597 pairs, 232 bonds and 0 virtual sites 52: 52: Total mass 1662.885 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (56 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 56 cmap torsion pairs 52: 52: There are 2524 dihedrals, 149 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 0 virtual sites 52: 52: Total mass 6908.566 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (154 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 39 pairs 52: Before cleaning: 39 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/monomer.pdb... 52: Read 'GLU', 9 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 52: 52: chain #res #atoms 52: 52: 1 'X' 1 9 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'X' (9 atoms, 1 residues) 52: 52: Identified residue GLU1 as a starting terminus. 52: 52: Identified residue GLU1 as a ending terminus. 52: Start terminus GLU-1: NH3+ 52: End terminus GLU-1: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 1 residues with 18 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 17, now 17 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 39 dihedrals, 2 impropers, 30 angles 52: 39 pairs, 17 bonds and 0 virtual sites 52: 52: Total mass 146.123 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/monomer.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file (37 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Marked 124 virtual sites 52: Added 16 dummy masses 52: Added 26 new constraints 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 14 cmap torsion pairs 52: 52: There are 663 dihedrals, 48 impropers, 457 angles 52: 650 pairs, 254 bonds and 130 virtual sites 52: 52: Total mass 1846.115 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (65 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Marked 132 virtual sites 52: Added 10 dummy masses 52: Added 19 new constraints 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 14 cmap torsion pairs 52: 52: There are 778 dihedrals, 49 impropers, 516 angles 52: 736 pairs, 290 bonds and 133 virtual sites 52: 52: Total mass 2088.361 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (54 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Marked 123 virtual sites 52: Added 22 dummy masses 52: Added 35 new constraints 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 14 cmap torsion pairs 52: 52: There are 696 dihedrals, 39 impropers, 472 angles 52: 667 pairs, 261 bonds and 132 virtual sites 52: 52: Total mass 1861.130 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (57 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Marked 111 virtual sites 52: Added 18 dummy masses 52: Added 31 new constraints 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 14 cmap torsion pairs 52: 52: There are 618 dihedrals, 38 impropers, 419 angles 52: 597 pairs, 232 bonds and 116 virtual sites 52: 52: Total mass 1662.885 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (37 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Marked 447 virtual sites 52: Added 58 dummy masses 52: Added 101 new constraints 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 56 cmap torsion pairs 52: 52: There are 2524 dihedrals, 149 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 462 virtual sites 52: 52: Total mass 6908.566 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (108 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Marked 8 virtual sites 52: Added 2 dummy masses 52: Added 3 new constraints 52: Before cleaning: 39 pairs 52: Before cleaning: 39 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/monomer.pdb... 52: Read 'GLU', 9 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 52: 52: chain #res #atoms 52: 52: 1 'X' 1 9 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'X' (9 atoms, 1 residues) 52: 52: Identified residue GLU1 as a starting terminus. 52: 52: Identified residue GLU1 as a ending terminus. 52: Start terminus GLU-1: NH3+ 52: End terminus GLU-1: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 1 residues with 18 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 17, now 17 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 39 dihedrals, 2 impropers, 30 angles 52: 39 pairs, 17 bonds and 9 virtual sites 52: 52: Total mass 146.123 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/monomer.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file (39 ms) 52: [----------] 12 tests from Charmm/Pdb2gmxTest (778 ms total) 52: 52: [----------] 8 tests from ChainSep/Pdb2gmxTest 52: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 651 pairs 52: Before cleaning: 661 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on changing chain id only (ignoring TER records). 52: 52: Merged chains into joint molecule definitions at 2 places. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 16 127 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (127 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue GLU5 as a ending terminus. 52: 52: Identified residue PHE6 as a starting terminus. 52: 52: Identified residue MET12 as a ending terminus. 52: 52: Identified residue ASN13 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus GLU-5: COO- 52: Start terminus PHE-6: NH3+ 52: End terminus MET-12: COO- 52: Start terminus ASN-13: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 258 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 258, now 258 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 10 cmap torsion pairs 52: 52: There are 661 dihedrals, 46 impropers, 463 angles 52: 648 pairs, 258 bonds and 0 virtual sites 52: 52: Total mass 1882.146 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file (80 ms) 52: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 123 pairs 52: Before cleaning: 123 dihedrals 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 10 donors and 7 acceptors were found. 52: There are 7 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS8 52: NE223 52: MET12 SD55 0.990 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 317 pairs 52: Before cleaning: 322 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 211 pairs 52: Before cleaning: 216 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on changing chain id only (ignoring TER records). 52: 52: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 4 28 52: 52: 2 'B' 7 58 52: 52: 3 'C' 5 41 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (28 atoms, 4 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue GLU5 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus GLU-5: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 4 residues with 51 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 50, now 50 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2 cmap torsion pairs 52: 52: There are 123 dihedrals, 9 impropers, 88 angles 52: 123 pairs, 50 bonds and 0 virtual sites 52: 52: Total mass 434.421 a.m.u. 52: 52: Total charge -2.000 e 52: 52: Writing topology 52: 52: Processing chain 2 'B' (58 atoms, 7 residues) 52: 52: Identified residue PHE6 as a starting terminus. 52: 52: Identified residue MET12 as a ending terminus. 52: Start terminus PHE-6: NH3+ 52: End terminus MET-12: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 7 residues with 124 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 125, now 125 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 5 cmap torsion pairs 52: 52: There are 322 dihedrals, 19 impropers, 227 angles 52: 314 pairs, 125 bonds and 0 virtual sites 52: 52: Total mass 846.083 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Processing chain 3 'C' (41 atoms, 5 residues) 52: 52: Identified residue ASN13 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ASN-13: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 5 residues with 83 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 83, now 83 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 3 cmap torsion pairs 52: 52: There are 216 dihedrals, 18 impropers, 148 angles 52: 211 pairs, 83 bonds and 0 virtual sites 52: 52: Total mass 601.643 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Including chain 1 in system: 51 atoms 4 residues 52: 52: Including chain 2 in system: 124 atoms 7 residues 52: 52: Including chain 3 in system: 83 atoms 5 residues 52: 52: Now there are 258 atoms and 16 residues 52: 52: Total mass in system 1882.146 a.m.u. 52: 52: Total charge in system 0.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file (82 ms) 52: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 651 pairs 52: Before cleaning: 661 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records only (ignoring chain id). 52: 52: Merged chains into joint molecule definitions at 2 places. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 16 127 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (127 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue ILE9 as a ending terminus. 52: 52: Identified residue LYS10 as a starting terminus. 52: 52: Identified residue MET12 as a ending terminus. 52: 52: Identified residue ASN13 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus ILE-9: COO- 52: Start terminus LYS-10: NH3+ 52: End terminus MET-12: COO- 52: Start terminus ASN-13: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 258 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 258, now 258 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 10 cmap torsion pairs 52: 52: There are 661 dihedrals, 46 impropers, 463 angles 52: 648 pairs, 258 bonds and 0 virtual sites 52: 52: Total mass 1882.146 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file (45 ms) 52: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 10 donors and 12 acceptors were found. 52: There are 13 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 52: SG9 52: HIS8 NE251 1.055 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 288 pairs 52: Before cleaning: 293 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 152 pairs 52: Before cleaning: 152 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 211 pairs 52: Before cleaning: 216 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records only (ignoring chain id). 52: 52: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 8 61 52: 52: 2 'B' 3 25 52: 52: 3 'C' 5 41 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (61 atoms, 8 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue ILE9 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus ILE-9: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 8 residues with 114 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 115, now 115 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 6 cmap torsion pairs 52: 52: There are 293 dihedrals, 23 impropers, 203 angles 52: 285 pairs, 115 bonds and 0 virtual sites 52: 52: Total mass 888.952 a.m.u. 52: 52: Total charge -2.000 e 52: 52: Writing topology 52: 52: Processing chain 2 'B' (25 atoms, 3 residues) 52: 52: Identified residue LYS10 as a starting terminus. 52: 52: Identified residue MET12 as a ending terminus. 52: Start terminus LYS-10: NH3+ 52: End terminus MET-12: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 3 residues with 61 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 60, now 60 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 1 cmap torsion pairs 52: 52: There are 152 dihedrals, 5 impropers, 112 angles 52: 152 pairs, 60 bonds and 0 virtual sites 52: 52: Total mass 391.552 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Processing chain 3 'C' (41 atoms, 5 residues) 52: 52: Identified residue ASN13 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ASN-13: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 5 residues with 83 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 83, now 83 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 3 cmap torsion pairs 52: 52: There are 216 dihedrals, 18 impropers, 148 angles 52: 211 pairs, 83 bonds and 0 virtual sites 52: 52: Total mass 601.643 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Including chain 1 in system: 114 atoms 8 residues 52: 52: Including chain 2 in system: 61 atoms 3 residues 52: 52: Including chain 3 in system: 83 atoms 5 residues 52: 52: Now there are 258 atoms and 16 residues 52: 52: Total mass in system 1882.146 a.m.u. 52: 52: Total charge in system 0.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file (42 ms) 52: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 650 pairs 52: Before cleaning: 660 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: Merged chains into joint molecule definitions at 3 places. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 16 127 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (127 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue GLU5 as a ending terminus. 52: 52: Identified residue PHE6 as a starting terminus. 52: 52: Identified residue ILE9 as a ending terminus. 52: 52: Identified residue LYS10 as a starting terminus. 52: 52: Identified residue MET12 as a ending terminus. 52: 52: Identified residue ASN13 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus GLU-5: COO- 52: Start terminus PHE-6: NH3+ 52: End terminus ILE-9: COO- 52: Start terminus LYS-10: NH3+ 52: End terminus MET-12: COO- 52: Start terminus ASN-13: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 261 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 260, now 260 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 8 cmap torsion pairs 52: 52: There are 660 dihedrals, 45 impropers, 466 angles 52: 647 pairs, 260 bonds and 0 virtual sites 52: 52: Total mass 1900.162 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file (40 ms) 52: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 52: 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 123 pairs 52: Before cleaning: 123 dihedrals 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 6 donors and 4 acceptors were found. 52: There are 3 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 164 pairs 52: Before cleaning: 169 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 152 pairs 52: Before cleaning: 152 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 211 pairs 52: Before cleaning: 216 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 52: 52: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 4 28 52: 52: 2 'B' 4 33 52: 52: 3 'B' 3 25 52: 52: 4 'C' 5 41 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (28 atoms, 4 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue GLU5 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus GLU-5: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 4 residues with 51 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 50, now 50 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2 cmap torsion pairs 52: 52: There are 123 dihedrals, 9 impropers, 88 angles 52: 123 pairs, 50 bonds and 0 virtual sites 52: 52: Total mass 434.421 a.m.u. 52: 52: Total charge -2.000 e 52: 52: Writing topology 52: 52: Processing chain 2 'B' (33 atoms, 4 residues) 52: 52: Identified residue PHE6 as a starting terminus. 52: 52: Identified residue ILE9 as a ending terminus. 52: Start terminus PHE-6: NH3+ 52: End terminus ILE-9: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 4 residues with 66 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 67, now 67 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2 cmap torsion pairs 52: 52: There are 169 dihedrals, 13 impropers, 118 angles 52: 161 pairs, 67 bonds and 0 virtual sites 52: 52: Total mass 472.547 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Processing chain 3 'B' (25 atoms, 3 residues) 52: 52: Identified residue LYS10 as a starting terminus. 52: 52: Identified residue MET12 as a ending terminus. 52: Start terminus LYS-10: NH3+ 52: End terminus MET-12: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 3 residues with 61 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 60, now 60 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 1 cmap torsion pairs 52: 52: There are 152 dihedrals, 5 impropers, 112 angles 52: 152 pairs, 60 bonds and 0 virtual sites 52: 52: Total mass 391.552 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Processing chain 4 'C' (41 atoms, 5 residues) 52: 52: Identified residue ASN13 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ASN-13: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 5 residues with 83 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 83, now 83 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 3 cmap torsion pairs 52: 52: There are 216 dihedrals, 18 impropers, 148 angles 52: 211 pairs, 83 bonds and 0 virtual sites 52: 52: Total mass 601.643 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Including chain 1 in system: 51 atoms 4 residues 52: 52: Including chain 2 in system: 66 atoms 4 residues 52: 52: Including chain 3 in system: 61 atoms 3 residues 52: 52: Including chain 4 in system: 83 atoms 5 residues 52: 52: Now there are 261 atoms and 16 residues 52: 52: Total mass in system 1900.162 a.m.u. 52: 52: Total charge in system 0.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file (46 ms) 52: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 652 pairs 52: Before cleaning: 662 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records and chain id changing. 52: 52: Merged chains into joint molecule definitions at 1 places. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 16 127 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (127 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue MET12 as a ending terminus. 52: 52: Identified residue ASN13 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus MET-12: COO- 52: Start terminus ASN-13: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 256, now 256 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 12 cmap torsion pairs 52: 52: There are 662 dihedrals, 47 impropers, 460 angles 52: 649 pairs, 256 bonds and 0 virtual sites 52: 52: Total mass 1864.131 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file (46 ms) 52: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 14 donors and 15 acceptors were found. 52: There are 20 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 441 pairs 52: Before cleaning: 446 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 211 pairs 52: Before cleaning: 216 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records and chain id changing. 52: 52: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 11 86 52: 52: 2 'C' 5 41 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (86 atoms, 11 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue MET12 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus MET-12: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 11 residues with 172 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 173, now 173 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 9 cmap torsion pairs 52: 52: There are 446 dihedrals, 29 impropers, 312 angles 52: 438 pairs, 173 bonds and 0 virtual sites 52: 52: Total mass 1262.488 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Processing chain 2 'C' (41 atoms, 5 residues) 52: 52: Identified residue ASN13 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ASN-13: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 5 residues with 83 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 83, now 83 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 3 cmap torsion pairs 52: 52: There are 216 dihedrals, 18 impropers, 148 angles 52: 211 pairs, 83 bonds and 0 virtual sites 52: 52: Total mass 601.643 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Including chain 1 in system: 172 atoms 11 residues 52: 52: Including chain 2 in system: 83 atoms 5 residues 52: 52: Now there are 255 atoms and 16 residues 52: 52: Total mass in system 1864.131 a.m.u. 52: 52: Total charge in system 0.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file (28 ms) 52: [----------] 8 tests from ChainSep/Pdb2gmxTest (413 ms total) 52: 52: [----------] 4 tests from ChainChanges/Pdb2gmxTest 52: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 83 pairs 52: Before cleaning: 83 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 145 pairs 52: Before cleaning: 150 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb... 52: Read 'Fragments of peptides and ions', 47 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on changing chain id only (ignoring TER records). 52: 52: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 3 19 52: 52: 2 'B' 3 28 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (19 atoms, 3 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue ASP4 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus ASP-4: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 3 residues with 36 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 35, now 35 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 1 cmap torsion pairs 52: 52: There are 83 dihedrals, 6 impropers, 61 angles 52: 83 pairs, 35 bonds and 0 virtual sites 52: 52: Total mass 306.314 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Processing chain 2 'B' (28 atoms, 3 residues) 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue TRP20 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus TRP-20: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 3 residues with 57 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 58, now 58 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 1 cmap torsion pairs 52: 52: There are 150 dihedrals, 5 impropers, 103 angles 52: 142 pairs, 58 bonds and 0 virtual sites 52: 52: Total mass 404.468 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Including chain 1 in system: 36 atoms 3 residues 52: 52: Including chain 2 in system: 57 atoms 3 residues 52: 52: Now there are 93 atoms and 6 residues 52: 52: Total mass in system 710.782 a.m.u. 52: 52: Total charge in system -1.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file (21 ms) 52: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 83 pairs 52: Before cleaning: 83 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 145 pairs 52: Before cleaning: 150 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb... 52: Read 'Fragments of peptides and ions', 47 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records only (ignoring chain id). 52: 52: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 3 19 52: 52: 2 'B' 3 28 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (19 atoms, 3 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue ASP4 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus ASP-4: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 3 residues with 36 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 35, now 35 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 1 cmap torsion pairs 52: 52: There are 83 dihedrals, 6 impropers, 61 angles 52: 83 pairs, 35 bonds and 0 virtual sites 52: 52: Total mass 306.314 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Processing chain 2 'B' (28 atoms, 3 residues) 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue TRP20 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus TRP-20: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 3 residues with 57 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 58, now 58 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 1 cmap torsion pairs 52: 52: There are 150 dihedrals, 5 impropers, 103 angles 52: 142 pairs, 58 bonds and 0 virtual sites 52: 52: Total mass 404.468 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Including chain 1 in system: 36 atoms 3 residues 52: 52: Including chain 2 in system: 57 atoms 3 residues 52: 52: Now there are 93 atoms and 6 residues 52: 52: Total mass in system 710.782 a.m.u. 52: 52: Total charge in system -1.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file (45 ms) 52: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 83 pairs 52: Before cleaning: 83 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 145 pairs 52: Before cleaning: 150 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb... 52: Read 'Fragments of peptides and ions', 47 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 3 19 52: 52: 2 'B' 3 28 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (19 atoms, 3 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue ASP4 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus ASP-4: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 3 residues with 36 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 35, now 35 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 1 cmap torsion pairs 52: 52: There are 83 dihedrals, 6 impropers, 61 angles 52: 83 pairs, 35 bonds and 0 virtual sites 52: 52: Total mass 306.314 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Processing chain 2 'B' (28 atoms, 3 residues) 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue TRP20 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus TRP-20: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 3 residues with 57 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 58, now 58 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 1 cmap torsion pairs 52: 52: There are 150 dihedrals, 5 impropers, 103 angles 52: 142 pairs, 58 bonds and 0 virtual sites 52: 52: Total mass 404.468 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Including chain 1 in system: 36 atoms 3 residues 52: 52: Including chain 2 in system: 57 atoms 3 residues 52: 52: Now there are 93 atoms and 6 residues 52: 52: Total mass in system 710.782 a.m.u. 52: 52: Total charge in system -1.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file (31 ms) 52: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 83 pairs 52: Before cleaning: 83 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 145 pairs 52: Before cleaning: 150 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb... 52: Read 'Fragments of peptides and ions', 47 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records and chain id changing. 52: 52: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 3 19 52: 52: 2 'B' 3 28 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (19 atoms, 3 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue ASP4 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus ASP-4: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 3 residues with 36 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 35, now 35 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 1 cmap torsion pairs 52: 52: There are 83 dihedrals, 6 impropers, 61 angles 52: 83 pairs, 35 bonds and 0 virtual sites 52: 52: Total mass 306.314 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Processing chain 2 'B' (28 atoms, 3 residues) 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue TRP20 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus TRP-20: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 3 residues with 57 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 58, now 58 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 1 cmap torsion pairs 52: 52: There are 150 dihedrals, 5 impropers, 103 angles 52: 142 pairs, 58 bonds and 0 virtual sites 52: 52: Total mass 404.468 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Including chain 1 in system: 36 atoms 3 residues 52: 52: Including chain 2 in system: 57 atoms 3 residues 52: 52: Now there are 93 atoms and 6 residues 52: 52: Total mass in system 710.782 a.m.u. 52: 52: Total charge in system -1.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file (32 ms) 52: [----------] 4 tests from ChainChanges/Pdb2gmxTest (136 ms total) 52: 52: [----------] 4 tests from Cyclic/Pdb2gmxTest 52: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: WARNING: all CONECT records are ignored 52: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 52: 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 6040 pairs 52: Before cleaning: 6605 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 6040 pairs 52: Before cleaning: 6605 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 52: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 52: 52: Moved all the water blocks to the end 52: 52: There are 3 chains and 2 blocks of water and 175 residues with 3087 atoms 52: 52: chain #res #atoms 52: 52: 1 'P' 71 1527 52: 52: 2 'Q' 71 1527 52: 52: 3 'Q' 7 7 52: 52: 4 ' ' 10 10 (only water) 52: 52: 5 ' ' 16 16 (only water) 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'P' (1527 atoms, 71 residues) 52: 52: Identified residue G1 as a starting terminus. 52: 52: Identified residue U71 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 71 residues with 2297 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 2481, now 2481 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 6605 dihedrals, 183 impropers, 4434 angles 52: 5827 pairs, 2481 bonds and 0 virtual sites 52: 52: Total mass 22984.514 a.m.u. 52: 52: Total charge -71.000 e 52: 52: Writing topology 52: 52: Processing chain 2 'Q' (1527 atoms, 71 residues) 52: 52: Identified residue G1 as a starting terminus. 52: 52: Identified residue U71 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 71 residues with 2297 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 2481, now 2481 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 6605 dihedrals, 183 impropers, 4434 angles 52: 5827 pairs, 2481 bonds and 0 virtual sites 52: 52: Total mass 22984.514 a.m.u. 52: 52: Total charge -71.000 e 52: 52: Writing topology 52: 52: Processing chain 3 'Q' (7 atoms, 7 residues) 52: 52: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 52: 52: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 52: 52: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 52: 52: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 52: 52: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 52: 52: Disabling further notes about ions. 52: 52: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 7 residues with 7 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: No bonds 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 0 dihedrals, 0 impropers, 0 angles 52: 0 pairs, 0 bonds and 0 virtual sites 52: 52: Total mass 170.135 a.m.u. 52: 52: Total charge 14.000 e 52: 52: Writing topology 52: 52: Processing chain 4 (10 atoms, 10 residues) 52: 52: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 10 residues with 30 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 30, now 30 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 0 dihedrals, 0 impropers, 30 angles 52: 0 pairs, 30 bonds and 0 virtual sites 52: 52: Total mass 180.154 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Processing chain 5 (16 atoms, 16 residues) 52: 52: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 48 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 48, now 48 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 0 dihedrals, 0 impropers, 48 angles 52: 0 pairs, 48 bonds and 0 virtual sites 52: 52: Total mass 288.246 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Including chain 1 in system: 2297 atoms 71 residues 52: 52: Including chain 2 in system: 2297 atoms 71 residues 52: 52: Including chain 3 in system: 7 atoms 7 residues 52: 52: Including chain 4 in system: 30 atoms 10 residues 52: 52: Including chain 5 in system: 48 atoms 16 residues 52: 52: Now there are 4679 atoms and 175 residues 52: 52: Total mass in system 46607.563 a.m.u. 52: 52: Total charge in system -128.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file (310 ms) 52: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 2325 pairs 52: Before cleaning: 2325 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 52: Read 'CARNOCYCLIN-A', 413 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 60 413 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (413 atoms, 60 residues) 52: 52: Identified residue LEU1 as a starting terminus. 52: 52: Identified residue LEU60 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 60 residues with 878 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 880, now 880 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 60 cmap torsion pairs 52: 52: There are 2325 dihedrals, 137 impropers, 1614 angles 52: 2319 pairs, 880 bonds and 0 virtual sites 52: 52: Total mass 5866.087 a.m.u. 52: 52: Total charge 4.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file (100 ms) 52: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: WARNING: all CONECT records are ignored 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 12080 pairs 52: Before cleaning: 13210 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 52: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: Moved all the water blocks to the end 52: 52: Merged chains into joint molecule definitions at 2 places. 52: 52: There are 1 chains and 2 blocks of water and 175 residues with 3087 atoms 52: 52: chain #res #atoms 52: 52: 1 'P' 149 3061 52: 52: 2 ' ' 10 10 (only water) 52: 52: 3 ' ' 16 16 (only water) 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'P' (3061 atoms, 149 residues) 52: 52: Identified residue G1 as a starting terminus. 52: 52: Identified residue U71 as a ending terminus. 52: 52: Identified residue G1 as a starting terminus. 52: 52: Identified residue U71 as a ending terminus. 52: 52: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 52: 52: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 52: 52: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 52: 52: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 52: 52: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 52: 52: Disabling further notes about ions. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 149 residues with 4601 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 4962, now 4962 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 13210 dihedrals, 366 impropers, 8868 angles 52: 11654 pairs, 4962 bonds and 0 virtual sites 52: 52: Total mass 46139.162 a.m.u. 52: 52: Total charge -128.000 e 52: 52: Writing topology 52: 52: Processing chain 2 (10 atoms, 10 residues) 52: 52: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 10 residues with 30 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 30, now 30 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 0 dihedrals, 0 impropers, 30 angles 52: 0 pairs, 30 bonds and 0 virtual sites 52: 52: Total mass 180.154 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Processing chain 3 (16 atoms, 16 residues) 52: 52: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 48 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 48, now 48 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 0 dihedrals, 0 impropers, 48 angles 52: 0 pairs, 48 bonds and 0 virtual sites 52: 52: Total mass 288.246 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Including chain 1 in system: 4601 atoms 149 residues 52: 52: Including chain 2 in system: 30 atoms 10 residues 52: 52: Including chain 3 in system: 48 atoms 16 residues 52: 52: Now there are 4679 atoms and 175 residues 52: 52: Total mass in system 46607.563 a.m.u. 52: 52: Total charge in system -128.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file (585 ms) 52: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 2325 pairs 52: Before cleaning: 2325 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 52: Read 'CARNOCYCLIN-A', 413 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 60 413 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (413 atoms, 60 residues) 52: 52: Identified residue LEU1 as a starting terminus. 52: 52: Identified residue LEU60 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 60 residues with 878 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 880, now 880 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 60 cmap torsion pairs 52: 52: There are 2325 dihedrals, 137 impropers, 1614 angles 52: 2319 pairs, 880 bonds and 0 virtual sites 52: 52: Total mass 5866.087 a.m.u. 52: 52: Total charge 4.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file (136 ms) 52: [----------] 4 tests from Cyclic/Pdb2gmxTest (1142 ms total) 52: 52: [----------] Global test environment tear-down 52: [==========] 39 tests from 6 test suites ran. (3148 ms total) 52: [ PASSED ] 39 tests. 52/87 Test #52: Pdb2gmx3Test .............................. Passed 3.18 sec test 53 Start 53: CorrelationsTest 53: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/correlations-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/CorrelationsTest.xml" 53: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/correlationfunctions/tests 53: Test timeout computed to be: 30 53: [==========] Running 21 tests from 3 test suites. 53: [----------] Global test environment set-up. 53: [----------] 10 tests from AutocorrTest 53: [ RUN ] AutocorrTest.EacNormal 53: [ OK ] AutocorrTest.EacNormal (60 ms) 53: [ RUN ] AutocorrTest.EacNoNormalize 53: [ OK ] AutocorrTest.EacNoNormalize (51 ms) 53: [ RUN ] AutocorrTest.EacCos 53: [ OK ] AutocorrTest.EacCos (88 ms) 53: [ RUN ] AutocorrTest.EacVector 53: [ OK ] AutocorrTest.EacVector (134 ms) 53: [ RUN ] AutocorrTest.EacRcross 53: [ OK ] AutocorrTest.EacRcross (3 ms) 53: [ RUN ] AutocorrTest.EacP0 53: [ OK ] AutocorrTest.EacP0 (136 ms) 53: [ RUN ] AutocorrTest.EacP1 53: [ OK ] AutocorrTest.EacP1 (136 ms) 53: [ RUN ] AutocorrTest.EacP2 53: [ OK ] AutocorrTest.EacP2 (307 ms) 53: [ RUN ] AutocorrTest.EacP3 53: [ OK ] AutocorrTest.EacP3 (2 ms) 53: [ RUN ] AutocorrTest.EacP4 53: [ OK ] AutocorrTest.EacP4 (133 ms) 53: [----------] 10 tests from AutocorrTest (1056 ms total) 53: 53: [----------] 10 tests from ExpfitTest 53: [ RUN ] ExpfitTest.EffnEXP1 53: [ OK ] ExpfitTest.EffnEXP1 (0 ms) 53: [ RUN ] ExpfitTest.EffnEXP2 53: [ OK ] ExpfitTest.EffnEXP2 (1 ms) 53: [ RUN ] ExpfitTest.EffnEXPEXP 53: [ OK ] ExpfitTest.EffnEXPEXP (1 ms) 53: [ RUN ] ExpfitTest.EffnEXP5 53: [ OK ] ExpfitTest.EffnEXP5 (2 ms) 53: [ RUN ] ExpfitTest.EffnEXP7 53: [ OK ] ExpfitTest.EffnEXP7 (1 ms) 53: [ RUN ] ExpfitTest.EffnEXP9 53: [ OK ] ExpfitTest.EffnEXP9 (10 ms) 53: [ RUN ] ExpfitTest.EffnERF 53: [ OK ] ExpfitTest.EffnERF (1 ms) 53: [ RUN ] ExpfitTest.EffnERREST 53: [ OK ] ExpfitTest.EffnERREST (1 ms) 53: [ RUN ] ExpfitTest.EffnVAC 53: [ OK ] ExpfitTest.EffnVAC (3 ms) 53: [ RUN ] ExpfitTest.EffnPRES 53: [ OK ] ExpfitTest.EffnPRES (10 ms) 53: [----------] 10 tests from ExpfitTest (54 ms total) 53: 53: [----------] 1 test from ManyAutocorrelationTest 53: [ RUN ] ManyAutocorrelationTest.Empty 53: [ OK ] ManyAutocorrelationTest.Empty (2 ms) 53: [----------] 1 test from ManyAutocorrelationTest (2 ms total) 53: 53: [----------] Global test environment tear-down 53: [==========] 21 tests from 3 test suites ran. (1126 ms total) 53: [ PASSED ] 21 tests. 53/87 Test #53: CorrelationsTest .......................... Passed 1.16 sec test 54 Start 54: AnalysisDataUnitTests 54: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/analysisdata-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/AnalysisDataUnitTests.xml" 54: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/analysisdata/tests 54: Test timeout computed to be: 30 54: [==========] Running 69 tests from 14 test suites. 54: [----------] Global test environment set-up. 54: [----------] 3 tests from AnalysisDataInitializationTest 54: [ RUN ] AnalysisDataInitializationTest.BasicInitialization 54: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms) 54: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules 54: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms) 54: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules 54: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms) 54: [----------] 3 tests from AnalysisDataInitializationTest (0 ms total) 54: 54: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = (anonymous namespace)::SimpleInputData 54: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (1 ms) 54: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly 54: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames 54: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 54: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks 54: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (0 ms) 54: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData 54: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (0 ms) 54: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks 54: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (0 ms) 54: [----------] 8 tests from AnalysisDataCommonTest/0 (2 ms total) 54: 54: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = (anonymous namespace)::DataSetsInputData 54: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly 54: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames 54: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (4 ms) 54: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks 54: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (0 ms) 54: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData 54: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (0 ms) 54: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks 54: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (0 ms) 54: [----------] 8 tests from AnalysisDataCommonTest/1 (5 ms total) 54: 54: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = (anonymous namespace)::MultipointInputData 54: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly 54: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames 54: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 54: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks 54: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (0 ms) 54: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData 54: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (0 ms) 54: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks 54: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (0 ms) 54: [----------] 8 tests from AnalysisDataCommonTest/2 (1 ms total) 54: 54: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = (anonymous namespace)::MultipointDataSetsInputData 54: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly 54: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames 54: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 54: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks 54: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (0 ms) 54: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData 54: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (0 ms) 54: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks 54: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (4 ms) 54: [----------] 8 tests from AnalysisDataCommonTest/3 (5 ms total) 54: 54: [----------] 4 tests from AnalysisArrayDataTest 54: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly 54: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (0 ms) 54: [ RUN ] AnalysisArrayDataTest.StorageWorks 54: [ OK ] AnalysisArrayDataTest.StorageWorks (0 ms) 54: [ RUN ] AnalysisArrayDataTest.CanSetXAxis 54: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms) 54: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount 54: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms) 54: [----------] 4 tests from AnalysisArrayDataTest (0 ms total) 54: 54: [----------] 6 tests from AverageModuleTest 54: [ RUN ] AverageModuleTest.BasicTest 54: [ OK ] AverageModuleTest.BasicTest (1 ms) 54: [ RUN ] AverageModuleTest.HandlesMultipointData 54: [ OK ] AverageModuleTest.HandlesMultipointData (1 ms) 54: [ RUN ] AverageModuleTest.HandlesMultipleDataSets 54: [ OK ] AverageModuleTest.HandlesMultipleDataSets (1 ms) 54: [ RUN ] AverageModuleTest.HandlesDataSetAveraging 54: [ OK ] AverageModuleTest.HandlesDataSetAveraging (1 ms) 54: [ RUN ] AverageModuleTest.CanCustomizeXAxis 54: [ OK ] AverageModuleTest.CanCustomizeXAxis (0 ms) 54: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis 54: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (0 ms) 54: [----------] 6 tests from AverageModuleTest (10 ms total) 54: 54: [----------] 2 tests from FrameAverageModuleTest 54: [ RUN ] FrameAverageModuleTest.BasicTest 54: [ OK ] FrameAverageModuleTest.BasicTest (0 ms) 54: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets 54: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (1 ms) 54: [----------] 2 tests from FrameAverageModuleTest (2 ms total) 54: 54: [----------] 7 tests from AnalysisHistogramSettingsTest 54: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins 54: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms) 54: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins 54: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms) 54: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount 54: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms) 54: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth 54: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms) 54: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins 54: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms) 54: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins 54: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms) 54: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange 54: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms) 54: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total) 54: 54: [----------] 2 tests from SimpleHistogramModuleTest 54: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly 54: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (5 ms) 54: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll 54: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (1 ms) 54: [----------] 2 tests from SimpleHistogramModuleTest (7 ms total) 54: 54: [----------] 3 tests from WeightedHistogramModuleTest 54: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly 54: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (1 ms) 54: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll 54: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (1 ms) 54: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets 54: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (1 ms) 54: [----------] 3 tests from WeightedHistogramModuleTest (8 ms total) 54: 54: [----------] 3 tests from BinAverageModuleTest 54: [ RUN ] BinAverageModuleTest.ComputesCorrectly 54: [ OK ] BinAverageModuleTest.ComputesCorrectly (1 ms) 54: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll 54: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (1 ms) 54: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets 54: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (1 ms) 54: [----------] 3 tests from BinAverageModuleTest (10 ms total) 54: 54: [----------] 4 tests from AbstractAverageHistogramTest 54: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly 54: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (0 ms) 54: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram 54: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (1 ms) 54: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth 54: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (1 ms) 54: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins 54: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (1 ms) 54: [----------] 4 tests from AbstractAverageHistogramTest (6 ms total) 54: 54: [----------] 3 tests from LifetimeModuleTest 54: [ RUN ] LifetimeModuleTest.BasicTest 54: [ OK ] LifetimeModuleTest.BasicTest (0 ms) 54: [ RUN ] LifetimeModuleTest.CumulativeTest 54: [ OK ] LifetimeModuleTest.CumulativeTest (0 ms) 54: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets 54: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (1 ms) 54: [----------] 3 tests from LifetimeModuleTest (3 ms total) 54: 54: [----------] Global test environment tear-down 54: [==========] 69 tests from 14 test suites ran. (67 ms total) 54: [ PASSED ] 69 tests. 54/87 Test #54: AnalysisDataUnitTests ..................... Passed 0.11 sec test 55 Start 55: CoordinateIOTests 55: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/coordinateio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/CoordinateIOTests.xml" 55: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/coordinateio/tests 55: Test timeout computed to be: 30 55: [==========] Running 67 tests from 20 test suites. 55: [----------] Global test environment set-up. 55: [----------] 1 test from OutputSelectorDeathTest 55: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (15 ms) 55: [----------] 1 test from OutputSelectorDeathTest (15 ms total) 55: 55: [----------] 5 tests from TrajectoryFrameWriterTest 55: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (1 ms) 55: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (0 ms) 55: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (1 ms) 55: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (1 ms) 55: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks 55: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms) 55: [----------] 5 tests from TrajectoryFrameWriterTest (5 ms total) 55: 55: [----------] 5 tests from OutputAdapterContainer 55: [ RUN ] OutputAdapterContainer.MakeEmpty 55: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms) 55: [ RUN ] OutputAdapterContainer.AddAdapter 55: [ OK ] OutputAdapterContainer.AddAdapter (0 ms) 55: [ RUN ] OutputAdapterContainer.RejectBadAdapter 55: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms) 55: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter 55: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms) 55: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters 55: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms) 55: [----------] 5 tests from OutputAdapterContainer (0 ms total) 55: 55: [----------] 3 tests from RegisterFrameConverterTest 55: [ RUN ] RegisterFrameConverterTest.NoConverterWorks 55: [ OK ] RegisterFrameConverterTest.NoConverterWorks (0 ms) 55: [ RUN ] RegisterFrameConverterTest.RegistrationWorks 55: [ OK ] RegisterFrameConverterTest.RegistrationWorks (0 ms) 55: [ RUN ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees 55: [ OK ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees (0 ms) 55: [----------] 3 tests from RegisterFrameConverterTest (0 ms total) 55: 55: [----------] 5 tests from FlagTest 55: [ RUN ] FlagTest.CanSetSimpleFlag 55: [ OK ] FlagTest.CanSetSimpleFlag (0 ms) 55: [ RUN ] FlagTest.CanAddNewBox 55: [ OK ] FlagTest.CanAddNewBox (0 ms) 55: [ RUN ] FlagTest.SetsImplicitPrecisionChange 55: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms) 55: [ RUN ] FlagTest.SetsImplicitStartTimeChange 55: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms) 55: [ RUN ] FlagTest.SetsImplicitTimeStepChange 55: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms) 55: [----------] 5 tests from FlagTest (0 ms total) 55: 55: [----------] 5 tests from SetAtomsTest 55: [ RUN ] SetAtomsTest.RemovesExistingAtoms 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] SetAtomsTest.RemovesExistingAtoms (1 ms) 55: [ RUN ] SetAtomsTest.AddsNewAtoms 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] SetAtomsTest.AddsNewAtoms (5 ms) 55: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (1 ms) 55: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (0 ms) 55: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (5 ms) 55: [----------] 5 tests from SetAtomsTest (13 ms total) 55: 55: [----------] 2 tests from SetBothTimeTest 55: [ RUN ] SetBothTimeTest.StartTimeZeroWorks 55: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms) 55: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks 55: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms) 55: [----------] 2 tests from SetBothTimeTest (0 ms total) 55: 55: [----------] 2 tests from SetStartTimeTest 55: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart 55: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms) 55: [ RUN ] SetStartTimeTest.WorksWithZeroStart 55: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms) 55: [----------] 2 tests from SetStartTimeTest (0 ms total) 55: 55: [----------] 1 test from SetTimeStepTest 55: [ RUN ] SetTimeStepTest.SetTimeStepWorks 55: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms) 55: [----------] 1 test from SetTimeStepTest (0 ms total) 55: 55: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest 55: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (1 ms) 55: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (1 ms) 55: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (1 ms) 55: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (5 ms) 55: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (0 ms) 55: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (0 ms) 55: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (10 ms total) 55: 55: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles 55: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (0 ms) 55: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (5 ms) 55: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (0 ms) 55: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (7 ms total) 55: 55: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles 55: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 55: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms) 55: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 55: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms) 55: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 55: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms) 55: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (0 ms total) 55: 55: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles 55: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (2 ms) 55: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (6 ms) 55: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (6 ms) 55: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (2 ms) 55: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (16 ms total) 55: 55: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles 55: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (0 ms) 55: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (5 ms) 55: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (0 ms) 55: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (7 ms total) 55: 55: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles 55: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 55: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms) 55: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 55: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms) 55: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 55: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms) 55: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (0 ms total) 55: 55: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles 55: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (0 ms) 55: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (0 ms) 55: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (1 ms total) 55: 55: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles 55: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 55: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms) 55: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 55: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms) 55: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 55: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms) 55: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 55: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms) 55: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (0 ms total) 55: 55: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles 55: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (5 ms) 55: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (0 ms) 55: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (6 ms total) 55: 55: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles 55: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 55: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms) 55: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 55: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms) 55: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 55: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms) 55: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 55: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms) 55: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (0 ms total) 55: 55: [----------] 4 tests from ModuleSupported/NoOptionalOutput 55: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (0 ms) 55: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (0 ms) 55: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (5 ms) 55: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (0 ms) 55: [----------] 4 tests from ModuleSupported/NoOptionalOutput (14 ms total) 55: 55: [----------] Global test environment tear-down 55: [==========] 67 tests from 20 test suites ran. (99 ms total) 55: [ PASSED ] 67 tests. 55/87 Test #55: CoordinateIOTests ......................... Passed 0.13 sec test 56 Start 56: TrajectoryAnalysisUnitTests 56: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/trajectoryanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/TrajectoryAnalysisUnitTests.xml" 56: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests 56: Test timeout computed to be: 1920 56: [==========] Running 385 tests from 24 test suites. 56: [----------] Global test environment set-up. 56: [----------] 11 tests from AngleModuleTest 56: [ RUN ] AngleModuleTest.ComputesSimpleAngles 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.ComputesSimpleAngles (3 ms) 56: [ RUN ] AngleModuleTest.ComputesDihedrals 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.ComputesDihedrals (1 ms) 56: [ RUN ] AngleModuleTest.ComputesVectorPairAngles 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.ComputesVectorPairAngles (5 ms) 56: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (1 ms) 56: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (1 ms) 56: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (4 ms) 56: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles 56: Reading frames from gro file 'Test system for different angles', 33 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (1 ms) 56: [ RUN ] AngleModuleTest.ComputesMultipleAngles 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.ComputesMultipleAngles (1 ms) 56: [ RUN ] AngleModuleTest.HandlesDynamicSelections 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.HandlesDynamicSelections (3 ms) 56: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (1 ms) 56: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (7 ms) 56: [----------] 11 tests from AngleModuleTest (34 ms total) 56: 56: [----------] 5 tests from ClustsizeTest 56: [ RUN ] ClustsizeTest.NoMolDefaultCutoff 56: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 56: There is one group in the index 56: '', 24 atoms 56: Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Total number of atoms in clusters = 24 56: cmid: 2, cmax: 4, max_size: 6 56: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 56: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (13 ms) 56: [ RUN ] ClustsizeTest.NoMolShortCutoff 56: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 56: There is one group in the index 56: '', 24 atoms 56: Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Total number of atoms in clusters = 24 56: cmid: 1, cmax: 6, max_size: 6 56: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 56: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (1 ms) 56: [ RUN ] ClustsizeTest.MolDefaultCutoff 56: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 56: '', 24 atoms 56: Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Total number of atoms in clusters = 8 56: cmid: 2, cmax: 4, max_size: 2 56: 50%100%cmid: 2, cmax: 6, max_size: 2 56: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (8 ms) 56: [ RUN ] ClustsizeTest.MolShortCutoff 56: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 56: '', 24 atoms 56: Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Total number of atoms in clusters = 8 56: cmid: 1, cmax: 6, max_size: 2 56: 50%100%cmid: 2, cmax: 6, max_size: 2 56: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (13 ms) 56: [ RUN ] ClustsizeTest.MolCSize 56: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 56: '', 24 atoms 56: Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Total number of atoms in clusters = 8 56: cmid: 2, cmax: 4, max_size: 2 56: 50%100%cmid: 2, cmax: 6, max_size: 2 56: 50%100%[ OK ] ClustsizeTest.MolCSize (7 ms) 56: [----------] 5 tests from ClustsizeTest (44 ms total) 56: 56: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest 56: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp 56: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (1 ms) 56: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory 56: Reading frames from gro file 'Test system', 8 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (4 ms) 56: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset 56: Reading frames from gro file 'Test system', 8 atoms. 56: Reading frame 0 time 0.000 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (4 ms) 56: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory 56: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (0 ms) 56: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (11 ms total) 56: 56: [----------] 4 tests from ConvertTrjModuleTest 56: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 56: Reading frame 0 time 0.000 Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (15 ms) 56: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 56: Reading frame 0 time 0.000 Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (12 ms) 56: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 56: Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (2 ms) 56: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 56: Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (1 ms) 56: [----------] 4 tests from ConvertTrjModuleTest (32 ms total) 56: 56: [----------] 6 tests from DistanceModuleTest 56: [ RUN ] DistanceModuleTest.ComputesDistances 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: atomname S1 S2: 56: Number of samples: 5 56: Average distance: 1.43246 nm 56: Standard deviation: 0.96700 nm 56: [ OK ] DistanceModuleTest.ComputesDistances (1 ms) 56: [ RUN ] DistanceModuleTest.ComputesMultipleDistances 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: atomname S1 S2: 56: Number of samples: 5 56: Average distance: 1.43246 nm 56: Standard deviation: 0.96700 nm 56: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB: 56: Number of samples: 4 56: Average distance: 1.81066 nm 56: Standard deviation: 0.79289 nm 56: [ OK ] DistanceModuleTest.ComputesMultipleDistances (2 ms) 56: [ RUN ] DistanceModuleTest.HandlesDynamicSelections 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: atomname S1 S2 and res_cog x < 2.8: 56: Number of samples: 3 56: Average distance: 1.72076 nm 56: Standard deviation: 1.24839 nm 56: [ OK ] DistanceModuleTest.HandlesDynamicSelections (2 ms) 56: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroup 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: Contacts: 56: Number of samples: 2 56: Average distance: 1.00000 nm 56: Standard deviation: 0.00000 nm 56: [ OK ] DistanceModuleTest.HandlesSelectionFromGroup (10 ms) 56: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: SuccessiveContacts: 56: Number of samples: 2 56: Average distance: 1.00000 nm 56: Standard deviation: 0.00000 nm 56: [ OK ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices (5 ms) 56: [ RUN ] DistanceModuleTest.HandlesSelectionFromLargeGroup 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: ManyContacts: 56: Number of samples: 10 56: Average distance: 1.82913 nm 56: Standard deviation: 0.78478 nm 56: [ OK ] DistanceModuleTest.HandlesSelectionFromLargeGroup (6 ms) 56: [----------] 6 tests from DistanceModuleTest (39 ms total) 56: 56: [----------] 2 tests from ExtractClusterModuleTest 56: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms 56: trr version: GMX_trn_file (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 56: Analyzed 26 frames, last time 0.050 56: There are 8 clusters containing 26 structures, highest framenr is 25 56: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (5 ms) 56: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset 56: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 56: Analyzed 26 frames, last time 0.050 56: There are 8 clusters containing 26 structures, highest framenr is 25 56: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (2 ms) 56: [----------] 2 tests from ExtractClusterModuleTest (7 ms total) 56: 56: [----------] 2 tests from FreeVolumeModuleTest 56: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 56: from the source below. This means the results may be different 56: compared to previous GROMACS versions. 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. Bondi 56: van der Waals Volumes and Radii 56: J. Phys. Chem. 68 (1964) pp. 441-451 56: -------- -------- --- Thank You --- -------- -------- 56: 56: Could not determine VDW radius for CO2-RM. Set to zero. 56: Could not determine VDW radius for CO2-RM. Set to zero. 56: Could not determine VDW radius for CO2-RM. Set to zero. 56: Could not determine VDW radius for CO2-RM. Set to zero. 56: Could not determine VDW radius for CO2-RM. Set to zero. 56: Could not determine VDW radius for CO2-RM. Set to zero. 56: Could not determine VDW radius for CO2-RM. Set to zero. 56: Could not determine VDW radius for CO2-RM. Set to zero. 56: Could not determine VDW radius for CO2-RM. Set to zero. 56: Could not determine VDW radius for 40 particles. These were set to zero. 56: Reading frame 0 time 0.000 Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: cutoff = 0.18 nm 56: probe_radius = 0 nm 56: seed = 13 56: ninsert = 1000 probes per nm^3 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. Bondi 56: van der Waals Volumes and Radii 56: J. Phys. Chem. 68 (1964) pp. 441-451 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David 56: van der Spoel and Luciano T. Costa 56: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 56: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 56: Environ. Sci. Technol. 47 (2013) pp. 7421-7429 56: -------- -------- --- Thank You --- -------- -------- 56: 56: Free volume 38.02 +/- 0.00 % 56: Total volume 68.92 +/- 0.00 nm^3 56: Number of molecules 340 total mass 63491.38 Dalton 56: Average molar mass: 186.74 Dalton 56: Density rho: 1529.71 +/- 0.00 nm^3 56: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 56: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3 56: Fractional free volume 0.194 +/- 0.000 56: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (80 ms) 56: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 56: from the source below. This means the results may be different 56: compared to previous GROMACS versions. 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. Bondi 56: van der Waals Volumes and Radii 56: J. Phys. Chem. 68 (1964) pp. 441-451 56: -------- -------- --- Thank You --- -------- -------- 56: 56: Reading frame 0 time 0.000 Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: cutoff = 0.18 nm 56: probe_radius = 0 nm 56: seed = 17 56: ninsert = 1000 probes per nm^3 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. Bondi 56: van der Waals Volumes and Radii 56: J. Phys. Chem. 68 (1964) pp. 441-451 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David 56: van der Spoel and Luciano T. Costa 56: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 56: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 56: Environ. Sci. Technol. 47 (2013) pp. 7421-7429 56: -------- -------- --- Thank You --- -------- -------- 56: 56: Free volume 38.48 +/- 0.00 % 56: Total volume 68.92 +/- 0.00 nm^3 56: Number of molecules 340 total mass 63491.38 Dalton 56: Average molar mass: 186.74 Dalton 56: Density rho: 1529.71 +/- 0.00 nm^3 56: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 56: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3 56: Fractional free volume 0.200 +/- 0.000 56: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (95 ms) 56: [----------] 2 tests from FreeVolumeModuleTest (176 ms total) 56: 56: [----------] 11 tests from MsdModuleTest 56: [ RUN ] MsdModuleTest.threeDimensionalDiffusion 56: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 56: Analyzed 10 frames, last time 9.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] MsdModuleTest.threeDimensionalDiffusion (10 ms) 56: [ RUN ] MsdModuleTest.twoDimensionalDiffusion 56: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 56: Analyzed 10 frames, last time 9.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] MsdModuleTest.twoDimensionalDiffusion (2 ms) 56: [ RUN ] MsdModuleTest.oneDimensionalDiffusion 56: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 56: Analyzed 10 frames, last time 9.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] MsdModuleTest.oneDimensionalDiffusion (4 ms) 56: [ RUN ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau 56: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 56: Analyzed 10 frames, last time 9.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau (6 ms) 56: [ RUN ] MsdModuleTest.roundingFail 56: Reading frame 0 time 0.000 Reading frame 1 time 0.001 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] MsdModuleTest.roundingFail (2 ms) 56: [ RUN ] MsdModuleTest.multipleGroupsWork 56: 56: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 56: For a correct single-point energy evaluation with nsteps = 0, use 56: continuation = yes to avoid constraining the input coordinates. 56: 56: Generating 1-4 interactions: fudge = 0.5 56: 56: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 56: For energy conservation with LINCS, lincs_iter should be 2 or larger. 56: 56: 56: Number of degrees of freedom in T-Coupling group rest is 1818.00 56: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 56: 56: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 56: NVE simulation: will use the initial temperature of 288.764 K for 56: determining the Verlet buffer size 56: 56: 56: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 56: There are 9 non-linear virtual site constructions. Their contribution to 56: the energy error is approximated. In most cases this does not affect the 56: error significantly. 56: 56: 56: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 56: You are using a plain Coulomb cut-off, which might produce artifacts. 56: You might want to consider using PME electrostatics. 56: 56: 56: 56: There were 5 NOTEs 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 2.000 56: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 56: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 56: Analyzed 21 frames, last time 40.000 56: Setting the LD random seed to -2229777 56: 56: Generated 2145 of the 2145 non-bonded parameter combinations 56: 56: Generated 2145 of the 2145 1-4 parameter combinations 56: 56: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 56: 56: Excluding 2 bonded neighbours molecule type 'SOL' 56: 56: Cleaning up constraints and constant bonded interactions with virtual sites 56: 56: Converted 15 Bonds with virtual sites to connections, 7 left 56: 56: Removed 18 Angles with virtual sites, 21 left 56: 56: Removed 10 Proper Dih.s with virtual sites, 44 left 56: 56: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 56: 56: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 56: 56: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 56: 56: Note that mdrun will redetermine rlist based on the actual pair-list setup 56: 56: This run will generate roughly 0 Mb of data 56: [ OK ] MsdModuleTest.multipleGroupsWork (50 ms) 56: [ DISABLED ] MsdModuleTest.DISABLED_trestartLessThanDt 56: [ RUN ] MsdModuleTest.trestartGreaterThanDt 56: 56: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 56: For a correct single-point energy evaluation with nsteps = 0, use 56: continuation = yes to avoid constraining the input coordinates. 56: 56: Generating 1-4 interactions: fudge = 0.5 56: 56: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 56: For energy conservation with LINCS, lincs_iter should be 2 or larger. 56: 56: 56: Number of degrees of freedom in T-Coupling group rest is 1818.00 56: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 56: 56: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 56: NVE simulation: will use the initial temperature of 288.764 K for 56: determining the Verlet buffer size 56: 56: 56: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 56: There are 9 non-linear virtual site constructions. Their contribution to 56: the energy error is approximated. In most cases this does not affect the 56: error significantly. 56: 56: 56: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 56: You are using a plain Coulomb cut-off, which might produce artifacts. 56: You might want to consider using PME electrostatics. 56: 56: 56: 56: There were 5 NOTEs 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 56: Analyzed 21 frames, last time 40.000 56: Setting the LD random seed to 926807799 56: 56: Generated 2145 of the 2145 non-bonded parameter combinations 56: 56: Generated 2145 of the 2145 1-4 parameter combinations 56: 56: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 56: 56: Excluding 2 bonded neighbours molecule type 'SOL' 56: 56: Cleaning up constraints and constant bonded interactions with virtual sites 56: 56: Converted 15 Bonds with virtual sites to connections, 7 left 56: 56: Removed 18 Angles with virtual sites, 21 left 56: 56: Removed 10 Proper Dih.s with virtual sites, 44 left 56: 56: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 56: 56: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 56: 56: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 56: 56: Note that mdrun will redetermine rlist based on the actual pair-list setup 56: 56: This run will generate roughly 0 Mb of data 56: [ OK ] MsdModuleTest.trestartGreaterThanDt (30 ms) 56: [ RUN ] MsdModuleTest.molTest 56: 56: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 56: For a correct single-point energy evaluation with nsteps = 0, use 56: continuation = yes to avoid constraining the input coordinates. 56: 56: Generating 1-4 interactions: fudge = 0.5 56: 56: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 56: For energy conservation with LINCS, lincs_iter should be 2 or larger. 56: 56: 56: Number of degrees of freedom in T-Coupling group rest is 1818.00 56: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 56: 56: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 56: NVE simulation: will use the initial temperature of 288.764 K for 56: determining the Verlet buffer size 56: 56: 56: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 56: There are 9 non-linear virtual site constructions. Their contribution to 56: the energy error is approximated. In most cases this does not affect the 56: error significantly. 56: 56: 56: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 56: You are using a plain Coulomb cut-off, which might produce artifacts. 56: You might want to consider using PME electrostatics. 56: 56: 56: 56: There were 5 NOTEs 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 56: Analyzed 21 frames, last time 40.000 56: Setting the LD random seed to 1033878015 56: 56: Generated 2145 of the 2145 non-bonded parameter combinations 56: 56: Generated 2145 of the 2145 1-4 parameter combinations 56: 56: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 56: 56: Excluding 2 bonded neighbours molecule type 'SOL' 56: 56: Cleaning up constraints and constant bonded interactions with virtual sites 56: 56: Converted 15 Bonds with virtual sites to connections, 7 left 56: 56: Removed 18 Angles with virtual sites, 21 left 56: 56: Removed 10 Proper Dih.s with virtual sites, 44 left 56: 56: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 56: 56: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 56: 56: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 56: 56: Note that mdrun will redetermine rlist based on the actual pair-list setup 56: 56: This run will generate roughly 0 Mb of data 56: [ OK ] MsdModuleTest.molTest (39 ms) 56: [ RUN ] MsdModuleTest.beginFit 56: 56: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 56: For a correct single-point energy evaluation with nsteps = 0, use 56: continuation = yes to avoid constraining the input coordinates. 56: 56: Generating 1-4 interactions: fudge = 0.5 56: 56: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 56: For energy conservation with LINCS, lincs_iter should be 2 or larger. 56: 56: 56: Number of degrees of freedom in T-Coupling group rest is 1818.00 56: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 56: 56: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 56: NVE simulation: will use the initial temperature of 288.764 K for 56: determining the Verlet buffer size 56: 56: 56: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 56: There are 9 non-linear virtual site constructions. Their contribution to 56: the energy error is approximated. In most cases this does not affect the 56: error significantly. 56: 56: 56: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 56: You are using a plain Coulomb cut-off, which might produce artifacts. 56: You might want to consider using PME electrostatics. 56: 56: 56: 56: There were 5 NOTEs 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 2.000 56: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 56: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 56: Analyzed 21 frames, last time 40.000 56: Setting the LD random seed to -218370101 56: 56: Generated 2145 of the 2145 non-bonded parameter combinations 56: 56: Generated 2145 of the 2145 1-4 parameter combinations 56: 56: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 56: 56: Excluding 2 bonded neighbours molecule type 'SOL' 56: 56: Cleaning up constraints and constant bonded interactions with virtual sites 56: 56: Converted 15 Bonds with virtual sites to connections, 7 left 56: 56: Removed 18 Angles with virtual sites, 21 left 56: 56: Removed 10 Proper Dih.s with virtual sites, 44 left 56: 56: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 56: 56: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 56: 56: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 56: 56: Note that mdrun will redetermine rlist based on the actual pair-list setup 56: 56: This run will generate roughly 0 Mb of data 56: [ OK ] MsdModuleTest.beginFit (25 ms) 56: [ RUN ] MsdModuleTest.endFit 56: 56: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 56: For a correct single-point energy evaluation with nsteps = 0, use 56: continuation = yes to avoid constraining the input coordinates. 56: 56: Generating 1-4 interactions: fudge = 0.5 56: 56: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 56: For energy conservation with LINCS, lincs_iter should be 2 or larger. 56: 56: 56: Number of degrees of freedom in T-Coupling group rest is 1818.00 56: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 56: 56: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 56: NVE simulation: will use the initial temperature of 288.764 K for 56: determining the Verlet buffer size 56: 56: 56: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 56: There are 9 non-linear virtual site constructions. Their contribution to 56: the energy error is approximated. In most cases this does not affect the 56: error significantly. 56: 56: 56: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 56: You are using a plain Coulomb cut-off, which might produce artifacts. 56: You might want to consider using PME electrostatics. 56: 56: 56: 56: There were 5 NOTEs 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 2.000 56: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 56: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 56: Analyzed 21 frames, last time 40.000 56: Setting the LD random seed to -1342324781 56: 56: Generated 2145 of the 2145 non-bonded parameter combinations 56: 56: Generated 2145 of the 2145 1-4 parameter combinations 56: 56: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 56: 56: Excluding 2 bonded neighbours molecule type 'SOL' 56: 56: Cleaning up constraints and constant bonded interactions with virtual sites 56: 56: Converted 15 Bonds with virtual sites to connections, 7 left 56: 56: Removed 18 Angles with virtual sites, 21 left 56: 56: Removed 10 Proper Dih.s with virtual sites, 44 left 56: 56: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 56: 56: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 56: 56: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 56: 56: Note that mdrun will redetermine rlist based on the actual pair-list setup 56: 56: This run will generate roughly 0 Mb of data 56: [ OK ] MsdModuleTest.endFit (22 ms) 56: [ RUN ] MsdModuleTest.notEnoughPointsForFitErrorEstimate 56: 56: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 56: For a correct single-point energy evaluation with nsteps = 0, use 56: continuation = yes to avoid constraining the input coordinates. 56: 56: Generating 1-4 interactions: fudge = 0.5 56: 56: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 56: For energy conservation with LINCS, lincs_iter should be 2 or larger. 56: 56: 56: Number of degrees of freedom in T-Coupling group rest is 1818.00 56: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 56: 56: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 56: NVE simulation: will use the initial temperature of 288.764 K for 56: determining the Verlet buffer size 56: 56: 56: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 56: There are 9 non-linear virtual site constructions. Their contribution to 56: the energy error is approximated. In most cases this does not affect the 56: error significantly. 56: 56: 56: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 56: You are using a plain Coulomb cut-off, which might produce artifacts. 56: You might want to consider using PME electrostatics. 56: 56: 56: 56: There were 5 NOTEs 56: NOTE: You provided an index file 56: /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/alanine_vsite_solvated.ndx 56: (with -n), but it was not used by any selection. 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 2.000 56: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 56: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 56: Analyzed 21 frames, last time 40.000 56: Setting the LD random seed to -312306305 56: 56: Generated 2145 of the 2145 non-bonded parameter combinations 56: 56: Generated 2145 of the 2145 1-4 parameter combinations 56: 56: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 56: 56: Excluding 2 bonded neighbours molecule type 'SOL' 56: 56: Cleaning up constraints and constant bonded interactions with virtual sites 56: 56: Converted 15 Bonds with virtual sites to connections, 7 left 56: 56: Removed 18 Angles with virtual sites, 21 left 56: 56: Removed 10 Proper Dih.s with virtual sites, 44 left 56: 56: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 56: 56: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 56: 56: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 56: 56: Note that mdrun will redetermine rlist based on the actual pair-list setup 56: 56: This run will generate roughly 0 Mb of data 56: [ OK ] MsdModuleTest.notEnoughPointsForFitErrorEstimate (26 ms) 56: [----------] 11 tests from MsdModuleTest (224 ms total) 56: 56: [----------] 9 tests from PairDistanceModuleTest 56: [ RUN ] PairDistanceModuleTest.ComputesAllDistances 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] PairDistanceModuleTest.ComputesAllDistances (4 ms) 56: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (1 ms) 56: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (4 ms) 56: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (1 ms) 56: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (4 ms) 56: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (4 ms) 56: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (1 ms) 56: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (1 ms) 56: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (7 ms) 56: [----------] 9 tests from PairDistanceModuleTest (37 ms total) 56: 56: [----------] 5 tests from RdfModuleTest 56: [ RUN ] RdfModuleTest.BasicTest 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] RdfModuleTest.BasicTest (40 ms) 56: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork 56: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms. 56: Reading frame 0 time 0.000 Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (25 ms) 56: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (27 ms) 56: [ RUN ] RdfModuleTest.CalculatesSurf 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] RdfModuleTest.CalculatesSurf (15 ms) 56: [ RUN ] RdfModuleTest.CalculatesXY 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] RdfModuleTest.CalculatesXY (26 ms) 56: [----------] 5 tests from RdfModuleTest (136 ms total) 56: 56: [----------] 5 tests from SasaModuleTest 56: [ RUN ] SasaModuleTest.BasicTest 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 56: Michael Scharf 56: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 56: of Surface Area and Volume and to Dot Surface Contouring of Molecular 56: Assemblies 56: J. Comp. Chem. 16 (1995) pp. 273-284 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 56: from the source below. This means the results may be different 56: compared to previous GROMACS versions. 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. Bondi 56: van der Waals Volumes and Radii 56: J. Phys. Chem. 68 (1964) pp. 441-451 56: -------- -------- --- Thank You --- -------- -------- 56: 56: Analyzed topology coordinates 56: [ OK ] SasaModuleTest.BasicTest (18 ms) 56: [ RUN ] SasaModuleTest.HandlesSelectedResidues 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 56: Michael Scharf 56: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 56: of Surface Area and Volume and to Dot Surface Contouring of Molecular 56: Assemblies 56: J. Comp. Chem. 16 (1995) pp. 273-284 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 56: from the source below. This means the results may be different 56: compared to previous GROMACS versions. 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. Bondi 56: van der Waals Volumes and Radii 56: J. Phys. Chem. 68 (1964) pp. 441-451 56: -------- -------- --- Thank You --- -------- -------- 56: 56: Analyzed topology coordinates 56: [ OK ] SasaModuleTest.HandlesSelectedResidues (7 ms) 56: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 56: Michael Scharf 56: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 56: of Surface Area and Volume and to Dot Surface Contouring of Molecular 56: Assemblies 56: J. Comp. Chem. 16 (1995) pp. 273-284 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 56: from the source below. This means the results may be different 56: compared to previous GROMACS versions. 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. Bondi 56: van der Waals Volumes and Radii 56: J. Phys. Chem. 68 (1964) pp. 441-451 56: -------- -------- --- Thank You --- -------- -------- 56: 56: Analyzed topology coordinates 56: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (59 ms) 56: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 56: Michael Scharf 56: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 56: of Surface Area and Volume and to Dot Surface Contouring of Molecular 56: Assemblies 56: J. Comp. Chem. 16 (1995) pp. 273-284 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 56: from the source below. This means the results may be different 56: compared to previous GROMACS versions. 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. Bondi 56: van der Waals Volumes and Radii 56: J. Phys. Chem. 68 (1964) pp. 441-451 56: -------- -------- --- Thank You --- -------- -------- 56: 56: Analyzed topology coordinates 56: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (55 ms) 56: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 56: Michael Scharf 56: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 56: of Surface Area and Volume and to Dot Surface Contouring of Molecular 56: Assemblies 56: J. Comp. Chem. 16 (1995) pp. 273-284 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 56: from the source below. This means the results may be different 56: compared to previous GROMACS versions. 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. Bondi 56: van der Waals Volumes and Radii 56: J. Phys. Chem. 68 (1964) pp. 441-451 56: -------- -------- --- Thank You --- -------- -------- 56: 56: Analyzed topology coordinates 56: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (16 ms) 56: [----------] 5 tests from SasaModuleTest (166 ms total) 56: 56: [----------] 8 tests from SelectModuleTest 56: [ RUN ] SelectModuleTest.BasicTest 56: Reading frames from gro file 'Test system', 15 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] SelectModuleTest.BasicTest (9 ms) 56: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput 56: Reading frames from gro file 'Test system', 15 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (6 ms) 56: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput 56: Reading frames from gro file 'Test system', 15 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (7 ms) 56: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput 56: Reading frames from gro file 'Test system', 15 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (10 ms) 56: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput 56: Reading frames from gro file 'Test system', 15 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (4 ms) 56: [ RUN ] SelectModuleTest.NormalizesSizes 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] SelectModuleTest.NormalizesSizes (2 ms) 56: [ RUN ] SelectModuleTest.WritesResidueNumbers 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] SelectModuleTest.WritesResidueNumbers (2 ms) 56: [ RUN ] SelectModuleTest.WritesResidueIndices 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] SelectModuleTest.WritesResidueIndices (3 ms) 56: [----------] 8 tests from SelectModuleTest (56 ms total) 56: 56: [----------] 10 tests from SurfaceAreaTest 56: [ RUN ] SurfaceAreaTest.ComputesSinglePoint 56: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms) 56: [ RUN ] SurfaceAreaTest.ComputesTwoPoints 56: [ OK ] SurfaceAreaTest.ComputesTwoPoints (0 ms) 56: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius 56: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (0 ms) 56: [ RUN ] SurfaceAreaTest.SurfacePoints12 56: [ OK ] SurfaceAreaTest.SurfacePoints12 (0 ms) 56: [ RUN ] SurfaceAreaTest.SurfacePoints32 56: [ OK ] SurfaceAreaTest.SurfacePoints32 (0 ms) 56: [ RUN ] SurfaceAreaTest.SurfacePoints42 56: [ OK ] SurfaceAreaTest.SurfacePoints42 (0 ms) 56: [ RUN ] SurfaceAreaTest.SurfacePoints122 56: [ OK ] SurfaceAreaTest.SurfacePoints122 (1 ms) 56: [ RUN ] SurfaceAreaTest.Computes100Points 56: [ OK ] SurfaceAreaTest.Computes100Points (3 ms) 56: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC 56: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (5 ms) 56: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC 56: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (7 ms) 56: [----------] 10 tests from SurfaceAreaTest (27 ms total) 56: 56: [----------] 4 tests from TopologyInformation 56: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile 56: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms) 56: [ RUN ] TopologyInformation.WorksWithGroFile 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] TopologyInformation.WorksWithGroFile (4 ms) 56: [ RUN ] TopologyInformation.WorksWithPdbFile 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] TopologyInformation.WorksWithPdbFile (1 ms) 56: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile 56: 56: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 56: For a correct single-point energy evaluation with nsteps = 0, use 56: continuation = yes to avoid constraining the input coordinates. 56: 56: Generating 1-4 interactions: fudge = 0.5 56: 56: NOTE 2 [file lysozyme.top, line 1465]: 56: System has non-zero total charge: 2.000000 56: Total charge should normally be an integer. See 56: https://manual.gromacs.org/current/user-guide/floating-point.html 56: for discussion on how close it should be to an integer. 56: 56: 56: 56: Number of degrees of freedom in T-Coupling group rest is 465.00 56: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 56: 56: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 56: NVE simulation with an initial temperature of zero: will use a Verlet 56: buffer of 10%. Check your energy drift! 56: 56: 56: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 56: You are using a plain Coulomb cut-off, which might produce artifacts. 56: You might want to consider using PME electrostatics. 56: 56: 56: 56: There were 4 NOTEs 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 56: Setting the LD random seed to -537406517 56: 56: Generated 330891 of the 330891 non-bonded parameter combinations 56: 56: Generated 330891 of the 330891 1-4 parameter combinations 56: 56: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 56: Analysing residue names: 56: There are: 10 Protein residues 56: Analysing Protein... 56: 56: This run will generate roughly 0 Mb of data 56: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (454 ms) 56: [----------] 4 tests from TopologyInformation (461 ms total) 56: 56: [----------] 4 tests from TrajectoryModuleTest 56: [ RUN ] TrajectoryModuleTest.BasicTest 56: Reading frames from gro file 'Test system', 15 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] TrajectoryModuleTest.BasicTest (3 ms) 56: [ RUN ] TrajectoryModuleTest.PlotsXOnly 56: Reading frames from gro file 'Test system', 15 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] TrajectoryModuleTest.PlotsXOnly (4 ms) 56: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities 56: Reading frames from gro file 'Test system', 15 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (7 ms) 56: [ RUN ] TrajectoryModuleTest.HandlesNoForces 56: Reading frames from gro file 'Test system', 15 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] TrajectoryModuleTest.HandlesNoForces (7 ms) 56: [----------] 4 tests from TrajectoryModuleTest (24 ms total) 56: 56: [----------] 5 tests from UnionFinderTest 56: [ RUN ] UnionFinderTest.WorksEmpty 56: [ OK ] UnionFinderTest.WorksEmpty (0 ms) 56: [ RUN ] UnionFinderTest.BasicMerges 56: [ OK ] UnionFinderTest.BasicMerges (0 ms) 56: [ RUN ] UnionFinderTest.LargerMerges 56: [ OK ] UnionFinderTest.LargerMerges (0 ms) 56: [ RUN ] UnionFinderTest.LongRightMerge 56: [ OK ] UnionFinderTest.LongRightMerge (0 ms) 56: [ RUN ] UnionFinderTest.LongLeftMerge 56: [ OK ] UnionFinderTest.LongLeftMerge (0 ms) 56: [----------] 5 tests from UnionFinderTest (0 ms total) 56: 56: [----------] 1 test from MappedUnionFinderTest 56: [ RUN ] MappedUnionFinderTest.BasicMerges 56: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms) 56: [----------] 1 test from MappedUnionFinderTest (0 ms total) 56: 56: [----------] 160 tests from MoleculeTests/DsspModuleTestDsspNB 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/0 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/0 (23 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/1 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/1 (8 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/2 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/2 (9 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/3 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/3 (15 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/4 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/4 (10 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/5 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/5 (11 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/6 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/6 (9 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/7 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/7 (92 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/8 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/8 (35 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/9 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/9 (21 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/10 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/10 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/11 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/11 (33 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/12 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/12 (30 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/13 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/13 (53 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/14 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/14 (17 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/15 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/15 (48 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/16 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/16 (55 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/17 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/17 (40 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/18 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/18 (34 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/19 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/19 (35 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/20 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/20 (38 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/21 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/21 (40 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/22 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/22 (26 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/23 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/23 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/24 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/24 (47 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/25 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/25 (68 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/26 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/26 (50 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/27 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/27 (38 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/28 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/28 (33 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/29 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/29 (26 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/30 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/30 (32 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/31 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/31 (27 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/32 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/32 (10 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/33 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/33 (8 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/34 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/34 (6 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/35 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/35 (8 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/36 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/36 (7 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/37 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/37 (12 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/38 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/38 (10 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/39 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/39 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/40 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/40 (21 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/41 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/41 (19 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/42 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/42 (15 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/43 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/43 (14 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/44 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/44 (14 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/45 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/45 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/46 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/46 (15 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/47 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/47 (15 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/48 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/48 (17 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/49 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/49 (7 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/50 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/50 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/51 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/51 (7 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/52 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/52 (14 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/53 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/53 (12 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/54 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/54 (25 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/55 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/55 (33 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/56 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/56 (58 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/57 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/57 (30 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/58 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/58 (41 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/59 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/59 (34 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/60 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/60 (42 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/61 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/61 (47 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/62 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/62 (55 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/63 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/63 (54 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/64 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/64 (35 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/65 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/65 (58 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/66 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/66 (46 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/67 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/67 (34 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/68 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/68 (29 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/69 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/69 (35 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/70 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/70 (26 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/71 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/71 (24 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/72 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/72 (30 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/73 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/73 (18 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/74 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/74 (26 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/75 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/75 (17 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/76 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/76 (18 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/77 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/77 (15 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/78 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/78 (14 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/79 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/79 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/80 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/80 (49 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/81 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/81 (27 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/82 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/82 (58 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/83 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/83 (53 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/84 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/84 (41 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/85 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/85 (49 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/86 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/86 (47 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/87 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/87 (39 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/88 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/88 (28 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/89 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/89 (15 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/90 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/90 (24 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/91 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/91 (23 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/92 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/92 (18 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/93 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/93 (15 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/94 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/94 (23 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/95 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/95 (21 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/96 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/96 (21 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/97 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/97 (24 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/98 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/98 (23 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/99 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/99 (23 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/100 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/100 (29 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/101 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/101 (23 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/102 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/102 (25 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/103 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/103 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/104 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/104 (32 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/105 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/105 (23 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/106 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/106 (25 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/107 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/107 (38 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/108 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/108 (33 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/109 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/109 (25 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/110 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/110 (39 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/111 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/111 (41 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/112 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/112 (27 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/113 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/113 (18 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/114 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/114 (15 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/115 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/115 (11 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/116 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/116 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/117 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/117 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/118 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/118 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/119 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/119 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/120 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/120 (77 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/121 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/121 (125 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/122 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/122 (95 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/123 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/123 (83 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/124 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/124 (89 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/125 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/125 (76 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/126 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/126 (84 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/127 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/127 (65 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/128 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/128 (19 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/129 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/129 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/130 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/130 (21 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/131 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/131 (32 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/132 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/132 (23 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/133 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/133 (10 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/134 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/134 (18 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/135 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/135 (18 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/136 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/136 (17 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/137 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/137 (17 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/138 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/138 (33 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/139 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/139 (27 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/140 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/140 (33 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/141 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/141 (38 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/142 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/142 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/143 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/143 (26 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/144 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/144 (16 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/145 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/145 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/146 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/146 (22 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/147 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/147 (27 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/148 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/148 (16 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/149 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/149 (19 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/150 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/150 (16 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/151 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/151 (21 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/152 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/152 (51 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/153 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/153 (64 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/154 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/154 (67 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/155 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/155 (67 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/156 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/156 (76 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/157 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/157 (77 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/158 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/158 (58 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/159 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/159 (36 ms) 56: [----------] 160 tests from MoleculeTests/DsspModuleTestDsspNB (5124 ms total) 56: 56: [----------] 24 tests from MoleculeTests/DsspModuleTestGromacsNB 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/0 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/0 (60 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/1 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/1 (45 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/2 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/2 (36 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/3 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/3 (69 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/4 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/4 (131 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/5 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/5 (68 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/6 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/6 (107 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/7 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/7 (64 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/8 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/8 (57 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/9 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/9 (26 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/10 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/10 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/11 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/11 (29 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/12 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/12 (25 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/13 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/13 (23 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/14 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/14 (24 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/15 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/15 (21 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/16 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/16 (14 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/17 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/17 (14 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/18 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/18 (17 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/19 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/19 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/20 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/20 (22 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/21 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/21 (16 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/22 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/22 (18 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/23 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/23 (24 ms) 56: [----------] 24 tests from MoleculeTests/DsspModuleTestGromacsNB (970 ms total) 56: 56: [----------] 80 tests from MoleculeTests/DsspModuleTestDsspNoNB 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/0 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/0 (34 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/1 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/1 (25 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/2 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/2 (9 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/3 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/3 (21 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/4 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/4 (26 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/5 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/5 (14 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/6 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/6 (58 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/7 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/7 (32 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/8 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/8 (41 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/9 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/9 (92 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/10 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/10 (44 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/11 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/11 (104 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/12 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/12 (50 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/13 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/13 (49 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/14 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/14 (62 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/15 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/15 (59 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/16 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/16 (10 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/17 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/17 (44 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/18 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/18 (16 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/19 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/19 (15 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/20 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/20 (12 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/21 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/21 (16 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/22 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/22 (12 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/23 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/23 (85 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/24 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/24 (15 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/25 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/25 (8 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/26 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/26 (18 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/27 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/27 (10 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/28 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/28 (71 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/29 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/29 (57 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/30 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/30 (43 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/31 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/31 (49 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/32 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/32 (39 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/33 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/33 (36 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/34 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/34 (24 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/35 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/35 (36 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/36 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/36 (17 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/37 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/37 (32 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/38 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/38 (17 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/39 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/39 (14 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/40 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/40 (37 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/41 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/41 (37 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/42 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/42 (26 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/43 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/43 (23 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/44 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/44 (14 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/45 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/45 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/46 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/46 (16 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/47 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/47 (17 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/48 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/48 (25 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/49 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/49 (26 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/50 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/50 (27 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/51 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/51 (29 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/52 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/52 (28 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/53 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/53 (15 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/54 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/54 (30 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/55 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/55 (29 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/56 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/56 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/57 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/57 (14 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/58 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/58 (21 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/59 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/59 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/60 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/60 (109 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/61 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/61 (77 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/62 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/62 (67 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/63 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/63 (84 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/64 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/64 (27 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/65 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/65 (18 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/66 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/66 (19 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/67 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/67 (12 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/68 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/68 (22 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/69 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/69 (21 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/70 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/70 (22 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/71 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/71 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/72 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/72 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/73 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/73 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/74 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/74 (15 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/75 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/75 (22 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/76 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/76 (31 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/77 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/77 (28 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/78 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/78 (30 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/79 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/79 (32 ms) 56: [----------] 80 tests from MoleculeTests/DsspModuleTestDsspNoNB (2630 ms total) 56: 56: [----------] 12 tests from MoleculeTests/DsspModuleTestGromacsNoNB 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/0 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/0 (66 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/1 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/1 (65 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/2 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/2 (105 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/3 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/3 (74 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/4 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/4 (36 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/5 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/5 (25 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/6 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/6 (17 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/7 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/7 (24 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/8 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/8 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/9 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/9 (17 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/10 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/10 (14 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/11 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/11 (24 ms) 56: [----------] 12 tests from MoleculeTests/DsspModuleTestGromacsNoNB (488 ms total) 56: 56: [----------] 3 tests from GyrateTests/GyrateModuleTest 56: [ RUN ] GyrateTests/GyrateModuleTest.Works/0 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 56: Analyzed 2 frames, last time 10.000 56: [ OK ] GyrateTests/GyrateModuleTest.Works/0 (20 ms) 56: [ RUN ] GyrateTests/GyrateModuleTest.Works/1 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 56: Analyzed 2 frames, last time 10.000 56: [ OK ] GyrateTests/GyrateModuleTest.Works/1 (20 ms) 56: [ RUN ] GyrateTests/GyrateModuleTest.Works/2 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 56: Analyzed 2 frames, last time 10.000 56: [ OK ] GyrateTests/GyrateModuleTest.Works/2 (11 ms) 56: [----------] 3 tests from GyrateTests/GyrateModuleTest (52 ms total) 56: 56: [----------] 6 tests from HBondTests/HbondModuleTest 56: [ RUN ] HBondTests/HbondModuleTest.Works/0 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 56: Analyzed 2 frames, last time 10.000 56: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 56: [ OK ] HBondTests/HbondModuleTest.Works/0 (37 ms) 56: [ RUN ] HBondTests/HbondModuleTest.Works/1 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 56: Analyzed 2 frames, last time 10.000 56: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 56: [ OK ] HBondTests/HbondModuleTest.Works/1 (24 ms) 56: [ RUN ] HBondTests/HbondModuleTest.Works/2 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 56: Analyzed 2 frames, last time 10.000 56: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 56: [ OK ] HBondTests/HbondModuleTest.Works/2 (62 ms) 56: [ RUN ] HBondTests/HbondModuleTest.Works/3 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 56: Analyzed 2 frames, last time 10.000 56: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 56: Merging hbonds with Acceptor and Donor swapped 56: [ OK ] HBondTests/HbondModuleTest.Works/3 (64 ms) 56: [ RUN ] HBondTests/HbondModuleTest.Works/4 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 56: Analyzed 2 frames, last time 10.000 56: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 56: [ OK ] HBondTests/HbondModuleTest.Works/4 (79 ms) 56: [ RUN ] HBondTests/HbondModuleTest.Works/5 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 56: Analyzed 2 frames, last time 10.000 56: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 56: [ OK ] HBondTests/HbondModuleTest.Works/5 (55 ms) 56: [----------] 6 tests from HBondTests/HbondModuleTest (363 ms total) 56: 56: [----------] 4 tests from MoleculeTests/ScatteringModule 56: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/0 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev & V. V. Isaev-Ivanov 56: Method for calculating small-angle neutron scattering spectra using all-atom 56: molecular dynamics trajectories 56: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques 7 (2013) pp. 1124–1127 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/ScatteringModule.DirectMode/0 (16 ms) 56: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/1 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev & V. V. Isaev-Ivanov 56: Method for calculating small-angle neutron scattering spectra using all-atom 56: molecular dynamics trajectories 56: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques 7 (2013) pp. 1124–1127 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: D. T. Cromer & J. B. Mann 56: X-ray scattering factors computed from numerical Hartree-Fock wave functions 56: Acta Cryst. A 24 (1968) pp. 321 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/ScatteringModule.DirectMode/1 (126 ms) 56: [ RUN ] MoleculeTests/ScatteringModule.MCMode/0 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev & V. V. Isaev-Ivanov 56: Method for calculating small-angle neutron scattering spectra using all-atom 56: molecular dynamics trajectories 56: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques 7 (2013) pp. 1124–1127 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/ScatteringModule.MCMode/0 (21 ms) 56: [ RUN ] MoleculeTests/ScatteringModule.MCMode/1 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev & V. V. Isaev-Ivanov 56: Method for calculating small-angle neutron scattering spectra using all-atom 56: molecular dynamics trajectories 56: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques 7 (2013) pp. 1124–1127 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: D. T. Cromer & J. B. Mann 56: X-ray scattering factors computed from numerical Hartree-Fock wave functions 56: Acta Cryst. A 24 (1968) pp. 321 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/ScatteringModule.MCMode/1 (34 ms) 56: [----------] 4 tests from MoleculeTests/ScatteringModule (203 ms total) 56: 56: [----------] Global test environment tear-down 56: [==========] 385 tests from 24 test suites ran. (11317 ms total) 56: [ PASSED ] 385 tests. 56: 56: YOU HAVE 1 DISABLED TEST 56: 56/87 Test #56: TrajectoryAnalysisUnitTests ............... Passed 11.35 sec test 57 Start 57: EnergyAnalysisUnitTests 57: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/energyanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/EnergyAnalysisUnitTests.xml" 57: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/energyanalysis/tests 57: Test timeout computed to be: 30 57: [==========] Running 11 tests from 5 test suites. 57: [----------] Global test environment set-up. 57: [----------] 2 tests from EnergyTermTest 57: [ RUN ] EnergyTermTest.ConstructWorks 57: [ OK ] EnergyTermTest.ConstructWorks (0 ms) 57: [ RUN ] EnergyTermTest.AddFrameWorks 57: [ OK ] EnergyTermTest.AddFrameWorks (0 ms) 57: [----------] 2 tests from EnergyTermTest (0 ms total) 57: 57: [----------] 1 test from DhdlTest 57: [ RUN ] DhdlTest.ExtractDhdl 57: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file 57: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision) 57: Note: file tpx version 110, software tpx version 134 57: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Reading energy frame 6 time 0.060 Reading energy frame 7 time 0.070 Reading energy frame 8 time 0.080 Reading energy frame 9 time 0.090 Reading energy frame 10 time 0.100 Reading energy frame 11 time 0.110 Reading energy frame 12 time 0.120 Reading energy frame 13 time 0.130 Reading energy frame 14 time 0.140 Reading energy frame 15 time 0.150 Reading energy frame 16 time 0.160 Reading energy frame 17 time 0.170 Reading energy frame 18 time 0.180 Reading energy frame 19 time 0.190 Reading energy frame 20 time 0.200 Reading energy frame 30 time 0.300 Reading energy frame 40 time 0.400 Reading energy frame 50 time 0.500 Reading energy frame 60 time 0.600 Reading energy frame 70 time 0.700 Reading energy frame 80 time 0.800 Reading energy frame 90 time 0.900 Reading energy frame 100 time 1.000 Last energy frame read 100 time 1.000 57: 57: 57: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg 57: [ OK ] DhdlTest.ExtractDhdl (16 ms) 57: [----------] 1 test from DhdlTest (16 ms total) 57: 57: [----------] 1 test from OriresTest 57: [ RUN ] OriresTest.ExtractOrires 57: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file 57: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision) 57: Note: file tpx version 111, software tpx version 134 57: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all) 57: End your selection with 0 57: Selecting all 7 orientation restraints 57: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Reading energy frame 3 time 0.006 Reading energy frame 4 time 0.008 Reading energy frame 5 time 0.010 Reading energy frame 6 time 0.012 Reading energy frame 7 time 0.014 Reading energy frame 8 time 0.016 Reading energy frame 9 time 0.018 Reading energy frame 10 time 0.020 Last energy frame read 10 time 0.020 57: [ OK ] OriresTest.ExtractOrires (16 ms) 57: [----------] 1 test from OriresTest (17 ms total) 57: 57: [----------] 5 tests from EnergyTest 57: [ RUN ] EnergyTest.ExtractEnergy 57: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 57: 57: Select the terms you want from the following list by 57: selecting either (part of) the name or the number or a combination. 57: End your selection with an empty line or a zero. 57: ------------------------------------------------------------------- 57: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 57: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 57: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 57: 13 Box-Z 14 Volume 15 Density 16 pV 57: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 57: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 57: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 57: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 57: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 57: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 57: 57: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 57: 57: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 57: All statistics are over 5001 points 57: 57: Energy Average Err.Est. RMSD Tot-Drift 57: ------------------------------------------------------------------------------- 57: Potential -34142.2 39 228.993 -62.8906 (kJ/mol) 57: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 57: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 57: [ OK ] EnergyTest.ExtractEnergy (7 ms) 57: [ RUN ] EnergyTest.ExtractEnergyByNumber 57: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 57: 57: Select the terms you want from the following list by 57: selecting either (part of) the name or the number or a combination. 57: End your selection with an empty line or a zero. 57: ------------------------------------------------------------------- 57: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 57: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 57: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 57: 13 Box-Z 14 Volume 15 Density 16 pV 57: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 57: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 57: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 57: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 57: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 57: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 57: 57: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 57: 57: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 57: All statistics are over 5001 points 57: 57: Energy Average Err.Est. RMSD Tot-Drift 57: ------------------------------------------------------------------------------- 57: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol) 57: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 57: Pres. DC -268.49 3 8.52175 13.2804 (bar) 57: [ OK ] EnergyTest.ExtractEnergyByNumber (6 ms) 57: [ RUN ] EnergyTest.ExtractEnergyMixed 57: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 57: 57: Select the terms you want from the following list by 57: selecting either (part of) the name or the number or a combination. 57: End your selection with an empty line or a zero. 57: ------------------------------------------------------------------- 57: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 57: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 57: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 57: 13 Box-Z 14 Volume 15 Density 16 pV 57: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 57: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 57: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 57: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 57: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 57: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 57: 57: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 57: 57: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets 57: All statistics are over 5001 points 57: 57: Energy Average Err.Est. RMSD Tot-Drift 57: ------------------------------------------------------------------------------- 57: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 57: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 57: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm) 57: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 57: [ OK ] EnergyTest.ExtractEnergyMixed (4 ms) 57: [ RUN ] EnergyTest.ExtractEnergyWithNumberInName 57: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 57: 57: Select the terms you want from the following list by 57: selecting either (part of) the name or the number or a combination. 57: End your selection with an empty line or a zero. 57: ------------------------------------------------------------------- 57: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 57: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 57: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 57: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 57: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 57: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 57: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 57: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 57: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 57: 37 1/Viscosity 38 T-System 39 Lamb-System 57: 57: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 57: 57: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 1 data sets 57: All statistics are over 3 points (frames) 57: 57: Energy Average Err.Est. RMSD Tot-Drift 57: ------------------------------------------------------------------------------- 57: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 57: [ OK ] EnergyTest.ExtractEnergyWithNumberInName (2 ms) 57: [ RUN ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber 57: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 57: 57: Select the terms you want from the following list by 57: selecting either (part of) the name or the number or a combination. 57: End your selection with an empty line or a zero. 57: ------------------------------------------------------------------- 57: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 57: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 57: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 57: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 57: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 57: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 57: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 57: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 57: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 57: 37 1/Viscosity 38 T-System 39 Lamb-System 57: 57: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 57: 57: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 2 data sets 57: All statistics are over 3 points (frames) 57: 57: Energy Average Err.Est. RMSD Tot-Drift 57: ------------------------------------------------------------------------------- 57: LJ (SR) -14.1095 -- 0.384124 0.932214 (kJ/mol) 57: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 57: [ OK ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber (2 ms) 57: [----------] 5 tests from EnergyTest (25 ms total) 57: 57: [----------] 2 tests from ViscosityTest 57: [ RUN ] ViscosityTest.EinsteinViscosity 57: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 57: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 57: 57: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 57: All statistics are over 5001 points 57: 57: Energy Average Err.Est. RMSD Tot-Drift 57: ------------------------------------------------------------------------------- 57: Pres-XX 20.2092 65 717.193 185.978 (bar) 57: Pres-XY -47.7351 39 372.522 207.456 (bar) 57: Pres-XZ 11.477 31 379.79 6.80818 (bar) 57: Pres-YX -47.7106 39 372.525 207.5 (bar) 57: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 57: Pres-YZ -41.3534 45 401.216 114.663 (bar) 57: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 57: Pres-ZY -41.3119 45 401.196 114.743 (bar) 57: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 57: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 57: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 57: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 57: 57: Computing shear viscosity using the Einstein relation with 14 start points separated by 0.2 ps 57: [ OK ] ViscosityTest.EinsteinViscosity (170 ms) 57: [ RUN ] ViscosityTest.EinsteinViscosityIntegral 57: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 57: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 57: 57: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 57: All statistics are over 5001 points 57: 57: Energy Average Err.Est. RMSD Tot-Drift 57: ------------------------------------------------------------------------------- 57: Pres-XX 20.2092 65 717.193 185.978 (bar) 57: Pres-XY -47.7351 39 372.522 207.456 (bar) 57: Pres-XZ 11.477 31 379.79 6.80818 (bar) 57: Pres-YX -47.7106 39 372.525 207.5 (bar) 57: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 57: Pres-YZ -41.3534 45 401.216 114.663 (bar) 57: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 57: Pres-ZY -41.3119 45 401.196 114.743 (bar) 57: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 57: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 57: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 57: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 57: 57: Computing shear viscosity using the Einstein relation with 14 start points separated by 0.2 ps 57: [ OK ] ViscosityTest.EinsteinViscosityIntegral (183 ms) 57: [----------] 2 tests from ViscosityTest (354 ms total) 57: 57: [----------] Global test environment tear-down 57: [==========] 11 tests from 5 test suites ran. (414 ms total) 57: [ PASSED ] 11 tests. 57/87 Test #57: EnergyAnalysisUnitTests ................... Passed 0.45 sec test 58 Start 58: ToolUnitTests 58: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/tool-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/ToolUnitTests.xml" 58: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests 58: Test timeout computed to be: 1920 58: [==========] Running 62 tests from 7 test suites. 58: [----------] Global test environment set-up. 58: [----------] 2 tests from DumpTest 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file lysozyme.top, line 1465]: 58: System has non-zero total charge: 2.000000 58: Total charge should normally be an integer. See 58: https://manual.gromacs.org/current/user-guide/floating-point.html 58: for discussion on how close it should be to an integer. 58: 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 465.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 58: NVE simulation with an initial temperature of zero: will use a Verlet 58: buffer of 10%. Check your energy drift! 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 4 NOTEs 58: Setting the LD random seed to -14699346 58: 58: Generated 330891 of the 330891 non-bonded parameter combinations 58: 58: Generated 330891 of the 330891 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 58: Analysing residue names: 58: There are: 10 Protein residues 58: Analysing Protein... 58: 58: This run will generate roughly 0 Mb of data 58: [ RUN ] DumpTest.WorksWithTpr 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 58: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr: 58: inputrec: 58: integrator = md 58: tinit = 0 58: dt = 0.001 58: nsteps = 0 58: init-step = 0 58: simulation-part = 1 58: mts = false 58: mass-repartition-factor = 1 58: comm-mode = Linear 58: nstcomm = 100 58: bd-fric = 0 58: ld-seed = -14699346 58: emtol = 10 58: emstep = 0.01 58: niter = 20 58: fcstep = 0 58: nstcgsteep = 1000 58: nbfgscorr = 10 58: rtpi = 0.05 58: nstxout = 0 58: nstvout = 0 58: nstfout = 0 58: nstlog = 1000 58: nstcalcenergy = 100 58: nstenergy = 1000 58: nstxout-compressed = 0 58: compressed-x-precision = 1000 58: cutoff-scheme = Verlet 58: nstlist = 10 58: pbc = xyz 58: periodic-molecules = false 58: verlet-buffer-tolerance = -1 58: verlet-buffer-pressure-tolerance = 0.5 58: rlist = 1.1 58: coulombtype = Cut-off 58: coulomb-modifier = Potential-shift 58: rcoulomb-switch = 0 58: rcoulomb = 1 58: epsilon-r = 1 58: epsilon-rf = inf 58: vdw-type = Cut-off 58: vdw-modifier = Potential-shift 58: rvdw-switch = 0 58: rvdw = 1 58: DispCorr = No 58: table-extension = 1 58: fourierspacing = 0.12 58: fourier-nx = 0 58: fourier-ny = 0 58: fourier-nz = 0 58: pme-order = 4 58: ewald-rtol = 1e-05 58: ewald-rtol-lj = 0.001 58: lj-pme-comb-rule = Geometric 58: ewald-geometry = 3d 58: epsilon-surface = 0 58: ensemble-temperature-setting = not available 58: tcoupl = No 58: nsttcouple = -1 58: nh-chain-length = 0 58: print-nose-hoover-chain-variables = false 58: pcoupl = No 58: refcoord-scaling = No 58: posres-com (3): 58: posres-com[0]= 0.00000e+00 58: posres-com[1]= 0.00000e+00 58: posres-com[2]= 0.00000e+00 58: posres-comB (3): 58: posres-comB[0]= 0.00000e+00 58: posres-comB[1]= 0.00000e+00 58: posres-comB[2]= 0.00000e+00 58: QMMM = false 58: qm-opts: 58: ngQM = 0 58: constraint-algorithm = Lincs 58: continuation = false 58: Shake-SOR = false 58: shake-tol = 0.0001 58: lincs-order = 4 58: lincs-iter = 1 58: lincs-warnangle = 30 58: nwall = 0 58: wall-type = 9-3 58: wall-r-linpot = -1 58: wall-atomtype[0] = -1 58: wall-atomtype[1] = -1 58: wall-density[0] = 0 58: wall-density[1] = 0 58: wall-ewald-zfac = 3 58: pull = false 58: awh = false 58: rotation = false 58: interactiveMD = false 58: disre = No 58: disre-weighting = Conservative 58: disre-mixed = false 58: dr-fc = 1000 58: dr-tau = 0 58: nstdisreout = 100 58: orire-fc = 0 58: orire-tau = 0 58: nstorireout = 100 58: free-energy = no 58: cos-acceleration = 0 58: deform (3x3): 58: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: simulated-tempering = false 58: swapcoords = no 58: userint1 = 0 58: userint2 = 0 58: userint3 = 0 58: userint4 = 0 58: userreal1 = 0 58: userreal2 = 0 58: userreal3 = 0 58: userreal4 = 0 58: applied-forces: 58: electric-field: 58: x: 58: E0 = 0 58: omega = 0 58: t0 = 0 58: sigma = 0 58: y: 58: E0 = 0 58: omega = 0 58: t0 = 0 58: sigma = 0 58: z: 58: E0 = 0 58: omega = 0 58: t0 = 0 58: sigma = 0 58: density-guided-simulation: 58: active = false 58: group = protein 58: similarity-measure = inner-product 58: atom-spreading-weight = unity 58: force-constant = 1e+09 58: gaussian-transform-spreading-width = 0.2 58: gaussian-transform-spreading-range-in-multiples-of-width = 4 58: reference-density-filename = reference.mrc 58: nst = 1 58: normalize-densities = true 58: adaptive-force-scaling = false 58: adaptive-force-scaling-time-constant = 4 58: shift-vector = 58: transformation-matrix = 58: qmmm-cp2k: 58: active = false 58: qmgroup = System 58: qmmethod = PBE 58: qmfilenames = 58: qmcharge = 0 58: qmmultiplicity = 1 58: colvars: 58: active = false 58: configfile = 58: seed = -1 58: grpopts: 58: nrdf: 465 58: ref-t: 0 58: tau-t: 0 58: annealing: No 58: annealing-npoints: 0 58: acc: 0 0 0 58: nfreeze: N N N 58: energygrp-flags[ 0]: 0 58: header: 58: bIr = present 58: bBox = present 58: bTop = present 58: bX = present 58: bV = present 58: bF = not present 58: natoms = 156 58: lambda = 0.000000e+00 58: buffer size = 56904 58: topology: 58: name="First 10 residues from 1AKI" 58: #atoms = 156 58: #molblock = 1 58: molblock (0): 58: moltype = 0 "Protein_chain_B" 58: #molecules = 1 58: #posres_xA = 0 58: #posres_xB = 0 58: bIntermolecularInteractions = false 58: ffparams: 58: atnr=10 58: ntypes=212 58: functype[0]=LJ_SR, c6= 3.35274678e-03, c12= 3.95094442e-06 58: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 58: functype[2]=LJ_SR, c6= 2.60916961e-03, c12= 3.84022374e-06 58: functype[3]=LJ_SR, c6= 6.41072082e-04, c12= 3.43856290e-07 58: functype[4]=LJ_SR, c6= 4.04775915e-03, c12= 7.32754594e-06 58: functype[5]=LJ_SR, c6= 2.81521126e-03, c12= 2.50631820e-06 58: functype[6]=LJ_SR, c6= 2.80388560e-03, c12= 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functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02 58: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02 58: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02 58: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02 58: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02 58: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02 58: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02 58: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02 58: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02 58: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39320000e+01, phiB= 1.80000000e+02, cpB= 4.39320000e+01, mult=2 58: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400000e+00, phiB= 1.80000000e+02, cpB= 4.18400000e+00, mult=2 58: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60240000e+00, phiB= 1.80000000e+02, cpB= 4.60240000e+00, mult=2 58: functype[143]=RBDIHS, rbcA[0]= 5.46010000e-01, rbcA[1]= 1.63803000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 5.46010000e-01, rbcB[1]= 1.63803000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[144]=RBDIHS, rbcA[0]= 7.25920000e-01, rbcA[1]= 2.17777000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 7.25920000e-01, rbcB[1]= 2.17777000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[145]=RBDIHS, rbcA[0]= 1.27612000e+00, rbcA[1]= 1.16734000e+00, rbcA[2]= 8.95380000e-01, rbcA[3]=-3.33884000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 1.27612000e+00, rbcB[1]= 1.16734000e+00, rbcB[2]= 8.95380000e-01, rbcB[3]=-3.33884000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[146]=RBDIHS, rbcA[0]=-6.91824000e+00, rbcA[1]= 4.67562000e+00, rbcA[2]= 2.24262000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-6.91824000e+00, rbcB[1]= 4.67562000e+00, rbcB[2]= 2.24262000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[147]=RBDIHS, rbcA[0]= 9.70690000e-01, rbcA[1]= 2.91206000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 9.70690000e-01, rbcB[1]= 2.91206000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[148]=RBDIHS, rbcA[0]= 6.27600000e-01, rbcA[1]= 1.88280000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 6.27600000e-01, rbcB[1]= 1.88280000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[149]=RBDIHS, rbcA[0]=-1.58990000e-01, rbcA[1]=-4.76980000e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35960000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-1.58990000e-01, rbcB[1]=-4.76980000e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35960000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654000e+00, rbcA[2]=-1.04934700e+01, rbcA[3]= 6.73624000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654000e+00, rbcB[2]=-1.04934700e+01, rbcB[3]= 6.73624000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[151]=RBDIHS, rbcA[0]= 5.00825000e+00, rbcA[1]=-1.69870000e+00, rbcA[2]=-3.72380000e-01, rbcA[3]=-2.93716000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 5.00825000e+00, rbcB[1]=-1.69870000e+00, rbcB[2]=-3.72380000e-01, rbcB[3]=-2.93716000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[152]=RBDIHS, rbcA[0]= 2.92880000e+00, rbcA[1]=-1.46440000e+00, rbcA[2]= 2.09200000e-01, rbcA[3]=-1.67360000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 2.92880000e+00, rbcB[1]=-1.46440000e+00, rbcB[2]= 2.09200000e-01, rbcB[3]=-1.67360000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[153]=RBDIHS, rbcA[0]= 5.77183000e+00, rbcA[1]=-2.67148000e+00, rbcA[2]= 9.58140000e-01, rbcA[3]=-4.05848000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 5.77183000e+00, rbcB[1]=-2.67148000e+00, rbcB[2]= 9.58140000e-01, rbcB[3]=-4.05848000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[154]=RBDIHS, rbcA[0]= 8.03330000e-01, rbcA[1]= 2.40999000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 8.03330000e-01, rbcB[1]= 2.40999000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[155]=RBDIHS, rbcA[0]= 2.05016000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 2.05016000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[156]=RBDIHS, rbcA[0]= 3.02879800e+01, rbcA[1]=-4.81160000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 3.02879800e+01, rbcB[1]=-4.81160000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[157]=RBDIHS, rbcA[0]= 2.54763800e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 2.54763800e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[158]=RBDIHS, rbcA[0]= 1.57025500e+01, rbcA[1]= 3.17565600e+01, rbcA[2]=-3.66936000e+00, rbcA[3]=-4.37897500e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 1.57025500e+01, rbcB[1]= 3.17565600e+01, rbcB[2]=-3.66936000e+00, rbcB[3]=-4.37897500e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[159]=RBDIHS, rbcA[0]=-1.03574900e+01, rbcA[1]=-2.95871600e+01, rbcA[2]=-1.16734000e+00, rbcA[3]= 4.11119900e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-1.03574900e+01, rbcB[1]=-2.95871600e+01, rbcB[2]=-1.16734000e+00, rbcB[3]= 4.11119900e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[160]=RBDIHS, rbcA[0]= 4.50199000e+00, rbcA[1]= 7.82410000e-01, rbcA[2]=-1.60247000e+00, rbcA[3]=-3.68192000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 4.50199000e+00, rbcB[1]= 7.82410000e-01, rbcB[2]=-1.60247000e+00, rbcB[3]=-3.68192000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[161]=RBDIHS, rbcA[0]= 4.22590000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]=-3.12964000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 4.22590000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]=-3.12964000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[162]=RBDIHS, rbcA[0]=-7.65670000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]= 4.02501000e+00, rbcA[3]=-5.96639000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-7.65670000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]= 4.02501000e+00, rbcB[3]=-5.96639000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[163]=RBDIHS, rbcA[0]= 9.66500000e-01, rbcA[1]= 2.89951000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86601000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 9.66500000e-01, rbcB[1]= 2.89951000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86601000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[164]=RBDIHS, rbcA[0]=-4.23421000e+00, rbcA[1]= 7.22159000e+00, rbcA[2]= 1.90790000e+00, rbcA[3]=-4.89528000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-4.23421000e+00, rbcB[1]= 7.22159000e+00, rbcB[2]= 1.90790000e+00, rbcB[3]=-4.89528000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[165]=RBDIHS, rbcA[0]= 3.03340000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03340000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 3.03340000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03340000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[166]=RBDIHS, rbcA[0]= 1.02319700e+01, rbcA[1]= 3.52083000e+00, rbcA[2]=-3.97899000e+00, rbcA[3]=-9.77382000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 1.02319700e+01, rbcB[1]= 3.52083000e+00, rbcB[2]=-3.97899000e+00, rbcB[3]=-9.77382000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[167]=RBDIHS, rbcA[0]= 5.49778000e+00, rbcA[1]= 1.41838000e+00, rbcA[2]=-6.91615000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 5.49778000e+00, rbcB[1]= 1.41838000e+00, rbcB[2]=-6.91615000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[168]=RBDIHS, rbcA[0]=-1.21755000e+00, rbcA[1]=-3.65264000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-1.21755000e+00, rbcB[1]=-3.65264000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[169]=RBDIHS, rbcA[0]=-1.26775000e+00, rbcA[1]= 3.02085000e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49782000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-1.26775000e+00, rbcB[1]= 3.02085000e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49782000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[170]=RBDIHS, rbcA[0]= 3.80117000e+00, rbcA[1]=-6.95172000e+00, rbcA[2]=-1.01671000e+00, rbcA[3]= 4.16726000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 3.80117000e+00, rbcB[1]=-6.95172000e+00, rbcB[2]=-1.01671000e+00, rbcB[3]= 4.16726000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[171]=RBDIHS, rbcA[0]= 3.70280000e-01, rbcA[1]= 1.11086000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 3.70280000e-01, rbcB[1]= 1.11086000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[172]=RBDIHS, rbcA[0]= 3.32042200e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042200e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 3.32042200e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042200e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[173]=RBDIHS, rbcA[0]= 1.63176000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 1.63176000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[174]=RBDIHS, rbcA[0]= 3.40787000e+00, rbcA[1]=-2.80537000e+00, rbcA[2]=-3.59820000e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 3.40787000e+00, rbcB[1]=-2.80537000e+00, rbcB[2]=-3.59820000e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[175]=RBDIHS, rbcA[0]=-1.62590200e+01, rbcA[1]= 9.08765000e+00, rbcA[2]= 7.17138000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-1.62590200e+01, rbcB[1]= 9.08765000e+00, rbcB[2]= 7.17138000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[176]=RBDIHS, rbcA[0]= 9.45590000e-01, rbcA[1]= 2.83675000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 9.45590000e-01, rbcB[1]= 2.83675000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[177]=RBDIHS, rbcA[0]=-1.50624000e+00, rbcA[1]= 5.37225000e+00, rbcA[2]= 1.17989000e+00, rbcA[3]=-5.04590000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-1.50624000e+00, rbcB[1]= 5.37225000e+00, rbcB[2]= 1.17989000e+00, rbcB[3]=-5.04590000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[178]=RBDIHS, rbcA[0]= 1.00416000e+00, rbcA[1]= 3.01248000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 1.00416000e+00, rbcB[1]= 3.01248000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[179]=RBDIHS, rbcA[0]= 8.79268000e+00, rbcA[1]=-1.18344400e+01, rbcA[2]= 1.07529000e+00, rbcA[3]= 1.96648000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 8.79268000e+00, rbcB[1]=-1.18344400e+01, rbcB[2]= 1.07529000e+00, rbcB[3]= 1.96648000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[180]=RBDIHS, rbcA[0]=-5.77392000e+00, rbcA[1]= 3.38485000e+00, rbcA[2]= 2.38906000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-5.77392000e+00, rbcB[1]= 3.38485000e+00, rbcB[2]= 2.38906000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[181]=RBDIHS, rbcA[0]=-9.08346000e+00, rbcA[1]= 9.75709000e+00, rbcA[2]= 3.45180000e+00, rbcA[3]=-4.12542000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-9.08346000e+00, rbcB[1]= 9.75709000e+00, rbcB[2]= 3.45180000e+00, rbcB[3]=-4.12542000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[182]=RBDIHS, rbcA[0]=-4.70700000e-01, rbcA[1]=-1.41210000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88280000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-4.70700000e-01, rbcB[1]=-1.41210000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88280000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[183]=RBDIHS, rbcA[0]= 3.43088000e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 3.43088000e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[184]=RBDIHS, rbcA[0]= 2.57316000e+00, rbcA[1]= 3.49782000e+00, rbcA[2]=-1.10039000e+00, rbcA[3]=-4.97059000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 2.57316000e+00, rbcB[1]= 3.49782000e+00, rbcB[2]=-1.10039000e+00, rbcB[3]=-4.97059000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[185]=RBDIHS, rbcA[0]=-8.22160000e-01, rbcA[1]= 1.12759000e+00, rbcA[2]=-3.05440000e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-8.22160000e-01, rbcB[1]= 1.12759000e+00, rbcB[2]=-3.05440000e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[186]=LJ14, c6A= 3.20536041e-04, c12A= 1.71928145e-07, c6B= 3.20536041e-04, c12B= 1.71928145e-07 58: functype[187]=LJ14, c6A= 1.30458481e-03, c12A= 1.92011187e-06, c6B= 1.30458481e-03, c12B= 1.92011187e-06 58: functype[188]=LJ14, c6A= 1.40760563e-03, c12A= 1.25315910e-06, c6B= 1.40760563e-03, c12B= 1.25315910e-06 58: functype[189]=LJ14, c6A= 1.67637339e-03, c12A= 1.97547221e-06, c6B= 1.67637339e-03, c12B= 1.97547221e-06 58: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00 58: functype[191]=LJ14, c6A= 2.49447081e-04, c12A= 1.67110056e-07, c6B= 2.49447081e-04, c12B= 1.67110056e-07 58: functype[192]=LJ14, c6A= 1.01525205e-03, c12A= 1.86630294e-06, c6B= 1.01525205e-03, c12B= 1.86630294e-06 58: functype[193]=LJ14, c6A= 6.12890625e-05, c12A= 1.49631500e-08, c6B= 6.12890625e-05, c12B= 1.49631500e-08 58: functype[194]=LJ14, c6A= 2.69145489e-04, c12A= 1.09064212e-07, c6B= 2.69145489e-04, c12B= 1.09064212e-07 58: functype[195]=LJ14, c6A= 1.09542476e-03, c12A= 1.21804075e-06, c6B= 1.09542476e-03, c12B= 1.21804075e-06 58: functype[196]=LJ14, c6A= 3.86982011e-04, c12A= 3.18863352e-07, c6B= 3.86982011e-04, c12B= 3.18863352e-07 58: functype[197]=LJ14, c6A= 1.57502055e-03, c12A= 3.56109993e-06, c6B= 1.57502055e-03, c12B= 3.56109993e-06 58: functype[198]=LJ14, c6A= 2.44342255e-03, c12A= 6.79494872e-06, c6B= 2.44342255e-03, c12B= 6.79494872e-06 58: functype[199]=LJ14, c6A= 1.40194280e-03, c12A= 2.15310613e-06, c6B= 1.40194280e-03, c12B= 2.15310613e-06 58: functype[200]=LJ14, c6A= 1.09101784e-03, c12A= 2.09276780e-06, c6B= 1.09101784e-03, c12B= 2.09276780e-06 58: functype[201]=LJ14, c6A= 2.68062710e-04, c12A= 1.87387876e-07, c6B= 2.68062710e-04, c12B= 1.87387876e-07 58: functype[202]=LJ14, c6A= 2.26258289e-04, c12A= 1.37484813e-07, c6B= 2.26258289e-04, c12B= 1.37484813e-07 58: functype[203]=LJ14, c6A= 2.43143395e-04, c12A= 1.54167785e-07, c6B= 2.43143395e-04, c12B= 1.54167785e-07 58: functype[204]=LJ14, c6A= 1.17243785e-03, c12A= 2.34671283e-06, c6B= 1.17243785e-03, c12B= 2.34671283e-06 58: functype[205]=LJ14, c6A= 1.69256051e-03, c12A= 3.99321842e-06, c6B= 1.69256051e-03, c12B= 3.99321842e-06 58: functype[206]=LJ14, c6A= 5.04237478e-05, c12A= 1.01280845e-08, c6B= 5.04237478e-05, c12B= 1.01280845e-08 58: functype[207]=LJ14, c6A= 2.34763367e-04, c12A= 1.14652101e-07, c6B= 2.34763367e-04, c12B= 1.14652101e-07 58: functype[208]=LJ14, c6A= 5.76812790e-05, c12A= 1.02660284e-08, c6B= 5.76812790e-05, c12B= 1.02660284e-08 58: functype[209]=LJ14, c6A= 3.60245183e-03, c12A= 5.76973368e-06, c6B= 3.60245183e-03, c12B= 5.76973368e-06 58: functype[210]=LJ14, c6A= 6.88817690e-04, c12A= 5.02148096e-07, c6B= 6.88817690e-04, c12B= 5.02148096e-07 58: functype[211]=LJ14, c6A= 4.34922716e-03, c12A= 1.07007298e-05, c6B= 4.34922716e-03, c12B= 1.07007298e-05 58: reppow = 12 58: fudgeQQ = 0.5 58: cmap 58: moltype (0): 58: name="Protein_chain_B" 58: atoms: 58: atom (156): 58: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 58: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 58: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 58: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 58: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6} 58: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 58: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 58: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 58: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 58: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 58: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 58: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 58: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 58: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 58: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 58: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6} 58: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 58: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 58: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 58: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 58: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 58: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 58: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6} 58: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8} 58: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7} 58: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1} 58: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6} 58: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 58: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6} 58: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 58: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 58: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 58: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 58: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 58: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 58: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 58: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 58: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 58: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6} 58: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8} 58: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7} 58: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1} 58: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6} 58: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 58: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6} 58: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 58: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 58: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 58: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 58: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 58: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 58: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 58: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 58: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 58: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 58: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 58: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 58: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 58: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6} 58: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8} 58: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7} 58: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1} 58: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6} 58: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 58: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 58: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6} 58: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8} 58: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7} 58: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1} 58: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6} 58: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 58: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6} 58: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 58: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 58: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6} 58: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 58: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 58: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6} 58: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 58: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 58: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7} 58: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1} 58: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6} 58: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 58: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 58: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 58: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 58: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 58: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 58: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6} 58: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8} 58: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7} 58: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1} 58: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6} 58: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 58: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6} 58: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 58: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 58: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16} 58: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1} 58: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6} 58: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8} 58: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7} 58: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1} 58: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6} 58: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 58: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6} 58: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 58: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 58: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6} 58: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 58: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 58: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6} 58: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 58: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 58: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6} 58: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8} 58: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7} 58: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1} 58: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6} 58: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 58: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6} 58: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 58: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 58: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6} 58: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 58: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 58: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 58: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 58: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 58: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 58: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 58: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 58: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 58: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6} 58: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8} 58: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7} 58: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1} 58: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6} 58: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 58: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6} 58: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 58: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 58: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 58: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6} 58: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8} 58: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7} 58: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1} 58: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6} 58: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 58: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6} 58: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 58: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 58: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 58: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6} 58: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8} 58: atom (156): 58: atom[0]={name="N"} 58: atom[1]={name="H1"} 58: atom[2]={name="H2"} 58: atom[3]={name="H3"} 58: atom[4]={name="CA"} 58: atom[5]={name="HA"} 58: atom[6]={name="CB"} 58: atom[7]={name="HB1"} 58: atom[8]={name="HB2"} 58: atom[9]={name="CG"} 58: atom[10]={name="HG1"} 58: atom[11]={name="HG2"} 58: atom[12]={name="CD"} 58: atom[13]={name="HD1"} 58: atom[14]={name="HD2"} 58: atom[15]={name="CE"} 58: atom[16]={name="HE1"} 58: atom[17]={name="HE2"} 58: atom[18]={name="NZ"} 58: atom[19]={name="HZ1"} 58: atom[20]={name="HZ2"} 58: atom[21]={name="HZ3"} 58: atom[22]={name="C"} 58: atom[23]={name="O"} 58: atom[24]={name="N"} 58: atom[25]={name="H"} 58: atom[26]={name="CA"} 58: atom[27]={name="HA"} 58: atom[28]={name="CB"} 58: atom[29]={name="HB"} 58: atom[30]={name="CG1"} 58: atom[31]={name="HG11"} 58: atom[32]={name="HG12"} 58: atom[33]={name="HG13"} 58: atom[34]={name="CG2"} 58: atom[35]={name="HG21"} 58: atom[36]={name="HG22"} 58: atom[37]={name="HG23"} 58: atom[38]={name="C"} 58: atom[39]={name="O"} 58: atom[40]={name="N"} 58: atom[41]={name="H"} 58: atom[42]={name="CA"} 58: atom[43]={name="HA"} 58: atom[44]={name="CB"} 58: atom[45]={name="HB1"} 58: atom[46]={name="HB2"} 58: atom[47]={name="CG"} 58: atom[48]={name="CD1"} 58: atom[49]={name="HD1"} 58: atom[50]={name="CD2"} 58: atom[51]={name="HD2"} 58: atom[52]={name="CE1"} 58: atom[53]={name="HE1"} 58: atom[54]={name="CE2"} 58: atom[55]={name="HE2"} 58: atom[56]={name="CZ"} 58: atom[57]={name="HZ"} 58: atom[58]={name="C"} 58: atom[59]={name="O"} 58: atom[60]={name="N"} 58: atom[61]={name="H"} 58: atom[62]={name="CA"} 58: atom[63]={name="HA1"} 58: atom[64]={name="HA2"} 58: atom[65]={name="C"} 58: atom[66]={name="O"} 58: atom[67]={name="N"} 58: atom[68]={name="H"} 58: atom[69]={name="CA"} 58: atom[70]={name="HA"} 58: atom[71]={name="CB"} 58: atom[72]={name="HB1"} 58: atom[73]={name="HB2"} 58: atom[74]={name="CG"} 58: atom[75]={name="HG1"} 58: atom[76]={name="HG2"} 58: atom[77]={name="CD"} 58: atom[78]={name="HD1"} 58: atom[79]={name="HD2"} 58: atom[80]={name="NE"} 58: atom[81]={name="HE"} 58: atom[82]={name="CZ"} 58: atom[83]={name="NH1"} 58: atom[84]={name="HH11"} 58: atom[85]={name="HH12"} 58: atom[86]={name="NH2"} 58: atom[87]={name="HH21"} 58: atom[88]={name="HH22"} 58: atom[89]={name="C"} 58: atom[90]={name="O"} 58: atom[91]={name="N"} 58: atom[92]={name="H"} 58: atom[93]={name="CA"} 58: atom[94]={name="HA"} 58: atom[95]={name="CB"} 58: atom[96]={name="HB1"} 58: atom[97]={name="HB2"} 58: atom[98]={name="SG"} 58: atom[99]={name="HG"} 58: atom[100]={name="C"} 58: atom[101]={name="O"} 58: atom[102]={name="N"} 58: atom[103]={name="H"} 58: atom[104]={name="CA"} 58: atom[105]={name="HA"} 58: atom[106]={name="CB"} 58: atom[107]={name="HB1"} 58: atom[108]={name="HB2"} 58: atom[109]={name="CG"} 58: atom[110]={name="HG1"} 58: atom[111]={name="HG2"} 58: atom[112]={name="CD"} 58: atom[113]={name="OE1"} 58: atom[114]={name="OE2"} 58: atom[115]={name="C"} 58: atom[116]={name="O"} 58: atom[117]={name="N"} 58: atom[118]={name="H"} 58: atom[119]={name="CA"} 58: atom[120]={name="HA"} 58: atom[121]={name="CB"} 58: atom[122]={name="HB1"} 58: atom[123]={name="HB2"} 58: atom[124]={name="CG"} 58: atom[125]={name="HG"} 58: atom[126]={name="CD1"} 58: atom[127]={name="HD11"} 58: atom[128]={name="HD12"} 58: atom[129]={name="HD13"} 58: atom[130]={name="CD2"} 58: atom[131]={name="HD21"} 58: atom[132]={name="HD22"} 58: atom[133]={name="HD23"} 58: atom[134]={name="C"} 58: atom[135]={name="O"} 58: atom[136]={name="N"} 58: atom[137]={name="H"} 58: atom[138]={name="CA"} 58: atom[139]={name="HA"} 58: atom[140]={name="CB"} 58: atom[141]={name="HB1"} 58: atom[142]={name="HB2"} 58: atom[143]={name="HB3"} 58: atom[144]={name="C"} 58: atom[145]={name="O"} 58: atom[146]={name="N"} 58: atom[147]={name="H"} 58: atom[148]={name="CA"} 58: atom[149]={name="HA"} 58: atom[150]={name="CB"} 58: atom[151]={name="HB1"} 58: atom[152]={name="HB2"} 58: atom[153]={name="HB3"} 58: atom[154]={name="C"} 58: atom[155]={name="O"} 58: type (156): 58: type[0]={name="opls_287",nameB="opls_287"} 58: type[1]={name="opls_290",nameB="opls_290"} 58: type[2]={name="opls_290",nameB="opls_290"} 58: type[3]={name="opls_290",nameB="opls_290"} 58: type[4]={name="opls_293B",nameB="opls_293B"} 58: type[5]={name="opls_140",nameB="opls_140"} 58: type[6]={name="opls_136",nameB="opls_136"} 58: type[7]={name="opls_140",nameB="opls_140"} 58: type[8]={name="opls_140",nameB="opls_140"} 58: type[9]={name="opls_136",nameB="opls_136"} 58: type[10]={name="opls_140",nameB="opls_140"} 58: type[11]={name="opls_140",nameB="opls_140"} 58: type[12]={name="opls_136",nameB="opls_136"} 58: type[13]={name="opls_140",nameB="opls_140"} 58: type[14]={name="opls_140",nameB="opls_140"} 58: type[15]={name="opls_292",nameB="opls_292"} 58: type[16]={name="opls_140",nameB="opls_140"} 58: type[17]={name="opls_140",nameB="opls_140"} 58: type[18]={name="opls_287",nameB="opls_287"} 58: type[19]={name="opls_290",nameB="opls_290"} 58: type[20]={name="opls_290",nameB="opls_290"} 58: type[21]={name="opls_290",nameB="opls_290"} 58: type[22]={name="opls_235",nameB="opls_235"} 58: type[23]={name="opls_236",nameB="opls_236"} 58: type[24]={name="opls_238",nameB="opls_238"} 58: type[25]={name="opls_241",nameB="opls_241"} 58: type[26]={name="opls_224B",nameB="opls_224B"} 58: type[27]={name="opls_140",nameB="opls_140"} 58: type[28]={name="opls_137",nameB="opls_137"} 58: type[29]={name="opls_140",nameB="opls_140"} 58: type[30]={name="opls_135",nameB="opls_135"} 58: type[31]={name="opls_140",nameB="opls_140"} 58: type[32]={name="opls_140",nameB="opls_140"} 58: type[33]={name="opls_140",nameB="opls_140"} 58: type[34]={name="opls_135",nameB="opls_135"} 58: type[35]={name="opls_140",nameB="opls_140"} 58: type[36]={name="opls_140",nameB="opls_140"} 58: type[37]={name="opls_140",nameB="opls_140"} 58: type[38]={name="opls_235",nameB="opls_235"} 58: type[39]={name="opls_236",nameB="opls_236"} 58: type[40]={name="opls_238",nameB="opls_238"} 58: type[41]={name="opls_241",nameB="opls_241"} 58: type[42]={name="opls_224B",nameB="opls_224B"} 58: type[43]={name="opls_140",nameB="opls_140"} 58: type[44]={name="opls_149",nameB="opls_149"} 58: type[45]={name="opls_140",nameB="opls_140"} 58: type[46]={name="opls_140",nameB="opls_140"} 58: type[47]={name="opls_145",nameB="opls_145"} 58: type[48]={name="opls_145",nameB="opls_145"} 58: type[49]={name="opls_146",nameB="opls_146"} 58: type[50]={name="opls_145",nameB="opls_145"} 58: type[51]={name="opls_146",nameB="opls_146"} 58: type[52]={name="opls_145",nameB="opls_145"} 58: type[53]={name="opls_146",nameB="opls_146"} 58: type[54]={name="opls_145",nameB="opls_145"} 58: type[55]={name="opls_146",nameB="opls_146"} 58: type[56]={name="opls_145",nameB="opls_145"} 58: type[57]={name="opls_146",nameB="opls_146"} 58: type[58]={name="opls_235",nameB="opls_235"} 58: type[59]={name="opls_236",nameB="opls_236"} 58: type[60]={name="opls_238",nameB="opls_238"} 58: type[61]={name="opls_241",nameB="opls_241"} 58: type[62]={name="opls_223B",nameB="opls_223B"} 58: type[63]={name="opls_140",nameB="opls_140"} 58: type[64]={name="opls_140",nameB="opls_140"} 58: type[65]={name="opls_235",nameB="opls_235"} 58: type[66]={name="opls_236",nameB="opls_236"} 58: type[67]={name="opls_238",nameB="opls_238"} 58: type[68]={name="opls_241",nameB="opls_241"} 58: type[69]={name="opls_224B",nameB="opls_224B"} 58: type[70]={name="opls_140",nameB="opls_140"} 58: type[71]={name="opls_136",nameB="opls_136"} 58: type[72]={name="opls_140",nameB="opls_140"} 58: type[73]={name="opls_140",nameB="opls_140"} 58: type[74]={name="opls_308",nameB="opls_308"} 58: type[75]={name="opls_140",nameB="opls_140"} 58: type[76]={name="opls_140",nameB="opls_140"} 58: type[77]={name="opls_307",nameB="opls_307"} 58: type[78]={name="opls_140",nameB="opls_140"} 58: type[79]={name="opls_140",nameB="opls_140"} 58: type[80]={name="opls_303",nameB="opls_303"} 58: type[81]={name="opls_304",nameB="opls_304"} 58: type[82]={name="opls_302",nameB="opls_302"} 58: type[83]={name="opls_300",nameB="opls_300"} 58: type[84]={name="opls_301",nameB="opls_301"} 58: type[85]={name="opls_301",nameB="opls_301"} 58: type[86]={name="opls_300",nameB="opls_300"} 58: type[87]={name="opls_301",nameB="opls_301"} 58: type[88]={name="opls_301",nameB="opls_301"} 58: type[89]={name="opls_235",nameB="opls_235"} 58: type[90]={name="opls_236",nameB="opls_236"} 58: type[91]={name="opls_238",nameB="opls_238"} 58: type[92]={name="opls_241",nameB="opls_241"} 58: type[93]={name="opls_224B",nameB="opls_224B"} 58: type[94]={name="opls_140",nameB="opls_140"} 58: type[95]={name="opls_206",nameB="opls_206"} 58: type[96]={name="opls_140",nameB="opls_140"} 58: type[97]={name="opls_140",nameB="opls_140"} 58: type[98]={name="opls_200",nameB="opls_200"} 58: type[99]={name="opls_204",nameB="opls_204"} 58: type[100]={name="opls_235",nameB="opls_235"} 58: type[101]={name="opls_236",nameB="opls_236"} 58: type[102]={name="opls_238",nameB="opls_238"} 58: type[103]={name="opls_241",nameB="opls_241"} 58: type[104]={name="opls_224B",nameB="opls_224B"} 58: type[105]={name="opls_140",nameB="opls_140"} 58: type[106]={name="opls_136",nameB="opls_136"} 58: type[107]={name="opls_140",nameB="opls_140"} 58: type[108]={name="opls_140",nameB="opls_140"} 58: type[109]={name="opls_274",nameB="opls_274"} 58: type[110]={name="opls_140",nameB="opls_140"} 58: type[111]={name="opls_140",nameB="opls_140"} 58: type[112]={name="opls_271",nameB="opls_271"} 58: type[113]={name="opls_272",nameB="opls_272"} 58: type[114]={name="opls_272",nameB="opls_272"} 58: type[115]={name="opls_235",nameB="opls_235"} 58: type[116]={name="opls_236",nameB="opls_236"} 58: type[117]={name="opls_238",nameB="opls_238"} 58: type[118]={name="opls_241",nameB="opls_241"} 58: type[119]={name="opls_224B",nameB="opls_224B"} 58: type[120]={name="opls_140",nameB="opls_140"} 58: type[121]={name="opls_136",nameB="opls_136"} 58: type[122]={name="opls_140",nameB="opls_140"} 58: type[123]={name="opls_140",nameB="opls_140"} 58: type[124]={name="opls_137",nameB="opls_137"} 58: type[125]={name="opls_140",nameB="opls_140"} 58: type[126]={name="opls_135",nameB="opls_135"} 58: type[127]={name="opls_140",nameB="opls_140"} 58: type[128]={name="opls_140",nameB="opls_140"} 58: type[129]={name="opls_140",nameB="opls_140"} 58: type[130]={name="opls_135",nameB="opls_135"} 58: type[131]={name="opls_140",nameB="opls_140"} 58: type[132]={name="opls_140",nameB="opls_140"} 58: type[133]={name="opls_140",nameB="opls_140"} 58: type[134]={name="opls_235",nameB="opls_235"} 58: type[135]={name="opls_236",nameB="opls_236"} 58: type[136]={name="opls_238",nameB="opls_238"} 58: type[137]={name="opls_241",nameB="opls_241"} 58: type[138]={name="opls_224B",nameB="opls_224B"} 58: type[139]={name="opls_140",nameB="opls_140"} 58: type[140]={name="opls_135",nameB="opls_135"} 58: type[141]={name="opls_140",nameB="opls_140"} 58: type[142]={name="opls_140",nameB="opls_140"} 58: type[143]={name="opls_140",nameB="opls_140"} 58: type[144]={name="opls_235",nameB="opls_235"} 58: type[145]={name="opls_236",nameB="opls_236"} 58: type[146]={name="opls_238",nameB="opls_238"} 58: type[147]={name="opls_241",nameB="opls_241"} 58: type[148]={name="opls_224B",nameB="opls_224B"} 58: type[149]={name="opls_140",nameB="opls_140"} 58: type[150]={name="opls_135",nameB="opls_135"} 58: type[151]={name="opls_140",nameB="opls_140"} 58: type[152]={name="opls_140",nameB="opls_140"} 58: type[153]={name="opls_140",nameB="opls_140"} 58: type[154]={name="opls_235",nameB="opls_235"} 58: type[155]={name="opls_236",nameB="opls_236"} 58: residue (10): 58: residue[0]={name="LYS", nr=1, ic=' '} 58: residue[1]={name="VAL", nr=2, ic=' '} 58: residue[2]={name="PHE", nr=3, ic=' '} 58: residue[3]={name="GLY", nr=4, ic=' '} 58: residue[4]={name="ARG", nr=5, ic=' '} 58: residue[5]={name="CYS", nr=6, ic=' '} 58: residue[6]={name="GLU", nr=7, ic=' '} 58: residue[7]={name="LEU", nr=8, ic=' '} 58: residue[8]={name="ALA", nr=9, ic=' '} 58: residue[9]={name="ALA", nr=10, ic=' '} 58: excls: 58: numLists=156 58: numElements=1828 58: excls[0][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 58: excls[1][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 58: excls[2][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 58: excls[3][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 58: excls[4][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 58: 23, 24, 25, 26} 58: excls[5][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 58: excls[6][num=19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 58: 14, 15, 22, 23, 24} 58: excls[7][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 58: excls[8][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 58: excls[9][num=17]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 58: 16, 17, 18, 22} 58: excls[10][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 58: excls[11][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 58: excls[12][num=17]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 58: 17, 18, 19, 20, 21} 58: excls[13][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 58: excls[14][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 58: excls[15][num=14]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 58: 20, 21} 58: excls[16][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 58: excls[17][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 58: excls[18][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 58: excls[19][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 58: excls[20][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 58: excls[21][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 58: excls[22][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 58: 26, 27, 28, 38} 58: excls[23][num=9]={0, 4, 5, 6, 22, 23, 24, 25, 26} 58: excls[24][num=17]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 58: 30, 34, 38, 39, 40} 58: excls[25][num=9]={4, 22, 23, 24, 25, 26, 27, 28, 38} 58: excls[26][num=22]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 58: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42} 58: excls[27][num=12]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 58: 40} 58: excls[28][num=18]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 58: 34, 35, 36, 37, 38, 39, 40} 58: excls[29][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 58: 36, 37, 38} 58: excls[30][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 58: 36, 37, 38} 58: excls[31][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 58: excls[32][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 58: excls[33][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 58: excls[34][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 58: 36, 37, 38} 58: excls[35][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 58: excls[36][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 58: excls[37][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 58: excls[38][num=17]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 58: 40, 41, 42, 43, 44, 58} 58: excls[39][num=9]={24, 26, 27, 28, 38, 39, 40, 41, 42} 58: excls[40][num=17]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 58: 45, 46, 47, 58, 59, 60} 58: excls[41][num=9]={26, 38, 39, 40, 41, 42, 43, 44, 58} 58: excls[42][num=18]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 58: 48, 50, 58, 59, 60, 61, 62} 58: excls[43][num=12]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 58: 60} 58: excls[44][num=18]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 58: 50, 51, 52, 54, 58, 59, 60} 58: excls[45][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 58: excls[46][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 58: excls[47][num=17]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 58: 52, 53, 54, 55, 56, 58} 58: excls[48][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 58: 54, 56, 57} 58: excls[49][num=8]={44, 47, 48, 49, 50, 52, 53, 56} 58: excls[50][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 58: 55, 56, 57} 58: excls[51][num=8]={44, 47, 48, 50, 51, 54, 55, 56} 58: excls[52][num=11]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57} 58: excls[53][num=8]={47, 48, 49, 52, 53, 54, 56, 57} 58: excls[54][num=11]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57} 58: excls[55][num=8]={47, 50, 51, 52, 54, 55, 56, 57} 58: excls[56][num=11]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57} 58: excls[57][num=8]={48, 50, 52, 53, 54, 55, 56, 57} 58: excls[58][num=17]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 58: 60, 61, 62, 63, 64, 65} 58: excls[59][num=9]={40, 42, 43, 44, 58, 59, 60, 61, 62} 58: excls[60][num=14]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64, 58: 65, 66, 67} 58: excls[61][num=9]={42, 58, 59, 60, 61, 62, 63, 64, 65} 58: excls[62][num=13]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 58: 68, 69} 58: excls[63][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 58: excls[64][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 58: excls[65][num=14]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 58: 70, 71, 89} 58: excls[66][num=9]={60, 62, 63, 64, 65, 66, 67, 68, 69} 58: excls[67][num=17]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 58: 72, 73, 74, 89, 90, 91} 58: excls[68][num=9]={62, 65, 66, 67, 68, 69, 70, 71, 89} 58: excls[69][num=19]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 58: 75, 76, 77, 89, 90, 91, 92, 93} 58: excls[70][num=12]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 58: 91} 58: excls[71][num=18]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 58: 77, 78, 79, 80, 89, 90, 91} 58: excls[72][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 58: excls[73][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 58: excls[74][num=16]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 58: 79, 80, 81, 82, 89} 58: excls[75][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 58: excls[76][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 58: excls[77][num=15]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 58: 81, 82, 83, 86} 58: excls[78][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 58: excls[79][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 58: excls[80][num=16]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 58: 84, 85, 86, 87, 88} 58: excls[81][num=9]={74, 77, 78, 79, 80, 81, 82, 83, 86} 58: excls[82][num=13]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 58: 87, 88} 58: excls[83][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 58: excls[84][num=6]={80, 82, 83, 84, 85, 86} 58: excls[85][num=6]={80, 82, 83, 84, 85, 86} 58: excls[86][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 58: excls[87][num=6]={80, 82, 83, 86, 87, 88} 58: excls[88][num=6]={80, 82, 83, 86, 87, 88} 58: excls[89][num=17]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 58: 91, 92, 93, 94, 95, 100} 58: excls[90][num=9]={67, 69, 70, 71, 89, 90, 91, 92, 93} 58: excls[91][num=17]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94, 95, 58: 96, 97, 98, 100, 101, 102} 58: excls[92][num=9]={69, 89, 90, 91, 92, 93, 94, 95, 100} 58: excls[93][num=17]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 58: 99, 100, 101, 102, 103, 104} 58: excls[94][num=12]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 58: 102} 58: excls[95][num=13]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 58: 101, 102} 58: excls[96][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 58: excls[97][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 58: excls[98][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 58: excls[99][num=6]={93, 95, 96, 97, 98, 99} 58: excls[100][num=17]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 58: 102, 103, 104, 105, 106, 115} 58: excls[101][num=9]={91, 93, 94, 95, 100, 101, 102, 103, 104} 58: excls[102][num=17]={91, 93, 94, 95, 100, 101, 102, 103, 104, 105, 58: 106, 107, 108, 109, 115, 116, 117} 58: excls[103][num=9]={93, 100, 101, 102, 103, 104, 105, 106, 115} 58: excls[104][num=19]={93, 100, 101, 102, 103, 104, 105, 106, 107, 58: 108, 109, 110, 111, 112, 115, 116, 117, 118, 119} 58: excls[105][num=12]={100, 102, 103, 104, 105, 106, 107, 108, 109, 58: 115, 116, 117} 58: excls[106][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 58: 110, 111, 112, 113, 114, 115, 116, 117} 58: excls[107][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 58: 112, 115} 58: excls[108][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 58: 112, 115} 58: excls[109][num=13]={102, 104, 105, 106, 107, 108, 109, 110, 111, 58: 112, 113, 114, 115} 58: excls[110][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 58: 114} 58: excls[111][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 58: 114} 58: excls[112][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 58: 114} 58: excls[113][num=7]={106, 109, 110, 111, 112, 113, 114} 58: excls[114][num=7]={106, 109, 110, 111, 112, 113, 114} 58: excls[115][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 58: 115, 116, 117, 118, 119, 120, 121, 134} 58: excls[116][num=9]={102, 104, 105, 106, 115, 116, 117, 118, 119} 58: excls[117][num=17]={102, 104, 105, 106, 115, 116, 117, 118, 119, 58: 120, 121, 122, 123, 124, 134, 135, 136} 58: excls[118][num=9]={104, 115, 116, 117, 118, 119, 120, 121, 134} 58: excls[119][num=19]={104, 115, 116, 117, 118, 119, 120, 121, 122, 58: 123, 124, 125, 126, 130, 134, 135, 136, 137, 138} 58: excls[120][num=12]={115, 117, 118, 119, 120, 121, 122, 123, 124, 58: 134, 135, 136} 58: excls[121][num=21]={115, 117, 118, 119, 120, 121, 122, 123, 124, 58: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136} 58: excls[122][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 58: 130, 134} 58: excls[123][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 58: 130, 134} 58: excls[124][num=17]={117, 119, 120, 121, 122, 123, 124, 125, 126, 58: 127, 128, 129, 130, 131, 132, 133, 134} 58: excls[125][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 58: 129, 130, 131, 132, 133} 58: excls[126][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 58: 129, 130, 131, 132, 133} 58: excls[127][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 58: excls[128][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 58: excls[129][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 58: excls[130][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 58: 129, 130, 131, 132, 133} 58: excls[131][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 58: excls[132][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 58: excls[133][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 58: excls[134][num=17]={115, 117, 118, 119, 120, 121, 122, 123, 124, 58: 134, 135, 136, 137, 138, 139, 140, 144} 58: excls[135][num=9]={117, 119, 120, 121, 134, 135, 136, 137, 138} 58: excls[136][num=17]={117, 119, 120, 121, 134, 135, 136, 137, 138, 58: 139, 140, 141, 142, 143, 144, 145, 146} 58: excls[137][num=9]={119, 134, 135, 136, 137, 138, 139, 140, 144} 58: excls[138][num=16]={119, 134, 135, 136, 137, 138, 139, 140, 141, 58: 142, 143, 144, 145, 146, 147, 148} 58: excls[139][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 58: 144, 145, 146} 58: excls[140][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 58: 144, 145, 146} 58: excls[141][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 58: excls[142][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 58: excls[143][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 58: excls[144][num=17]={134, 136, 137, 138, 139, 140, 141, 142, 143, 58: 144, 145, 146, 147, 148, 149, 150, 154} 58: excls[145][num=9]={136, 138, 139, 140, 144, 145, 146, 147, 148} 58: excls[146][num=16]={136, 138, 139, 140, 144, 145, 146, 147, 148, 58: 149, 150, 151, 152, 153, 154, 155} 58: excls[147][num=9]={138, 144, 145, 146, 147, 148, 149, 150, 154} 58: excls[148][num=13]={138, 144, 145, 146, 147, 148, 149, 150, 151, 58: 152, 153, 154, 155} 58: excls[149][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 58: 154, 155} 58: excls[150][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 58: 154, 155} 58: excls[151][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 58: excls[152][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 58: excls[153][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 58: excls[154][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 58: 154, 155} 58: excls[155][num=6]={146, 148, 149, 150, 154, 155} 58: Bond: 58: nr: 468 58: iatoms: 58: 0 type=100 (BONDS) 0 1 58: 1 type=100 (BONDS) 0 2 58: 2 type=100 (BONDS) 0 3 58: 3 type=101 (BONDS) 0 4 58: 4 type=102 (BONDS) 4 5 58: 5 type=103 (BONDS) 4 6 58: 6 type=104 (BONDS) 4 22 58: 7 type=102 (BONDS) 6 7 58: 8 type=102 (BONDS) 6 8 58: 9 type=103 (BONDS) 6 9 58: 10 type=102 (BONDS) 9 10 58: 11 type=102 (BONDS) 9 11 58: 12 type=103 (BONDS) 9 12 58: 13 type=102 (BONDS) 12 13 58: 14 type=102 (BONDS) 12 14 58: 15 type=103 (BONDS) 12 15 58: 16 type=102 (BONDS) 15 16 58: 17 type=102 (BONDS) 15 17 58: 18 type=101 (BONDS) 15 18 58: 19 type=100 (BONDS) 18 19 58: 20 type=100 (BONDS) 18 20 58: 21 type=100 (BONDS) 18 21 58: 22 type=105 (BONDS) 22 23 58: 23 type=106 (BONDS) 22 24 58: 24 type=100 (BONDS) 24 25 58: 25 type=107 (BONDS) 24 26 58: 26 type=102 (BONDS) 26 27 58: 27 type=103 (BONDS) 26 28 58: 28 type=104 (BONDS) 26 38 58: 29 type=102 (BONDS) 28 29 58: 30 type=103 (BONDS) 28 30 58: 31 type=103 (BONDS) 28 34 58: 32 type=102 (BONDS) 30 31 58: 33 type=102 (BONDS) 30 32 58: 34 type=102 (BONDS) 30 33 58: 35 type=102 (BONDS) 34 35 58: 36 type=102 (BONDS) 34 36 58: 37 type=102 (BONDS) 34 37 58: 38 type=105 (BONDS) 38 39 58: 39 type=106 (BONDS) 38 40 58: 40 type=100 (BONDS) 40 41 58: 41 type=107 (BONDS) 40 42 58: 42 type=102 (BONDS) 42 43 58: 43 type=103 (BONDS) 42 44 58: 44 type=104 (BONDS) 42 58 58: 45 type=102 (BONDS) 44 45 58: 46 type=102 (BONDS) 44 46 58: 47 type=108 (BONDS) 44 47 58: 48 type=109 (BONDS) 47 48 58: 49 type=109 (BONDS) 47 50 58: 50 type=110 (BONDS) 48 49 58: 51 type=109 (BONDS) 48 52 58: 52 type=110 (BONDS) 50 51 58: 53 type=109 (BONDS) 50 54 58: 54 type=110 (BONDS) 52 53 58: 55 type=109 (BONDS) 52 56 58: 56 type=110 (BONDS) 54 55 58: 57 type=109 (BONDS) 54 56 58: 58 type=110 (BONDS) 56 57 58: 59 type=105 (BONDS) 58 59 58: 60 type=106 (BONDS) 58 60 58: 61 type=100 (BONDS) 60 61 58: 62 type=107 (BONDS) 60 62 58: 63 type=102 (BONDS) 62 63 58: 64 type=102 (BONDS) 62 64 58: 65 type=104 (BONDS) 62 65 58: 66 type=105 (BONDS) 65 66 58: 67 type=106 (BONDS) 65 67 58: 68 type=100 (BONDS) 67 68 58: 69 type=107 (BONDS) 67 69 58: 70 type=102 (BONDS) 69 70 58: 71 type=103 (BONDS) 69 71 58: 72 type=104 (BONDS) 69 89 58: 73 type=102 (BONDS) 71 72 58: 74 type=102 (BONDS) 71 73 58: 75 type=103 (BONDS) 71 74 58: 76 type=102 (BONDS) 74 75 58: 77 type=102 (BONDS) 74 76 58: 78 type=103 (BONDS) 74 77 58: 79 type=102 (BONDS) 77 78 58: 80 type=102 (BONDS) 77 79 58: 81 type=111 (BONDS) 77 80 58: 82 type=100 (BONDS) 80 81 58: 83 type=112 (BONDS) 80 82 58: 84 type=112 (BONDS) 82 83 58: 85 type=112 (BONDS) 82 86 58: 86 type=100 (BONDS) 83 84 58: 87 type=100 (BONDS) 83 85 58: 88 type=100 (BONDS) 86 87 58: 89 type=100 (BONDS) 86 88 58: 90 type=105 (BONDS) 89 90 58: 91 type=106 (BONDS) 89 91 58: 92 type=100 (BONDS) 91 92 58: 93 type=107 (BONDS) 91 93 58: 94 type=102 (BONDS) 93 94 58: 95 type=103 (BONDS) 93 95 58: 96 type=104 (BONDS) 93 100 58: 97 type=102 (BONDS) 95 96 58: 98 type=102 (BONDS) 95 97 58: 99 type=113 (BONDS) 95 98 58: 100 type=114 (BONDS) 98 99 58: 101 type=105 (BONDS) 100 101 58: 102 type=106 (BONDS) 100 102 58: 103 type=100 (BONDS) 102 103 58: 104 type=107 (BONDS) 102 104 58: 105 type=102 (BONDS) 104 105 58: 106 type=103 (BONDS) 104 106 58: 107 type=104 (BONDS) 104 115 58: 108 type=102 (BONDS) 106 107 58: 109 type=102 (BONDS) 106 108 58: 110 type=103 (BONDS) 106 109 58: 111 type=102 (BONDS) 109 110 58: 112 type=102 (BONDS) 109 111 58: 113 type=104 (BONDS) 109 112 58: 114 type=115 (BONDS) 112 113 58: 115 type=115 (BONDS) 112 114 58: 116 type=105 (BONDS) 115 116 58: 117 type=106 (BONDS) 115 117 58: 118 type=100 (BONDS) 117 118 58: 119 type=107 (BONDS) 117 119 58: 120 type=102 (BONDS) 119 120 58: 121 type=103 (BONDS) 119 121 58: 122 type=104 (BONDS) 119 134 58: 123 type=102 (BONDS) 121 122 58: 124 type=102 (BONDS) 121 123 58: 125 type=103 (BONDS) 121 124 58: 126 type=102 (BONDS) 124 125 58: 127 type=103 (BONDS) 124 126 58: 128 type=103 (BONDS) 124 130 58: 129 type=102 (BONDS) 126 127 58: 130 type=102 (BONDS) 126 128 58: 131 type=102 (BONDS) 126 129 58: 132 type=102 (BONDS) 130 131 58: 133 type=102 (BONDS) 130 132 58: 134 type=102 (BONDS) 130 133 58: 135 type=105 (BONDS) 134 135 58: 136 type=106 (BONDS) 134 136 58: 137 type=100 (BONDS) 136 137 58: 138 type=107 (BONDS) 136 138 58: 139 type=102 (BONDS) 138 139 58: 140 type=103 (BONDS) 138 140 58: 141 type=104 (BONDS) 138 144 58: 142 type=102 (BONDS) 140 141 58: 143 type=102 (BONDS) 140 142 58: 144 type=102 (BONDS) 140 143 58: 145 type=105 (BONDS) 144 145 58: 146 type=106 (BONDS) 144 146 58: 147 type=100 (BONDS) 146 147 58: 148 type=107 (BONDS) 146 148 58: 149 type=102 (BONDS) 148 149 58: 150 type=103 (BONDS) 148 150 58: 151 type=104 (BONDS) 148 154 58: 152 type=102 (BONDS) 150 151 58: 153 type=102 (BONDS) 150 152 58: 154 type=102 (BONDS) 150 153 58: 155 type=105 (BONDS) 154 155 58: G96Bond: 58: nr: 0 58: Morse: 58: nr: 0 58: Cubic Bonds: 58: nr: 0 58: Connect Bonds: 58: nr: 0 58: Harmonic Pot.: 58: nr: 0 58: FENE Bonds: 58: nr: 0 58: Tab. Bonds: 58: nr: 0 58: Tab. Bonds NC: 58: nr: 0 58: Restraint Pot.: 58: nr: 0 58: Angle: 58: nr: 1124 58: iatoms: 58: 0 type=116 (ANGLES) 1 0 2 58: 1 type=116 (ANGLES) 1 0 3 58: 2 type=116 (ANGLES) 1 0 4 58: 3 type=116 (ANGLES) 2 0 3 58: 4 type=116 (ANGLES) 2 0 4 58: 5 type=116 (ANGLES) 3 0 4 58: 6 type=116 (ANGLES) 0 4 5 58: 7 type=117 (ANGLES) 0 4 6 58: 8 type=117 (ANGLES) 0 4 22 58: 9 type=118 (ANGLES) 5 4 6 58: 10 type=116 (ANGLES) 5 4 22 58: 11 type=119 (ANGLES) 6 4 22 58: 12 type=118 (ANGLES) 4 6 7 58: 13 type=118 (ANGLES) 4 6 8 58: 14 type=120 (ANGLES) 4 6 9 58: 15 type=121 (ANGLES) 7 6 8 58: 16 type=118 (ANGLES) 7 6 9 58: 17 type=118 (ANGLES) 8 6 9 58: 18 type=118 (ANGLES) 6 9 10 58: 19 type=118 (ANGLES) 6 9 11 58: 20 type=120 (ANGLES) 6 9 12 58: 21 type=121 (ANGLES) 10 9 11 58: 22 type=118 (ANGLES) 10 9 12 58: 23 type=118 (ANGLES) 11 9 12 58: 24 type=118 (ANGLES) 9 12 13 58: 25 type=118 (ANGLES) 9 12 14 58: 26 type=120 (ANGLES) 9 12 15 58: 27 type=121 (ANGLES) 13 12 14 58: 28 type=118 (ANGLES) 13 12 15 58: 29 type=118 (ANGLES) 14 12 15 58: 30 type=118 (ANGLES) 12 15 16 58: 31 type=118 (ANGLES) 12 15 17 58: 32 type=117 (ANGLES) 12 15 18 58: 33 type=121 (ANGLES) 16 15 17 58: 34 type=116 (ANGLES) 16 15 18 58: 35 type=116 (ANGLES) 17 15 18 58: 36 type=116 (ANGLES) 15 18 19 58: 37 type=116 (ANGLES) 15 18 20 58: 38 type=116 (ANGLES) 15 18 21 58: 39 type=116 (ANGLES) 19 18 20 58: 40 type=116 (ANGLES) 19 18 21 58: 41 type=116 (ANGLES) 20 18 21 58: 42 type=122 (ANGLES) 4 22 23 58: 43 type=123 (ANGLES) 4 22 24 58: 44 type=124 (ANGLES) 23 22 24 58: 45 type=125 (ANGLES) 22 24 25 58: 46 type=126 (ANGLES) 22 24 26 58: 47 type=127 (ANGLES) 25 24 26 58: 48 type=116 (ANGLES) 24 26 27 58: 49 type=128 (ANGLES) 24 26 28 58: 50 type=129 (ANGLES) 24 26 38 58: 51 type=118 (ANGLES) 27 26 28 58: 52 type=116 (ANGLES) 27 26 38 58: 53 type=119 (ANGLES) 28 26 38 58: 54 type=118 (ANGLES) 26 28 29 58: 55 type=120 (ANGLES) 26 28 30 58: 56 type=120 (ANGLES) 26 28 34 58: 57 type=118 (ANGLES) 29 28 30 58: 58 type=118 (ANGLES) 29 28 34 58: 59 type=120 (ANGLES) 30 28 34 58: 60 type=118 (ANGLES) 28 30 31 58: 61 type=118 (ANGLES) 28 30 32 58: 62 type=118 (ANGLES) 28 30 33 58: 63 type=121 (ANGLES) 31 30 32 58: 64 type=121 (ANGLES) 31 30 33 58: 65 type=121 (ANGLES) 32 30 33 58: 66 type=118 (ANGLES) 28 34 35 58: 67 type=118 (ANGLES) 28 34 36 58: 68 type=118 (ANGLES) 28 34 37 58: 69 type=121 (ANGLES) 35 34 36 58: 70 type=121 (ANGLES) 35 34 37 58: 71 type=121 (ANGLES) 36 34 37 58: 72 type=122 (ANGLES) 26 38 39 58: 73 type=123 (ANGLES) 26 38 40 58: 74 type=124 (ANGLES) 39 38 40 58: 75 type=125 (ANGLES) 38 40 41 58: 76 type=126 (ANGLES) 38 40 42 58: 77 type=127 (ANGLES) 41 40 42 58: 78 type=116 (ANGLES) 40 42 43 58: 79 type=128 (ANGLES) 40 42 44 58: 80 type=129 (ANGLES) 40 42 58 58: 81 type=118 (ANGLES) 43 42 44 58: 82 type=116 (ANGLES) 43 42 58 58: 83 type=119 (ANGLES) 44 42 58 58: 84 type=118 (ANGLES) 42 44 45 58: 85 type=118 (ANGLES) 42 44 46 58: 86 type=130 (ANGLES) 42 44 47 58: 87 type=121 (ANGLES) 45 44 46 58: 88 type=116 (ANGLES) 45 44 47 58: 89 type=116 (ANGLES) 46 44 47 58: 90 type=131 (ANGLES) 44 47 48 58: 91 type=131 (ANGLES) 44 47 50 58: 92 type=132 (ANGLES) 48 47 50 58: 93 type=133 (ANGLES) 47 48 49 58: 94 type=132 (ANGLES) 47 48 52 58: 95 type=133 (ANGLES) 49 48 52 58: 96 type=133 (ANGLES) 47 50 51 58: 97 type=132 (ANGLES) 47 50 54 58: 98 type=133 (ANGLES) 51 50 54 58: 99 type=133 (ANGLES) 48 52 53 58: 100 type=132 (ANGLES) 48 52 56 58: 101 type=133 (ANGLES) 53 52 56 58: 102 type=133 (ANGLES) 50 54 55 58: 103 type=132 (ANGLES) 50 54 56 58: 104 type=133 (ANGLES) 55 54 56 58: 105 type=132 (ANGLES) 52 56 54 58: 106 type=133 (ANGLES) 52 56 57 58: 107 type=133 (ANGLES) 54 56 57 58: 108 type=122 (ANGLES) 42 58 59 58: 109 type=123 (ANGLES) 42 58 60 58: 110 type=124 (ANGLES) 59 58 60 58: 111 type=125 (ANGLES) 58 60 61 58: 112 type=126 (ANGLES) 58 60 62 58: 113 type=127 (ANGLES) 61 60 62 58: 114 type=116 (ANGLES) 60 62 63 58: 115 type=116 (ANGLES) 60 62 64 58: 116 type=129 (ANGLES) 60 62 65 58: 117 type=121 (ANGLES) 63 62 64 58: 118 type=116 (ANGLES) 63 62 65 58: 119 type=116 (ANGLES) 64 62 65 58: 120 type=122 (ANGLES) 62 65 66 58: 121 type=123 (ANGLES) 62 65 67 58: 122 type=124 (ANGLES) 66 65 67 58: 123 type=125 (ANGLES) 65 67 68 58: 124 type=126 (ANGLES) 65 67 69 58: 125 type=127 (ANGLES) 68 67 69 58: 126 type=116 (ANGLES) 67 69 70 58: 127 type=128 (ANGLES) 67 69 71 58: 128 type=129 (ANGLES) 67 69 89 58: 129 type=118 (ANGLES) 70 69 71 58: 130 type=116 (ANGLES) 70 69 89 58: 131 type=119 (ANGLES) 71 69 89 58: 132 type=118 (ANGLES) 69 71 72 58: 133 type=118 (ANGLES) 69 71 73 58: 134 type=120 (ANGLES) 69 71 74 58: 135 type=121 (ANGLES) 72 71 73 58: 136 type=118 (ANGLES) 72 71 74 58: 137 type=118 (ANGLES) 73 71 74 58: 138 type=118 (ANGLES) 71 74 75 58: 139 type=118 (ANGLES) 71 74 76 58: 140 type=120 (ANGLES) 71 74 77 58: 141 type=121 (ANGLES) 75 74 76 58: 142 type=118 (ANGLES) 75 74 77 58: 143 type=118 (ANGLES) 76 74 77 58: 144 type=118 (ANGLES) 74 77 78 58: 145 type=118 (ANGLES) 74 77 79 58: 146 type=117 (ANGLES) 74 77 80 58: 147 type=121 (ANGLES) 78 77 79 58: 148 type=116 (ANGLES) 78 77 80 58: 149 type=116 (ANGLES) 79 77 80 58: 150 type=134 (ANGLES) 77 80 81 58: 151 type=135 (ANGLES) 77 80 82 58: 152 type=133 (ANGLES) 81 80 82 58: 153 type=131 (ANGLES) 80 82 83 58: 154 type=131 (ANGLES) 80 82 86 58: 155 type=131 (ANGLES) 83 82 86 58: 156 type=133 (ANGLES) 82 83 84 58: 157 type=133 (ANGLES) 82 83 85 58: 158 type=133 (ANGLES) 84 83 85 58: 159 type=133 (ANGLES) 82 86 87 58: 160 type=133 (ANGLES) 82 86 88 58: 161 type=133 (ANGLES) 87 86 88 58: 162 type=122 (ANGLES) 69 89 90 58: 163 type=123 (ANGLES) 69 89 91 58: 164 type=124 (ANGLES) 90 89 91 58: 165 type=125 (ANGLES) 89 91 92 58: 166 type=126 (ANGLES) 89 91 93 58: 167 type=127 (ANGLES) 92 91 93 58: 168 type=116 (ANGLES) 91 93 94 58: 169 type=128 (ANGLES) 91 93 95 58: 170 type=129 (ANGLES) 91 93 100 58: 171 type=118 (ANGLES) 94 93 95 58: 172 type=116 (ANGLES) 94 93 100 58: 173 type=119 (ANGLES) 95 93 100 58: 174 type=118 (ANGLES) 93 95 96 58: 175 type=118 (ANGLES) 93 95 97 58: 176 type=136 (ANGLES) 93 95 98 58: 177 type=121 (ANGLES) 96 95 97 58: 178 type=116 (ANGLES) 96 95 98 58: 179 type=116 (ANGLES) 97 95 98 58: 180 type=137 (ANGLES) 95 98 99 58: 181 type=122 (ANGLES) 93 100 101 58: 182 type=123 (ANGLES) 93 100 102 58: 183 type=124 (ANGLES) 101 100 102 58: 184 type=125 (ANGLES) 100 102 103 58: 185 type=126 (ANGLES) 100 102 104 58: 186 type=127 (ANGLES) 103 102 104 58: 187 type=116 (ANGLES) 102 104 105 58: 188 type=128 (ANGLES) 102 104 106 58: 189 type=129 (ANGLES) 102 104 115 58: 190 type=118 (ANGLES) 105 104 106 58: 191 type=116 (ANGLES) 105 104 115 58: 192 type=119 (ANGLES) 106 104 115 58: 193 type=118 (ANGLES) 104 106 107 58: 194 type=118 (ANGLES) 104 106 108 58: 195 type=120 (ANGLES) 104 106 109 58: 196 type=121 (ANGLES) 107 106 108 58: 197 type=118 (ANGLES) 107 106 109 58: 198 type=118 (ANGLES) 108 106 109 58: 199 type=118 (ANGLES) 106 109 110 58: 200 type=118 (ANGLES) 106 109 111 58: 201 type=119 (ANGLES) 106 109 112 58: 202 type=121 (ANGLES) 110 109 111 58: 203 type=116 (ANGLES) 110 109 112 58: 204 type=116 (ANGLES) 111 109 112 58: 205 type=138 (ANGLES) 109 112 113 58: 206 type=138 (ANGLES) 109 112 114 58: 207 type=139 (ANGLES) 113 112 114 58: 208 type=122 (ANGLES) 104 115 116 58: 209 type=123 (ANGLES) 104 115 117 58: 210 type=124 (ANGLES) 116 115 117 58: 211 type=125 (ANGLES) 115 117 118 58: 212 type=126 (ANGLES) 115 117 119 58: 213 type=127 (ANGLES) 118 117 119 58: 214 type=116 (ANGLES) 117 119 120 58: 215 type=128 (ANGLES) 117 119 121 58: 216 type=129 (ANGLES) 117 119 134 58: 217 type=118 (ANGLES) 120 119 121 58: 218 type=116 (ANGLES) 120 119 134 58: 219 type=119 (ANGLES) 121 119 134 58: 220 type=118 (ANGLES) 119 121 122 58: 221 type=118 (ANGLES) 119 121 123 58: 222 type=120 (ANGLES) 119 121 124 58: 223 type=121 (ANGLES) 122 121 123 58: 224 type=118 (ANGLES) 122 121 124 58: 225 type=118 (ANGLES) 123 121 124 58: 226 type=118 (ANGLES) 121 124 125 58: 227 type=120 (ANGLES) 121 124 126 58: 228 type=120 (ANGLES) 121 124 130 58: 229 type=118 (ANGLES) 125 124 126 58: 230 type=118 (ANGLES) 125 124 130 58: 231 type=120 (ANGLES) 126 124 130 58: 232 type=118 (ANGLES) 124 126 127 58: 233 type=118 (ANGLES) 124 126 128 58: 234 type=118 (ANGLES) 124 126 129 58: 235 type=121 (ANGLES) 127 126 128 58: 236 type=121 (ANGLES) 127 126 129 58: 237 type=121 (ANGLES) 128 126 129 58: 238 type=118 (ANGLES) 124 130 131 58: 239 type=118 (ANGLES) 124 130 132 58: 240 type=118 (ANGLES) 124 130 133 58: 241 type=121 (ANGLES) 131 130 132 58: 242 type=121 (ANGLES) 131 130 133 58: 243 type=121 (ANGLES) 132 130 133 58: 244 type=122 (ANGLES) 119 134 135 58: 245 type=123 (ANGLES) 119 134 136 58: 246 type=124 (ANGLES) 135 134 136 58: 247 type=125 (ANGLES) 134 136 137 58: 248 type=126 (ANGLES) 134 136 138 58: 249 type=127 (ANGLES) 137 136 138 58: 250 type=116 (ANGLES) 136 138 139 58: 251 type=128 (ANGLES) 136 138 140 58: 252 type=129 (ANGLES) 136 138 144 58: 253 type=118 (ANGLES) 139 138 140 58: 254 type=116 (ANGLES) 139 138 144 58: 255 type=119 (ANGLES) 140 138 144 58: 256 type=118 (ANGLES) 138 140 141 58: 257 type=118 (ANGLES) 138 140 142 58: 258 type=118 (ANGLES) 138 140 143 58: 259 type=121 (ANGLES) 141 140 142 58: 260 type=121 (ANGLES) 141 140 143 58: 261 type=121 (ANGLES) 142 140 143 58: 262 type=122 (ANGLES) 138 144 145 58: 263 type=123 (ANGLES) 138 144 146 58: 264 type=124 (ANGLES) 145 144 146 58: 265 type=125 (ANGLES) 144 146 147 58: 266 type=126 (ANGLES) 144 146 148 58: 267 type=127 (ANGLES) 147 146 148 58: 268 type=116 (ANGLES) 146 148 149 58: 269 type=128 (ANGLES) 146 148 150 58: 270 type=129 (ANGLES) 146 148 154 58: 271 type=118 (ANGLES) 149 148 150 58: 272 type=116 (ANGLES) 149 148 154 58: 273 type=119 (ANGLES) 150 148 154 58: 274 type=118 (ANGLES) 148 150 151 58: 275 type=118 (ANGLES) 148 150 152 58: 276 type=118 (ANGLES) 148 150 153 58: 277 type=121 (ANGLES) 151 150 152 58: 278 type=121 (ANGLES) 151 150 153 58: 279 type=121 (ANGLES) 152 150 153 58: 280 type=122 (ANGLES) 148 154 155 58: G96Angle: 58: nr: 0 58: Restr. Angles: 58: nr: 0 58: Lin. Angle: 58: nr: 0 58: Bond-Cross: 58: nr: 0 58: BA-Cross: 58: nr: 0 58: U-B: 58: nr: 0 58: Quartic Angles: 58: nr: 0 58: Tab. Angles: 58: nr: 0 58: Proper Dih.: 58: nr: 145 58: iatoms: 58: 0 type=140 (PDIHS) 4 24 22 23 58: 1 type=141 (PDIHS) 22 26 24 25 58: 2 type=140 (PDIHS) 26 40 38 39 58: 3 type=141 (PDIHS) 38 42 40 41 58: 4 type=140 (PDIHS) 42 60 58 59 58: 5 type=142 (PDIHS) 44 47 50 48 58: 6 type=142 (PDIHS) 47 52 48 49 58: 7 type=142 (PDIHS) 47 54 50 51 58: 8 type=142 (PDIHS) 48 56 52 53 58: 9 type=142 (PDIHS) 50 56 54 55 58: 10 type=142 (PDIHS) 52 54 56 57 58: 11 type=141 (PDIHS) 58 62 60 61 58: 12 type=140 (PDIHS) 62 67 65 66 58: 13 type=141 (PDIHS) 65 69 67 68 58: 14 type=140 (PDIHS) 69 91 89 90 58: 15 type=141 (PDIHS) 77 82 80 81 58: 16 type=140 (PDIHS) 80 83 82 86 58: 17 type=141 (PDIHS) 82 84 83 85 58: 18 type=141 (PDIHS) 82 87 86 88 58: 19 type=141 (PDIHS) 89 93 91 92 58: 20 type=140 (PDIHS) 93 102 100 101 58: 21 type=141 (PDIHS) 100 104 102 103 58: 22 type=140 (PDIHS) 104 117 115 116 58: 23 type=140 (PDIHS) 109 113 112 114 58: 24 type=141 (PDIHS) 115 119 117 118 58: 25 type=140 (PDIHS) 119 136 134 135 58: 26 type=141 (PDIHS) 134 138 136 137 58: 27 type=140 (PDIHS) 138 146 144 145 58: 28 type=141 (PDIHS) 144 148 146 147 58: Ryckaert-Bell.: 58: nr: 1565 58: iatoms: 58: 0 type=143 (RBDIHS) 1 0 4 5 58: 1 type=144 (RBDIHS) 1 0 4 6 58: 2 type=144 (RBDIHS) 1 0 4 22 58: 3 type=143 (RBDIHS) 2 0 4 5 58: 4 type=144 (RBDIHS) 2 0 4 6 58: 5 type=144 (RBDIHS) 2 0 4 22 58: 6 type=143 (RBDIHS) 3 0 4 5 58: 7 type=144 (RBDIHS) 3 0 4 6 58: 8 type=144 (RBDIHS) 3 0 4 22 58: 9 type=145 (RBDIHS) 0 4 6 9 58: 10 type=146 (RBDIHS) 22 4 6 9 58: 11 type=147 (RBDIHS) 0 4 6 7 58: 12 type=147 (RBDIHS) 0 4 6 8 58: 13 type=148 (RBDIHS) 5 4 6 7 58: 14 type=148 (RBDIHS) 5 4 6 8 58: 15 type=148 (RBDIHS) 5 4 6 9 58: 16 type=149 (RBDIHS) 22 4 6 7 58: 17 type=149 (RBDIHS) 22 4 6 8 58: 18 type=150 (RBDIHS) 0 4 22 24 58: 19 type=151 (RBDIHS) 6 4 22 24 58: 20 type=148 (RBDIHS) 4 6 9 10 58: 21 type=148 (RBDIHS) 4 6 9 11 58: 22 type=152 (RBDIHS) 4 6 9 12 58: 23 type=148 (RBDIHS) 7 6 9 10 58: 24 type=148 (RBDIHS) 7 6 9 11 58: 25 type=148 (RBDIHS) 7 6 9 12 58: 26 type=148 (RBDIHS) 8 6 9 10 58: 27 type=148 (RBDIHS) 8 6 9 11 58: 28 type=148 (RBDIHS) 8 6 9 12 58: 29 type=148 (RBDIHS) 6 9 12 13 58: 30 type=148 (RBDIHS) 6 9 12 14 58: 31 type=152 (RBDIHS) 6 9 12 15 58: 32 type=148 (RBDIHS) 10 9 12 13 58: 33 type=148 (RBDIHS) 10 9 12 14 58: 34 type=148 (RBDIHS) 10 9 12 15 58: 35 type=148 (RBDIHS) 11 9 12 13 58: 36 type=148 (RBDIHS) 11 9 12 14 58: 37 type=148 (RBDIHS) 11 9 12 15 58: 38 type=148 (RBDIHS) 9 12 15 16 58: 39 type=148 (RBDIHS) 9 12 15 17 58: 40 type=153 (RBDIHS) 9 12 15 18 58: 41 type=148 (RBDIHS) 13 12 15 16 58: 42 type=148 (RBDIHS) 13 12 15 17 58: 43 type=154 (RBDIHS) 13 12 15 18 58: 44 type=148 (RBDIHS) 14 12 15 16 58: 45 type=148 (RBDIHS) 14 12 15 17 58: 46 type=154 (RBDIHS) 14 12 15 18 58: 47 type=144 (RBDIHS) 12 15 18 19 58: 48 type=144 (RBDIHS) 12 15 18 20 58: 49 type=144 (RBDIHS) 12 15 18 21 58: 50 type=143 (RBDIHS) 16 15 18 19 58: 51 type=143 (RBDIHS) 16 15 18 20 58: 52 type=143 (RBDIHS) 16 15 18 21 58: 53 type=143 (RBDIHS) 17 15 18 19 58: 54 type=143 (RBDIHS) 17 15 18 20 58: 55 type=143 (RBDIHS) 17 15 18 21 58: 56 type=155 (RBDIHS) 4 22 24 25 58: 57 type=156 (RBDIHS) 4 22 24 26 58: 58 type=155 (RBDIHS) 23 22 24 25 58: 59 type=157 (RBDIHS) 23 22 24 26 58: 60 type=158 (RBDIHS) 22 24 26 28 58: 61 type=159 (RBDIHS) 22 24 26 38 58: 62 type=160 (RBDIHS) 24 26 28 30 58: 63 type=160 (RBDIHS) 24 26 28 34 58: 64 type=161 (RBDIHS) 38 26 28 30 58: 65 type=161 (RBDIHS) 38 26 28 34 58: 66 type=147 (RBDIHS) 24 26 28 29 58: 67 type=148 (RBDIHS) 27 26 28 29 58: 68 type=148 (RBDIHS) 27 26 28 30 58: 69 type=148 (RBDIHS) 27 26 28 34 58: 70 type=149 (RBDIHS) 38 26 28 29 58: 71 type=150 (RBDIHS) 24 26 38 40 58: 72 type=151 (RBDIHS) 28 26 38 40 58: 73 type=148 (RBDIHS) 26 28 30 31 58: 74 type=148 (RBDIHS) 26 28 30 32 58: 75 type=148 (RBDIHS) 26 28 30 33 58: 76 type=148 (RBDIHS) 29 28 30 31 58: 77 type=148 (RBDIHS) 29 28 30 32 58: 78 type=148 (RBDIHS) 29 28 30 33 58: 79 type=148 (RBDIHS) 34 28 30 31 58: 80 type=148 (RBDIHS) 34 28 30 32 58: 81 type=148 (RBDIHS) 34 28 30 33 58: 82 type=148 (RBDIHS) 26 28 34 35 58: 83 type=148 (RBDIHS) 26 28 34 36 58: 84 type=148 (RBDIHS) 26 28 34 37 58: 85 type=148 (RBDIHS) 29 28 34 35 58: 86 type=148 (RBDIHS) 29 28 34 36 58: 87 type=148 (RBDIHS) 29 28 34 37 58: 88 type=148 (RBDIHS) 30 28 34 35 58: 89 type=148 (RBDIHS) 30 28 34 36 58: 90 type=148 (RBDIHS) 30 28 34 37 58: 91 type=155 (RBDIHS) 26 38 40 41 58: 92 type=156 (RBDIHS) 26 38 40 42 58: 93 type=155 (RBDIHS) 39 38 40 41 58: 94 type=157 (RBDIHS) 39 38 40 42 58: 95 type=158 (RBDIHS) 38 40 42 44 58: 96 type=159 (RBDIHS) 38 40 42 58 58: 97 type=147 (RBDIHS) 40 42 44 45 58: 98 type=147 (RBDIHS) 40 42 44 46 58: 99 type=162 (RBDIHS) 40 42 44 47 58: 100 type=148 (RBDIHS) 43 42 44 45 58: 101 type=148 (RBDIHS) 43 42 44 46 58: 102 type=163 (RBDIHS) 43 42 44 47 58: 103 type=149 (RBDIHS) 58 42 44 45 58: 104 type=149 (RBDIHS) 58 42 44 46 58: 105 type=164 (RBDIHS) 58 42 44 47 58: 106 type=150 (RBDIHS) 40 42 58 60 58: 107 type=151 (RBDIHS) 44 42 58 60 58: 108 type=165 (RBDIHS) 44 47 48 49 58: 109 type=165 (RBDIHS) 44 47 48 52 58: 110 type=165 (RBDIHS) 50 47 48 49 58: 111 type=165 (RBDIHS) 50 47 48 52 58: 112 type=165 (RBDIHS) 44 47 50 51 58: 113 type=165 (RBDIHS) 44 47 50 54 58: 114 type=165 (RBDIHS) 48 47 50 51 58: 115 type=165 (RBDIHS) 48 47 50 54 58: 116 type=165 (RBDIHS) 47 48 52 53 58: 117 type=165 (RBDIHS) 47 48 52 56 58: 118 type=165 (RBDIHS) 49 48 52 53 58: 119 type=165 (RBDIHS) 49 48 52 56 58: 120 type=165 (RBDIHS) 47 50 54 55 58: 121 type=165 (RBDIHS) 47 50 54 56 58: 122 type=165 (RBDIHS) 51 50 54 55 58: 123 type=165 (RBDIHS) 51 50 54 56 58: 124 type=165 (RBDIHS) 48 52 56 54 58: 125 type=165 (RBDIHS) 48 52 56 57 58: 126 type=165 (RBDIHS) 53 52 56 54 58: 127 type=165 (RBDIHS) 53 52 56 57 58: 128 type=165 (RBDIHS) 50 54 56 52 58: 129 type=165 (RBDIHS) 50 54 56 57 58: 130 type=165 (RBDIHS) 55 54 56 52 58: 131 type=165 (RBDIHS) 55 54 56 57 58: 132 type=155 (RBDIHS) 42 58 60 61 58: 133 type=156 (RBDIHS) 42 58 60 62 58: 134 type=155 (RBDIHS) 59 58 60 61 58: 135 type=157 (RBDIHS) 59 58 60 62 58: 136 type=159 (RBDIHS) 58 60 62 65 58: 137 type=150 (RBDIHS) 60 62 65 67 58: 138 type=155 (RBDIHS) 62 65 67 68 58: 139 type=156 (RBDIHS) 62 65 67 69 58: 140 type=155 (RBDIHS) 66 65 67 68 58: 141 type=157 (RBDIHS) 66 65 67 69 58: 142 type=158 (RBDIHS) 65 67 69 71 58: 143 type=159 (RBDIHS) 65 67 69 89 58: 144 type=166 (RBDIHS) 67 69 71 74 58: 145 type=167 (RBDIHS) 89 69 71 74 58: 146 type=147 (RBDIHS) 67 69 71 72 58: 147 type=147 (RBDIHS) 67 69 71 73 58: 148 type=148 (RBDIHS) 70 69 71 72 58: 149 type=148 (RBDIHS) 70 69 71 73 58: 150 type=148 (RBDIHS) 70 69 71 74 58: 151 type=149 (RBDIHS) 89 69 71 72 58: 152 type=149 (RBDIHS) 89 69 71 73 58: 153 type=150 (RBDIHS) 67 69 89 91 58: 154 type=151 (RBDIHS) 71 69 89 91 58: 155 type=148 (RBDIHS) 69 71 74 75 58: 156 type=148 (RBDIHS) 69 71 74 76 58: 157 type=152 (RBDIHS) 69 71 74 77 58: 158 type=148 (RBDIHS) 72 71 74 75 58: 159 type=148 (RBDIHS) 72 71 74 76 58: 160 type=148 (RBDIHS) 72 71 74 77 58: 161 type=148 (RBDIHS) 73 71 74 75 58: 162 type=148 (RBDIHS) 73 71 74 76 58: 163 type=148 (RBDIHS) 73 71 74 77 58: 164 type=148 (RBDIHS) 71 74 77 78 58: 165 type=148 (RBDIHS) 71 74 77 79 58: 166 type=153 (RBDIHS) 71 74 77 80 58: 167 type=148 (RBDIHS) 75 74 77 78 58: 168 type=148 (RBDIHS) 75 74 77 79 58: 169 type=168 (RBDIHS) 75 74 77 80 58: 170 type=148 (RBDIHS) 76 74 77 78 58: 171 type=148 (RBDIHS) 76 74 77 79 58: 172 type=168 (RBDIHS) 76 74 77 80 58: 173 type=169 (RBDIHS) 74 77 80 81 58: 174 type=170 (RBDIHS) 74 77 80 82 58: 175 type=171 (RBDIHS) 78 77 80 82 58: 176 type=171 (RBDIHS) 79 77 80 82 58: 177 type=172 (RBDIHS) 77 80 82 83 58: 178 type=172 (RBDIHS) 77 80 82 86 58: 179 type=173 (RBDIHS) 81 80 82 83 58: 180 type=173 (RBDIHS) 81 80 82 86 58: 181 type=173 (RBDIHS) 80 82 83 84 58: 182 type=173 (RBDIHS) 80 82 83 85 58: 183 type=173 (RBDIHS) 86 82 83 84 58: 184 type=173 (RBDIHS) 86 82 83 85 58: 185 type=173 (RBDIHS) 80 82 86 87 58: 186 type=173 (RBDIHS) 80 82 86 88 58: 187 type=173 (RBDIHS) 83 82 86 87 58: 188 type=173 (RBDIHS) 83 82 86 88 58: 189 type=155 (RBDIHS) 69 89 91 92 58: 190 type=156 (RBDIHS) 69 89 91 93 58: 191 type=155 (RBDIHS) 90 89 91 92 58: 192 type=157 (RBDIHS) 90 89 91 93 58: 193 type=158 (RBDIHS) 89 91 93 95 58: 194 type=159 (RBDIHS) 89 91 93 100 58: 195 type=174 (RBDIHS) 91 93 95 98 58: 196 type=175 (RBDIHS) 100 93 95 98 58: 197 type=147 (RBDIHS) 91 93 95 96 58: 198 type=147 (RBDIHS) 91 93 95 97 58: 199 type=148 (RBDIHS) 94 93 95 96 58: 200 type=148 (RBDIHS) 94 93 95 97 58: 201 type=176 (RBDIHS) 94 93 95 98 58: 202 type=149 (RBDIHS) 100 93 95 96 58: 203 type=149 (RBDIHS) 100 93 95 97 58: 204 type=150 (RBDIHS) 91 93 100 102 58: 205 type=151 (RBDIHS) 95 93 100 102 58: 206 type=177 (RBDIHS) 93 95 98 99 58: 207 type=178 (RBDIHS) 96 95 98 99 58: 208 type=178 (RBDIHS) 97 95 98 99 58: 209 type=155 (RBDIHS) 93 100 102 103 58: 210 type=156 (RBDIHS) 93 100 102 104 58: 211 type=155 (RBDIHS) 101 100 102 103 58: 212 type=157 (RBDIHS) 101 100 102 104 58: 213 type=158 (RBDIHS) 100 102 104 106 58: 214 type=159 (RBDIHS) 100 102 104 115 58: 215 type=179 (RBDIHS) 102 104 106 109 58: 216 type=180 (RBDIHS) 115 104 106 109 58: 217 type=147 (RBDIHS) 102 104 106 107 58: 218 type=147 (RBDIHS) 102 104 106 108 58: 219 type=148 (RBDIHS) 105 104 106 107 58: 220 type=148 (RBDIHS) 105 104 106 108 58: 221 type=148 (RBDIHS) 105 104 106 109 58: 222 type=149 (RBDIHS) 115 104 106 107 58: 223 type=149 (RBDIHS) 115 104 106 108 58: 224 type=150 (RBDIHS) 102 104 115 117 58: 225 type=151 (RBDIHS) 106 104 115 117 58: 226 type=148 (RBDIHS) 104 106 109 110 58: 227 type=148 (RBDIHS) 104 106 109 111 58: 228 type=181 (RBDIHS) 104 106 109 112 58: 229 type=148 (RBDIHS) 107 106 109 110 58: 230 type=148 (RBDIHS) 107 106 109 111 58: 231 type=182 (RBDIHS) 107 106 109 112 58: 232 type=148 (RBDIHS) 108 106 109 110 58: 233 type=148 (RBDIHS) 108 106 109 111 58: 234 type=182 (RBDIHS) 108 106 109 112 58: 235 type=183 (RBDIHS) 106 109 112 113 58: 236 type=183 (RBDIHS) 106 109 112 114 58: 237 type=155 (RBDIHS) 104 115 117 118 58: 238 type=156 (RBDIHS) 104 115 117 119 58: 239 type=155 (RBDIHS) 116 115 117 118 58: 240 type=157 (RBDIHS) 116 115 117 119 58: 241 type=158 (RBDIHS) 115 117 119 121 58: 242 type=159 (RBDIHS) 115 117 119 134 58: 243 type=184 (RBDIHS) 117 119 121 124 58: 244 type=185 (RBDIHS) 134 119 121 124 58: 245 type=147 (RBDIHS) 117 119 121 122 58: 246 type=147 (RBDIHS) 117 119 121 123 58: 247 type=148 (RBDIHS) 120 119 121 122 58: 248 type=148 (RBDIHS) 120 119 121 123 58: 249 type=148 (RBDIHS) 120 119 121 124 58: 250 type=149 (RBDIHS) 134 119 121 122 58: 251 type=149 (RBDIHS) 134 119 121 123 58: 252 type=150 (RBDIHS) 117 119 134 136 58: 253 type=151 (RBDIHS) 121 119 134 136 58: 254 type=148 (RBDIHS) 119 121 124 125 58: 255 type=152 (RBDIHS) 119 121 124 126 58: 256 type=152 (RBDIHS) 119 121 124 130 58: 257 type=148 (RBDIHS) 122 121 124 125 58: 258 type=148 (RBDIHS) 122 121 124 126 58: 259 type=148 (RBDIHS) 122 121 124 130 58: 260 type=148 (RBDIHS) 123 121 124 125 58: 261 type=148 (RBDIHS) 123 121 124 126 58: 262 type=148 (RBDIHS) 123 121 124 130 58: 263 type=148 (RBDIHS) 121 124 126 127 58: 264 type=148 (RBDIHS) 121 124 126 128 58: 265 type=148 (RBDIHS) 121 124 126 129 58: 266 type=148 (RBDIHS) 125 124 126 127 58: 267 type=148 (RBDIHS) 125 124 126 128 58: 268 type=148 (RBDIHS) 125 124 126 129 58: 269 type=148 (RBDIHS) 130 124 126 127 58: 270 type=148 (RBDIHS) 130 124 126 128 58: 271 type=148 (RBDIHS) 130 124 126 129 58: 272 type=148 (RBDIHS) 121 124 130 131 58: 273 type=148 (RBDIHS) 121 124 130 132 58: 274 type=148 (RBDIHS) 121 124 130 133 58: 275 type=148 (RBDIHS) 125 124 130 131 58: 276 type=148 (RBDIHS) 125 124 130 132 58: 277 type=148 (RBDIHS) 125 124 130 133 58: 278 type=148 (RBDIHS) 126 124 130 131 58: 279 type=148 (RBDIHS) 126 124 130 132 58: 280 type=148 (RBDIHS) 126 124 130 133 58: 281 type=155 (RBDIHS) 119 134 136 137 58: 282 type=156 (RBDIHS) 119 134 136 138 58: 283 type=155 (RBDIHS) 135 134 136 137 58: 284 type=157 (RBDIHS) 135 134 136 138 58: 285 type=158 (RBDIHS) 134 136 138 140 58: 286 type=159 (RBDIHS) 134 136 138 144 58: 287 type=147 (RBDIHS) 136 138 140 141 58: 288 type=147 (RBDIHS) 136 138 140 142 58: 289 type=147 (RBDIHS) 136 138 140 143 58: 290 type=148 (RBDIHS) 139 138 140 141 58: 291 type=148 (RBDIHS) 139 138 140 142 58: 292 type=148 (RBDIHS) 139 138 140 143 58: 293 type=149 (RBDIHS) 144 138 140 141 58: 294 type=149 (RBDIHS) 144 138 140 142 58: 295 type=149 (RBDIHS) 144 138 140 143 58: 296 type=150 (RBDIHS) 136 138 144 146 58: 297 type=151 (RBDIHS) 140 138 144 146 58: 298 type=155 (RBDIHS) 138 144 146 147 58: 299 type=156 (RBDIHS) 138 144 146 148 58: 300 type=155 (RBDIHS) 145 144 146 147 58: 301 type=157 (RBDIHS) 145 144 146 148 58: 302 type=158 (RBDIHS) 144 146 148 150 58: 303 type=159 (RBDIHS) 144 146 148 154 58: 304 type=147 (RBDIHS) 146 148 150 151 58: 305 type=147 (RBDIHS) 146 148 150 152 58: 306 type=147 (RBDIHS) 146 148 150 153 58: 307 type=148 (RBDIHS) 149 148 150 151 58: 308 type=148 (RBDIHS) 149 148 150 152 58: 309 type=148 (RBDIHS) 149 148 150 153 58: 310 type=149 (RBDIHS) 154 148 150 151 58: 311 type=149 (RBDIHS) 154 148 150 152 58: 312 type=149 (RBDIHS) 154 148 150 153 58: Restr. Dih.: 58: nr: 0 58: CBT Dih.: 58: nr: 0 58: Fourier Dih.: 58: nr: 0 58: Improper Dih.: 58: nr: 0 58: Per. Imp. Dih.: 58: nr: 0 58: Tab. Dih.: 58: nr: 0 58: CMAP Dih.: 58: nr: 0 58: GB 1-2 Pol.: 58: nr: 0 58: GB 1-3 Pol.: 58: nr: 0 58: GB 1-4 Pol.: 58: nr: 0 58: GB Polariz.: 58: nr: 0 58: Nonpolar Sol.: 58: nr: 0 58: LJ-14: 58: nr: 1197 58: iatoms: 58: 0 type=186 (LJ14) 0 7 58: 1 type=186 (LJ14) 0 8 58: 2 type=187 (LJ14) 0 9 58: 3 type=188 (LJ14) 0 23 58: 4 type=189 (LJ14) 0 24 58: 5 type=190 (LJ14) 1 5 58: 6 type=190 (LJ14) 1 6 58: 7 type=190 (LJ14) 1 22 58: 8 type=190 (LJ14) 2 5 58: 9 type=190 (LJ14) 2 6 58: 10 type=190 (LJ14) 2 22 58: 11 type=190 (LJ14) 3 5 58: 12 type=190 (LJ14) 3 6 58: 13 type=190 (LJ14) 3 22 58: 14 type=191 (LJ14) 4 10 58: 15 type=191 (LJ14) 4 11 58: 16 type=192 (LJ14) 4 12 58: 17 type=190 (LJ14) 4 25 58: 18 type=192 (LJ14) 4 26 58: 19 type=193 (LJ14) 5 7 58: 20 type=193 (LJ14) 5 8 58: 21 type=191 (LJ14) 5 9 58: 22 type=194 (LJ14) 5 23 58: 23 type=186 (LJ14) 5 24 58: 24 type=191 (LJ14) 6 13 58: 25 type=191 (LJ14) 6 14 58: 26 type=192 (LJ14) 6 15 58: 27 type=195 (LJ14) 6 23 58: 28 type=187 (LJ14) 6 24 58: 29 type=193 (LJ14) 7 10 58: 30 type=193 (LJ14) 7 11 58: 31 type=191 (LJ14) 7 12 58: 32 type=196 (LJ14) 7 22 58: 33 type=193 (LJ14) 8 10 58: 34 type=193 (LJ14) 8 11 58: 35 type=191 (LJ14) 8 12 58: 36 type=196 (LJ14) 8 22 58: 37 type=191 (LJ14) 9 16 58: 38 type=191 (LJ14) 9 17 58: 39 type=187 (LJ14) 9 18 58: 40 type=197 (LJ14) 9 22 58: 41 type=193 (LJ14) 10 13 58: 42 type=193 (LJ14) 10 14 58: 43 type=191 (LJ14) 10 15 58: 44 type=193 (LJ14) 11 13 58: 45 type=193 (LJ14) 11 14 58: 46 type=191 (LJ14) 11 15 58: 47 type=190 (LJ14) 12 19 58: 48 type=190 (LJ14) 12 20 58: 49 type=190 (LJ14) 12 21 58: 50 type=193 (LJ14) 13 16 58: 51 type=193 (LJ14) 13 17 58: 52 type=186 (LJ14) 13 18 58: 53 type=193 (LJ14) 14 16 58: 54 type=193 (LJ14) 14 17 58: 55 type=186 (LJ14) 14 18 58: 56 type=190 (LJ14) 16 19 58: 57 type=190 (LJ14) 16 20 58: 58 type=190 (LJ14) 16 21 58: 59 type=190 (LJ14) 17 19 58: 60 type=190 (LJ14) 17 20 58: 61 type=190 (LJ14) 17 21 58: 62 type=196 (LJ14) 22 27 58: 63 type=197 (LJ14) 22 28 58: 64 type=198 (LJ14) 22 38 58: 65 type=190 (LJ14) 23 25 58: 66 type=195 (LJ14) 23 26 58: 67 type=186 (LJ14) 24 29 58: 68 type=187 (LJ14) 24 30 58: 69 type=187 (LJ14) 24 34 58: 70 type=188 (LJ14) 24 39 58: 71 type=189 (LJ14) 24 40 58: 72 type=190 (LJ14) 25 27 58: 73 type=190 (LJ14) 25 28 58: 74 type=190 (LJ14) 25 38 58: 75 type=191 (LJ14) 26 31 58: 76 type=191 (LJ14) 26 32 58: 77 type=191 (LJ14) 26 33 58: 78 type=191 (LJ14) 26 35 58: 79 type=191 (LJ14) 26 36 58: 80 type=191 (LJ14) 26 37 58: 81 type=190 (LJ14) 26 41 58: 82 type=192 (LJ14) 26 42 58: 83 type=193 (LJ14) 27 29 58: 84 type=191 (LJ14) 27 30 58: 85 type=191 (LJ14) 27 34 58: 86 type=194 (LJ14) 27 39 58: 87 type=186 (LJ14) 27 40 58: 88 type=195 (LJ14) 28 39 58: 89 type=187 (LJ14) 28 40 58: 90 type=193 (LJ14) 29 31 58: 91 type=193 (LJ14) 29 32 58: 92 type=193 (LJ14) 29 33 58: 93 type=193 (LJ14) 29 35 58: 94 type=193 (LJ14) 29 36 58: 95 type=193 (LJ14) 29 37 58: 96 type=196 (LJ14) 29 38 58: 97 type=191 (LJ14) 30 35 58: 98 type=191 (LJ14) 30 36 58: 99 type=191 (LJ14) 30 37 58: 100 type=197 (LJ14) 30 38 58: 101 type=191 (LJ14) 31 34 58: 102 type=191 (LJ14) 32 34 58: 103 type=191 (LJ14) 33 34 58: 104 type=197 (LJ14) 34 38 58: 105 type=196 (LJ14) 38 43 58: 106 type=197 (LJ14) 38 44 58: 107 type=198 (LJ14) 38 58 58: 108 type=190 (LJ14) 39 41 58: 109 type=195 (LJ14) 39 42 58: 110 type=186 (LJ14) 40 45 58: 111 type=186 (LJ14) 40 46 58: 112 type=199 (LJ14) 40 47 58: 113 type=188 (LJ14) 40 59 58: 114 type=189 (LJ14) 40 60 58: 115 type=190 (LJ14) 41 43 58: 116 type=190 (LJ14) 41 44 58: 117 type=190 (LJ14) 41 58 58: 118 type=200 (LJ14) 42 48 58: 119 type=200 (LJ14) 42 50 58: 120 type=190 (LJ14) 42 61 58: 121 type=192 (LJ14) 42 62 58: 122 type=193 (LJ14) 43 45 58: 123 type=193 (LJ14) 43 46 58: 124 type=201 (LJ14) 43 47 58: 125 type=194 (LJ14) 43 59 58: 126 type=186 (LJ14) 43 60 58: 127 type=202 (LJ14) 44 49 58: 128 type=202 (LJ14) 44 51 58: 129 type=200 (LJ14) 44 52 58: 130 type=200 (LJ14) 44 54 58: 131 type=195 (LJ14) 44 59 58: 132 type=187 (LJ14) 44 60 58: 133 type=201 (LJ14) 45 48 58: 134 type=201 (LJ14) 45 50 58: 135 type=196 (LJ14) 45 58 58: 136 type=201 (LJ14) 46 48 58: 137 type=201 (LJ14) 46 50 58: 138 type=196 (LJ14) 46 58 58: 139 type=203 (LJ14) 47 53 58: 140 type=203 (LJ14) 47 55 58: 141 type=204 (LJ14) 47 56 58: 142 type=205 (LJ14) 47 58 58: 143 type=203 (LJ14) 48 51 58: 144 type=204 (LJ14) 48 54 58: 145 type=203 (LJ14) 48 57 58: 146 type=203 (LJ14) 49 50 58: 147 type=206 (LJ14) 49 53 58: 148 type=203 (LJ14) 49 56 58: 149 type=204 (LJ14) 50 52 58: 150 type=203 (LJ14) 50 57 58: 151 type=206 (LJ14) 51 55 58: 152 type=203 (LJ14) 51 56 58: 153 type=203 (LJ14) 52 55 58: 154 type=203 (LJ14) 53 54 58: 155 type=206 (LJ14) 53 57 58: 156 type=206 (LJ14) 55 57 58: 157 type=196 (LJ14) 58 63 58: 158 type=196 (LJ14) 58 64 58: 159 type=198 (LJ14) 58 65 58: 160 type=190 (LJ14) 59 61 58: 161 type=195 (LJ14) 59 62 58: 162 type=188 (LJ14) 60 66 58: 163 type=189 (LJ14) 60 67 58: 164 type=190 (LJ14) 61 63 58: 165 type=190 (LJ14) 61 64 58: 166 type=190 (LJ14) 61 65 58: 167 type=190 (LJ14) 62 68 58: 168 type=192 (LJ14) 62 69 58: 169 type=194 (LJ14) 63 66 58: 170 type=186 (LJ14) 63 67 58: 171 type=194 (LJ14) 64 66 58: 172 type=186 (LJ14) 64 67 58: 173 type=196 (LJ14) 65 70 58: 174 type=197 (LJ14) 65 71 58: 175 type=198 (LJ14) 65 89 58: 176 type=190 (LJ14) 66 68 58: 177 type=195 (LJ14) 66 69 58: 178 type=186 (LJ14) 67 72 58: 179 type=186 (LJ14) 67 73 58: 180 type=187 (LJ14) 67 74 58: 181 type=188 (LJ14) 67 90 58: 182 type=189 (LJ14) 67 91 58: 183 type=190 (LJ14) 68 70 58: 184 type=190 (LJ14) 68 71 58: 185 type=190 (LJ14) 68 89 58: 186 type=191 (LJ14) 69 75 58: 187 type=191 (LJ14) 69 76 58: 188 type=192 (LJ14) 69 77 58: 189 type=190 (LJ14) 69 92 58: 190 type=192 (LJ14) 69 93 58: 191 type=193 (LJ14) 70 72 58: 192 type=193 (LJ14) 70 73 58: 193 type=191 (LJ14) 70 74 58: 194 type=194 (LJ14) 70 90 58: 195 type=186 (LJ14) 70 91 58: 196 type=191 (LJ14) 71 78 58: 197 type=191 (LJ14) 71 79 58: 198 type=187 (LJ14) 71 80 58: 199 type=195 (LJ14) 71 90 58: 200 type=187 (LJ14) 71 91 58: 201 type=193 (LJ14) 72 75 58: 202 type=193 (LJ14) 72 76 58: 203 type=191 (LJ14) 72 77 58: 204 type=196 (LJ14) 72 89 58: 205 type=193 (LJ14) 73 75 58: 206 type=193 (LJ14) 73 76 58: 207 type=191 (LJ14) 73 77 58: 208 type=196 (LJ14) 73 89 58: 209 type=190 (LJ14) 74 81 58: 210 type=207 (LJ14) 74 82 58: 211 type=197 (LJ14) 74 89 58: 212 type=193 (LJ14) 75 78 58: 213 type=193 (LJ14) 75 79 58: 214 type=186 (LJ14) 75 80 58: 215 type=193 (LJ14) 76 78 58: 216 type=193 (LJ14) 76 79 58: 217 type=186 (LJ14) 76 80 58: 218 type=187 (LJ14) 77 83 58: 219 type=187 (LJ14) 77 86 58: 220 type=190 (LJ14) 78 81 58: 221 type=208 (LJ14) 78 82 58: 222 type=190 (LJ14) 79 81 58: 223 type=208 (LJ14) 79 82 58: 224 type=190 (LJ14) 80 84 58: 225 type=190 (LJ14) 80 85 58: 226 type=190 (LJ14) 80 87 58: 227 type=190 (LJ14) 80 88 58: 228 type=190 (LJ14) 81 83 58: 229 type=190 (LJ14) 81 86 58: 230 type=190 (LJ14) 83 87 58: 231 type=190 (LJ14) 83 88 58: 232 type=190 (LJ14) 84 86 58: 233 type=190 (LJ14) 85 86 58: 234 type=196 (LJ14) 89 94 58: 235 type=197 (LJ14) 89 95 58: 236 type=198 (LJ14) 89 100 58: 237 type=190 (LJ14) 90 92 58: 238 type=195 (LJ14) 90 93 58: 239 type=186 (LJ14) 91 96 58: 240 type=186 (LJ14) 91 97 58: 241 type=209 (LJ14) 91 98 58: 242 type=188 (LJ14) 91 101 58: 243 type=189 (LJ14) 91 102 58: 244 type=190 (LJ14) 92 94 58: 245 type=190 (LJ14) 92 95 58: 246 type=190 (LJ14) 92 100 58: 247 type=190 (LJ14) 93 99 58: 248 type=190 (LJ14) 93 103 58: 249 type=192 (LJ14) 93 104 58: 250 type=193 (LJ14) 94 96 58: 251 type=193 (LJ14) 94 97 58: 252 type=210 (LJ14) 94 98 58: 253 type=194 (LJ14) 94 101 58: 254 type=186 (LJ14) 94 102 58: 255 type=195 (LJ14) 95 101 58: 256 type=187 (LJ14) 95 102 58: 257 type=190 (LJ14) 96 99 58: 258 type=196 (LJ14) 96 100 58: 259 type=190 (LJ14) 97 99 58: 260 type=196 (LJ14) 97 100 58: 261 type=211 (LJ14) 98 100 58: 262 type=196 (LJ14) 100 105 58: 263 type=197 (LJ14) 100 106 58: 264 type=198 (LJ14) 100 115 58: 265 type=190 (LJ14) 101 103 58: 266 type=195 (LJ14) 101 104 58: 267 type=186 (LJ14) 102 107 58: 268 type=186 (LJ14) 102 108 58: 269 type=187 (LJ14) 102 109 58: 270 type=188 (LJ14) 102 116 58: 271 type=189 (LJ14) 102 117 58: 272 type=190 (LJ14) 103 105 58: 273 type=190 (LJ14) 103 106 58: 274 type=190 (LJ14) 103 115 58: 275 type=191 (LJ14) 104 110 58: 276 type=191 (LJ14) 104 111 58: 277 type=197 (LJ14) 104 112 58: 278 type=190 (LJ14) 104 118 58: 279 type=192 (LJ14) 104 119 58: 280 type=193 (LJ14) 105 107 58: 281 type=193 (LJ14) 105 108 58: 282 type=191 (LJ14) 105 109 58: 283 type=194 (LJ14) 105 116 58: 284 type=186 (LJ14) 105 117 58: 285 type=195 (LJ14) 106 113 58: 286 type=195 (LJ14) 106 114 58: 287 type=195 (LJ14) 106 116 58: 288 type=187 (LJ14) 106 117 58: 289 type=193 (LJ14) 107 110 58: 290 type=193 (LJ14) 107 111 58: 291 type=196 (LJ14) 107 112 58: 292 type=196 (LJ14) 107 115 58: 293 type=193 (LJ14) 108 110 58: 294 type=193 (LJ14) 108 111 58: 295 type=196 (LJ14) 108 112 58: 296 type=196 (LJ14) 108 115 58: 297 type=197 (LJ14) 109 115 58: 298 type=194 (LJ14) 110 113 58: 299 type=194 (LJ14) 110 114 58: 300 type=194 (LJ14) 111 113 58: 301 type=194 (LJ14) 111 114 58: 302 type=196 (LJ14) 115 120 58: 303 type=197 (LJ14) 115 121 58: 304 type=198 (LJ14) 115 134 58: 305 type=190 (LJ14) 116 118 58: 306 type=195 (LJ14) 116 119 58: 307 type=186 (LJ14) 117 122 58: 308 type=186 (LJ14) 117 123 58: 309 type=187 (LJ14) 117 124 58: 310 type=188 (LJ14) 117 135 58: 311 type=189 (LJ14) 117 136 58: 312 type=190 (LJ14) 118 120 58: 313 type=190 (LJ14) 118 121 58: 314 type=190 (LJ14) 118 134 58: 315 type=191 (LJ14) 119 125 58: 316 type=192 (LJ14) 119 126 58: 317 type=192 (LJ14) 119 130 58: 318 type=190 (LJ14) 119 137 58: 319 type=192 (LJ14) 119 138 58: 320 type=193 (LJ14) 120 122 58: 321 type=193 (LJ14) 120 123 58: 322 type=191 (LJ14) 120 124 58: 323 type=194 (LJ14) 120 135 58: 324 type=186 (LJ14) 120 136 58: 325 type=191 (LJ14) 121 127 58: 326 type=191 (LJ14) 121 128 58: 327 type=191 (LJ14) 121 129 58: 328 type=191 (LJ14) 121 131 58: 329 type=191 (LJ14) 121 132 58: 330 type=191 (LJ14) 121 133 58: 331 type=195 (LJ14) 121 135 58: 332 type=187 (LJ14) 121 136 58: 333 type=193 (LJ14) 122 125 58: 334 type=191 (LJ14) 122 126 58: 335 type=191 (LJ14) 122 130 58: 336 type=196 (LJ14) 122 134 58: 337 type=193 (LJ14) 123 125 58: 338 type=191 (LJ14) 123 126 58: 339 type=191 (LJ14) 123 130 58: 340 type=196 (LJ14) 123 134 58: 341 type=197 (LJ14) 124 134 58: 342 type=193 (LJ14) 125 127 58: 343 type=193 (LJ14) 125 128 58: 344 type=193 (LJ14) 125 129 58: 345 type=193 (LJ14) 125 131 58: 346 type=193 (LJ14) 125 132 58: 347 type=193 (LJ14) 125 133 58: 348 type=191 (LJ14) 126 131 58: 349 type=191 (LJ14) 126 132 58: 350 type=191 (LJ14) 126 133 58: 351 type=191 (LJ14) 127 130 58: 352 type=191 (LJ14) 128 130 58: 353 type=191 (LJ14) 129 130 58: 354 type=196 (LJ14) 134 139 58: 355 type=197 (LJ14) 134 140 58: 356 type=198 (LJ14) 134 144 58: 357 type=190 (LJ14) 135 137 58: 358 type=195 (LJ14) 135 138 58: 359 type=186 (LJ14) 136 141 58: 360 type=186 (LJ14) 136 142 58: 361 type=186 (LJ14) 136 143 58: 362 type=188 (LJ14) 136 145 58: 363 type=189 (LJ14) 136 146 58: 364 type=190 (LJ14) 137 139 58: 365 type=190 (LJ14) 137 140 58: 366 type=190 (LJ14) 137 144 58: 367 type=190 (LJ14) 138 147 58: 368 type=192 (LJ14) 138 148 58: 369 type=193 (LJ14) 139 141 58: 370 type=193 (LJ14) 139 142 58: 371 type=193 (LJ14) 139 143 58: 372 type=194 (LJ14) 139 145 58: 373 type=186 (LJ14) 139 146 58: 374 type=195 (LJ14) 140 145 58: 375 type=187 (LJ14) 140 146 58: 376 type=196 (LJ14) 141 144 58: 377 type=196 (LJ14) 142 144 58: 378 type=196 (LJ14) 143 144 58: 379 type=196 (LJ14) 144 149 58: 380 type=197 (LJ14) 144 150 58: 381 type=198 (LJ14) 144 154 58: 382 type=190 (LJ14) 145 147 58: 383 type=195 (LJ14) 145 148 58: 384 type=186 (LJ14) 146 151 58: 385 type=186 (LJ14) 146 152 58: 386 type=186 (LJ14) 146 153 58: 387 type=188 (LJ14) 146 155 58: 388 type=190 (LJ14) 147 149 58: 389 type=190 (LJ14) 147 150 58: 390 type=190 (LJ14) 147 154 58: 391 type=193 (LJ14) 149 151 58: 392 type=193 (LJ14) 149 152 58: 393 type=193 (LJ14) 149 153 58: 394 type=194 (LJ14) 149 155 58: 395 type=195 (LJ14) 150 155 58: 396 type=196 (LJ14) 151 154 58: 397 type=196 (LJ14) 152 154 58: 398 type=196 (LJ14) 153 154 58: Coulomb-14: 58: nr: 0 58: LJC-14 q: 58: nr: 0 58: LJC Pairs NB: 58: nr: 0 58: LJ (SR): 58: nr: 0 58: Buck.ham (SR): 58: nr: 0 58: LJ: 58: nr: 0 58: B.ham: 58: nr: 0 58: Disper. corr.: 58: nr: 0 58: Coulomb (SR): 58: nr: 0 58: Coul: 58: nr: 0 58: RF excl.: 58: nr: 0 58: Coul. recip.: 58: nr: 0 58: LJ recip.: 58: nr: 0 58: DPD: 58: nr: 0 58: Polarization: 58: nr: 0 58: Water Pol.: 58: nr: 0 58: Thole Pol.: 58: nr: 0 58: Anharm. Pol.: 58: nr: 0 58: Position Rest.: 58: nr: 0 58: Flat-b. P-R.: 58: nr: 0 58: Dis. Rest.: 58: nr: 0 58: D.R.Viol. (nm): 58: nr: 0 58: Orient. Rest.: 58: nr: 0 58: Ori. R. RMSD: 58: nr: 0 58: Angle Rest.: 58: nr: 0 58: Angle Rest. Z: 58: nr: 0 58: Dih. Rest.: 58: nr: 0 58: Dih. Rest. Vi.: 58: nr: 0 58: Constraint: 58: nr: 0 58: Constr. No Co.: 58: nr: 0 58: Settle: 58: nr: 0 58: Virtual site 1: 58: nr: 0 58: Virtual site 2: 58: nr: 0 58: Virt. site 2fd: 58: nr: 0 58: Virtual site 3: 58: nr: 0 58: Virt. site 3fd: 58: nr: 0 58: Vir. site 3fad: 58: nr: 0 58: Vir. site 3out: 58: nr: 0 58: Virt. site 4fd: 58: nr: 0 58: Vir. site 4fdn: 58: nr: 0 58: Virtual site N: 58: nr: 0 58: COM Pull En.: 58: nr: 0 58: Dens. fitting: 58: nr: 0 58: Quantum En.: 58: nr: 0 58: Potential: 58: nr: 0 58: Kinetic En.: 58: nr: 0 58: Total Energy: 58: nr: 0 58: Conserved En.: 58: nr: 0 58: Temperature: 58: nr: 0 58: Vir. Temp.: 58: nr: 0 58: Pres. DC: 58: nr: 0 58: Pressure: 58: nr: 0 58: dH/dl constr.: 58: nr: 0 58: dVremain/dl: 58: nr: 0 58: dEkin/dl: 58: nr: 0 58: dVcoul/dl: 58: nr: 0 58: dVvdw/dl: 58: nr: 0 58: dVbonded/dl: 58: nr: 0 58: dVrestraint/dl: 58: nr: 0 58: dVtemp/dl: 58: nr: 0 58: grp[T-Coupling ] nr=1, name=[ rest] 58: grp[Energy Mon. ] nr=1, name=[ rest] 58: grp[Acc. not used] nr=1, name=[ rest] 58: grp[Freeze ] nr=1, name=[ rest] 58: grp[User1 ] nr=1, name=[ rest] 58: grp[User2 ] nr=1, name=[ rest] 58: grp[VCM ] nr=1, name=[ rest] 58: grp[Compressed X] nr=1, name=[ rest] 58: grp[Or. Res. Fit] nr=1, name=[ rest] 58: grp[QMMM ] nr=1, name=[ rest] 58: grpname (11): 58: grpname[0]={name="System"} 58: grpname[1]={name="Protein"} 58: grpname[2]={name="Protein-H"} 58: grpname[3]={name="C-alpha"} 58: grpname[4]={name="Backbone"} 58: grpname[5]={name="MainChain"} 58: grpname[6]={name="MainChain+Cb"} 58: grpname[7]={name="MainChain+H"} 58: grpname[8]={name="SideChain"} 58: grpname[9]={name="SideChain-H"} 58: grpname[10]={name="rest"} 58: groups T-Cou Energ Acc. Freez User1 User2 VCM Compr Or. R QMMM 58: allocated 0 0 0 0 0 0 0 0 0 0 58: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0 58: box (3x3): 58: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00} 58: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00} 58: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00} 58: box_rel (3x3): 58: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: boxv (3x3): 58: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: pres_prev (3x3): 58: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: svir_prev (3x3): 58: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: fvir_prev (3x3): 58: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: nosehoover_xi: not available 58: x (156x3): 58: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00} 58: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00} 58: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00} 58: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00} 58: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00} 58: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00} 58: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00} 58: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00} 58: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01} 58: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01} 58: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01} 58: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00} 58: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01} 58: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01} 58: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01} 58: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01} 58: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01} 58: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01} 58: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01} 58: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01} 58: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01} 58: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01} 58: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00} 58: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00} 58: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00} 58: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00} 58: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00} 58: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01} 58: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00} 58: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00} 58: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00} 58: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00} 58: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01} 58: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01} 58: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00} 58: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00} 58: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00} 58: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00} 58: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01} 58: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01} 58: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01} 58: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01} 58: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01} 58: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01} 58: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01} 58: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01} 58: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01} 58: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01} 58: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01} 58: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01} 58: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01} 58: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01} 58: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01} 58: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01} 58: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01} 58: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01} 58: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01} 58: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01} 58: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01} 58: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01} 58: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01} 58: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01} 58: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01} 58: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01} 58: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01} 58: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01} 58: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01} 58: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01} 58: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01} 58: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01} 58: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01} 58: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01} 58: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01} 58: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01} 58: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02} 58: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02} 58: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02} 58: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02} 58: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02} 58: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01} 58: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02} 58: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01} 58: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02} 58: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01} 58: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01} 58: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01} 58: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02} 58: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01} 58: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02} 58: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01} 58: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02} 58: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01} 58: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01} 58: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02} 58: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02} 58: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02} 58: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01} 58: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02} 58: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02} 58: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02} 58: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02} 58: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02} 58: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01} 58: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01} 58: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01} 58: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01} 58: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01} 58: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01} 58: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01} 58: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01} 58: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01} 58: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01} 58: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01} 58: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01} 58: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01} 58: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01} 58: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01} 58: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01} 58: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01} 58: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01} 58: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01} 58: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01} 58: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01} 58: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01} 58: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01} 58: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02} 58: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01} 58: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01} 58: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01} 58: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01} 58: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01} 58: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01} 58: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01} 58: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01} 58: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02} 58: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02} 58: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02} 58: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02} 58: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01} 58: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01} 58: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01} 58: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01} 58: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01} 58: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01} 58: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01} 58: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01} 58: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01} 58: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01} 58: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01} 58: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01} 58: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01} 58: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01} 58: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01} 58: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02} 58: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01} 58: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01} 58: v (156x3): 58: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: Group statistics 58: T-Coupling : 156 (total 156 atoms) 58: Energy Mon. : 156 (total 156 atoms) 58: Acc. not used: 156 (total 156 atoms) 58: Freeze : 156 (total 156 atoms) 58: User1 : 156 (total 156 atoms) 58: User2 : 156 (total 156 atoms) 58: VCM : 156 (total 156 atoms) 58: Compressed X: 156 (total 156 atoms) 58: Or. Res. Fit: 156 (total 156 atoms) 58: QMMM : 156 (total 156 atoms) 58: [ OK ] DumpTest.WorksWithTpr (18 ms) 58: [ RUN ] DumpTest.WorksWithTprAndMdpWriting 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 58: [ OK ] DumpTest.WorksWithTprAndMdpWriting (0 ms) 58: [----------] 2 tests from DumpTest (19 ms total) 58: 58: [----------] 3 tests from HelpwritingTest 58: [ RUN ] HelpwritingTest.ConvertTprWritesHelp 58: [ OK ] HelpwritingTest.ConvertTprWritesHelp (6 ms) 58: [ RUN ] HelpwritingTest.DumpWritesHelp 58: [ OK ] HelpwritingTest.DumpWritesHelp (0 ms) 58: [ RUN ] HelpwritingTest.ReportMethodsWritesHelp 58: [ OK ] HelpwritingTest.ReportMethodsWritesHelp (2 ms) 58: [----------] 3 tests from HelpwritingTest (9 ms total) 58: 58: [----------] 7 tests from GmxMakeNdx 58: [ RUN ] GmxMakeNdx.WritesDefaultProteinIndexGroups 58: 58: Reading structure file 58: Going to read 0 old index file(s) 58: Analysing residue names: 58: There are: 16 Protein residues 58: Analysing Protein... 58: 58: 0 System : 256 atoms 58: 1 Protein : 256 atoms 58: 2 Protein-H : 139 atoms 58: 3 C-alpha : 16 atoms 58: 4 Backbone : 48 atoms 58: 5 MainChain : 63 atoms 58: 6 MainChain+Cb : 78 atoms 58: 7 MainChain+H : 81 atoms 58: 8 SideChain : 175 atoms 58: 9 SideChain-H : 76 atoms 58: 58: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 58: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 58: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 58: 'r': residue 'res' nr 'chain' char 58: "name": group 'case': case sensitive 'q': save and quit 58: 'ri': residue index 58: 58: > 58: [ OK ] GmxMakeNdx.WritesDefaultProteinIndexGroups (12 ms) 58: [ RUN ] GmxMakeNdx.HandlesNoStructureInput 58: Going to read 1 old index file(s) 58: Deducing 22 atoms in the system from indices in the index file 58: 58: 0 System : 22 atoms 58: 1 Protein : 22 atoms 58: 2 Protein-H : 10 atoms 58: 3 C-alpha : 1 atoms 58: 4 Backbone : 5 atoms 58: 5 MainChain : 7 atoms 58: 6 MainChain+Cb : 8 atoms 58: 7 MainChain+H : 9 atoms 58: 8 SideChain : 13 atoms 58: 9 SideChain-H : 3 atoms 58: 10 CA : 1 atoms 58: 11 C_&_r_1 : 1 atoms 58: 12 C_&_r_2 : 1 atoms 58: 13 N_&_r_2 : 1 atoms 58: 14 N_&_r_3 : 1 atoms 58: 58: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 58: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 58: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 58: 'r': residue 'res' nr 'chain' char 58: "name": group 'case': case sensitive 'q': save and quit 58: 'ri': residue index 58: 58: > 58: Copied index group 1 'Protein' 58: Copied index group 2 'Protein-H' 58: Merged two groups with OR: 22 10 -> 22 58: 58: > 58: [ OK ] GmxMakeNdx.HandlesNoStructureInput (13 ms) 58: [ RUN ] GmxMakeNdx.HandlesNotProtein 58: Going to read 1 old index file(s) 58: Deducing 6 atoms in the system from indices in the index file 58: 58: 0 System : 6 atoms 58: 58: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 58: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 58: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 58: 'r': residue 'res' nr 'chain' char 58: "name": group 'case': case sensitive 'q': save and quit 58: 'ri': residue index 58: 58: > 58: [ OK ] GmxMakeNdx.HandlesNotProtein (2 ms) 58: [ RUN ] GmxMakeNdx.HandlesEmptyIndexResult 58: Going to read 1 old index file(s) 58: Deducing 22 atoms in the system from indices in the index file 58: 58: 0 System : 22 atoms 58: 1 Protein : 22 atoms 58: 2 Protein-H : 10 atoms 58: 3 C-alpha : 1 atoms 58: 4 Backbone : 5 atoms 58: 5 MainChain : 7 atoms 58: 6 MainChain+Cb : 8 atoms 58: 7 MainChain+H : 9 atoms 58: 8 SideChain : 13 atoms 58: 9 SideChain-H : 3 atoms 58: 10 CA : 1 atoms 58: 11 C_&_r_1 : 1 atoms 58: 12 C_&_r_2 : 1 atoms 58: 13 N_&_r_2 : 1 atoms 58: 14 N_&_r_3 : 1 atoms 58: 58: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 58: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 58: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 58: 'r': residue 'res' nr 'chain' char 58: "name": group 'case': case sensitive 'q': save and quit 58: 'ri': residue index 58: 58: > 58: Copied index group 4 'Backbone' 58: Copied index group 8 'SideChain' 58: Merged two groups with AND: 5 13 -> 0 58: Group is empty 58: 58: > 58: [ OK ] GmxMakeNdx.HandlesEmptyIndexResult (9 ms) 58: [ RUN ] GmxMakeNdx.HandlesEmptyIndexFile 58: Going to read 1 old index file(s) 58: Deducing 6 atoms in the system from indices in the index file 58: 58: 0 System : 6 atoms 58: 58: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 58: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 58: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 58: 'r': residue 'res' nr 'chain' char 58: "name": group 'case': case sensitive 'q': save and quit 58: 'ri': residue index 58: 58: > 58: Removed group 0 'System' 58: 58: > 58: [ OK ] GmxMakeNdx.HandlesEmptyIndexFile (1 ms) 58: [ RUN ] GmxMakeNdx.Splitres 58: 58: Reading structure file 58: Going to read 0 old index file(s) 58: Analysing residue names: 58: There are: 2 Water residues 58: 58: 0 System : 6 atoms 58: 1 Water : 6 atoms 58: 2 SOL : 6 atoms 58: 58: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 58: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 58: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 58: 'r': residue 'res' nr 'chain' char 58: "name": group 'case': case sensitive 'q': save and quit 58: 'ri': residue index 58: 58: > 58: Splitting group 1 'Water' into residues 58: 58: > 58: [ OK ] GmxMakeNdx.Splitres (9 ms) 58: [ RUN ] GmxMakeNdx.Splitat 58: 58: Reading structure file 58: Going to read 0 old index file(s) 58: Analysing residue names: 58: There are: 2 Water residues 58: 58: 0 System : 6 atoms 58: 1 Water : 6 atoms 58: 2 SOL : 6 atoms 58: 58: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 58: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 58: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 58: 'r': residue 'res' nr 'chain' char 58: "name": group 'case': case sensitive 'q': save and quit 58: 'ri': residue index 58: 58: > 58: Splitting group 1 'Water' into atoms 58: 58: > 58: [ OK ] GmxMakeNdx.Splitat (1 ms) 58: [----------] 7 tests from GmxMakeNdx (50 ms total) 58: 58: [----------] 4 tests from ReportMethodsTest 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file lysozyme.top, line 1465]: 58: System has non-zero total charge: 2.000000 58: Total charge should normally be an integer. See 58: https://manual.gromacs.org/current/user-guide/floating-point.html 58: for discussion on how close it should be to an integer. 58: 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 465.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 58: NVE simulation with an initial temperature of zero: will use a Verlet 58: buffer of 10%. Check your energy drift! 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 4 NOTEs 58: Setting the LD random seed to -875180092 58: 58: Generated 330891 of the 330891 non-bonded parameter combinations 58: 58: Generated 330891 of the 330891 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 58: Analysing residue names: 58: There are: 10 Protein residues 58: Analysing Protein... 58: 58: This run will generate roughly 0 Mb of data 58: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated 58: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms) 58: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted 58: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms) 58: [ RUN ] ReportMethodsTest.WritesCorrectInformation 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 58: [ OK ] ReportMethodsTest.WritesCorrectInformation (0 ms) 58: [ RUN ] ReportMethodsTest.ToolEndToEndTest 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 58: section: Methods 58: subsection: Simulation system 58: A system of 1 molecules (156 atoms) was simulated. 58: 58: subsection: Simulation settings 58: A total of 0 ns were simulated with a time step of 1 fs. 58: Neighbor searching was performed every 10 steps. 58: The Cut-off algorithm was used for electrostatic interactions. 58: with a cut-off of 1 nm. 58: A single cut-off of 1.1 nm was used for Van der Waals interactions. 58: [ OK ] ReportMethodsTest.ToolEndToEndTest (0 ms) 58: [----------] 4 tests from ReportMethodsTest (2 ms total) 58: 58: [----------] 4 tests from ConvertTprTest 58: [ RUN ] ConvertTprTest.ExtendRuntimeExtensionTest 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file lysozyme.top, line 1465]: 58: System has non-zero total charge: 2.000000 58: Total charge should normally be an integer. See 58: https://manual.gromacs.org/current/user-guide/floating-point.html 58: for discussion on how close it should be to an integer. 58: 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 465.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 58: NVE simulation with an initial temperature of zero: will use a Verlet 58: buffer of 10%. Check your energy drift! 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 4 NOTEs 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended_again.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 58: Setting the LD random seed to -294920195 58: 58: Generated 330891 of the 330891 non-bonded parameter combinations 58: 58: Generated 330891 of the 330891 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 58: Analysing residue names: 58: There are: 10 Protein residues 58: Analysing Protein... 58: 58: This run will generate roughly 0 Mb of data 58: Input file: 58: Run start step 0 58: Run start time 0 ps 58: Step to be made during run 0 58: Runtime for the run 0 ps 58: Run end step 0 58: Run end time 0 ps 58: 58: Extending remaining runtime by 100 ps 58: 58: Output file: 58: Run start step 0 58: Run start time 0 ps 58: Step to be made during run 100000 58: Runtime for the run 100 ps 58: Run end step 100000 58: Run end time 100 ps 58: 58: Input file: 58: Run start step 0 58: Run start time 0 ps 58: Step to be made during run 100000 58: Runtime for the run 100 ps 58: Run end step 100000 58: Run end time 100 ps 58: 58: Extending remaining runtime by 100 ps 58: 58: Output file: 58: Run start step 0 58: Run start time 0 ps 58: Step to be made during run 200000 58: Runtime for the run 200 ps 58: Run end step 200000 58: Run end time 200 ps 58: 58: [ OK ] ConvertTprTest.ExtendRuntimeExtensionTest (331 ms) 58: [ RUN ] ConvertTprTest.UntilRuntimeExtensionTest 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file lysozyme.top, line 1465]: 58: System has non-zero total charge: 2.000000 58: Total charge should normally be an integer. See 58: https://manual.gromacs.org/current/user-guide/floating-point.html 58: for discussion on how close it should be to an integer. 58: 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 465.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 58: NVE simulation with an initial temperature of zero: will use a Verlet 58: buffer of 10%. Check your energy drift! 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 4 NOTEs 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_extended.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 58: Setting the LD random seed to -1367363587 58: 58: Generated 330891 of the 330891 non-bonded parameter combinations 58: 58: Generated 330891 of the 330891 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 58: Analysing residue names: 58: There are: 10 Protein residues 58: Analysing Protein... 58: 58: This run will generate roughly 0 Mb of data 58: Input file: 58: Run start step 0 58: Run start time 0 ps 58: Step to be made during run 0 58: Runtime for the run 0 ps 58: Run end step 0 58: Run end time 0 ps 58: 58: Extending remaining runtime to 100 ps 58: 58: Output file: 58: Run start step 0 58: Run start time 0 ps 58: Step to be made during run 100000 58: Runtime for the run 100 ps 58: Run end step 100000 58: Run end time 100 ps 58: 58: [ OK ] ConvertTprTest.UntilRuntimeExtensionTest (404 ms) 58: [ RUN ] ConvertTprTest.nstepRuntimeExtensionTest 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file lysozyme.top, line 1465]: 58: System has non-zero total charge: 2.000000 58: Total charge should normally be an integer. See 58: https://manual.gromacs.org/current/user-guide/floating-point.html 58: for discussion on how close it should be to an integer. 58: 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 465.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 58: NVE simulation with an initial temperature of zero: will use a Verlet 58: buffer of 10%. Check your energy drift! 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 4 NOTEs 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 58: Setting nsteps to 102 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_extended.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 58: Setting the LD random seed to -1343374531 58: 58: Generated 330891 of the 330891 non-bonded parameter combinations 58: 58: Generated 330891 of the 330891 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 58: Analysing residue names: 58: There are: 10 Protein residues 58: Analysing Protein... 58: 58: This run will generate roughly 0 Mb of data 58: Input file: 58: Run start step 0 58: Run start time 0 ps 58: Step to be made during run 0 58: Runtime for the run 0 ps 58: Run end step 0 58: Run end time 0 ps 58: 58: 58: Output file: 58: Run start step 0 58: Run start time 0 ps 58: Step to be made during run 102 58: Runtime for the run 0.102 ps 58: Run end step 102 58: Run end time 0.102 ps 58: 58: [ OK ] ConvertTprTest.nstepRuntimeExtensionTest (500 ms) 58: [ RUN ] ConvertTprTest.generateVelocitiesTest 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file lysozyme.top, line 1465]: 58: System has non-zero total charge: 2.000000 58: Total charge should normally be an integer. See 58: https://manual.gromacs.org/current/user-guide/floating-point.html 58: for discussion on how close it should be to an integer. 58: 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 465.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 58: NVE simulation with an initial temperature of zero: will use a Verlet 58: buffer of 10%. Check your energy drift! 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 4 NOTEs 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_new_velocities.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 58: Setting the LD random seed to 2046525429 58: 58: Generated 330891 of the 330891 non-bonded parameter combinations 58: 58: Generated 330891 of the 330891 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 58: Analysing residue names: 58: There are: 10 Protein residues 58: Analysing Protein... 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] ConvertTprTest.generateVelocitiesTest (470 ms) 58: [----------] 4 tests from ConvertTprTest (1711 ms total) 58: 58: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: trr version: GMX_trn_file (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr (2 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 58: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng (0 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc (0 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 58: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro (0 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 58: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 58: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb (0 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 (7 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr (1 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 58: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng (2 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc (2 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 58: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro (1 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 58: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 58: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb (1 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 (1 ms) 58: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats (26 ms total) 58: 58: [----------] 30 tests from Works/TrjconvDumpTest 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 58: Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 58: Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 58: Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 58: Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 58: Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 (4 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 (1 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 (1 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 (1 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 58: Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 (6 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 58: Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 58: Will write trr: Trajectory in portable xdr format 58: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 58: Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 58: Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 58: Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 58: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 58: Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 58: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 58: Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 58: Will write trr: Trajectory in portable xdr format 58: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 58: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 58: Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 58: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 58: Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 58: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 58: Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 (0 ms) 58: [----------] 30 tests from Works/TrjconvDumpTest (24 ms total) 58: 58: [----------] Global test environment tear-down 58: [==========] 62 tests from 7 test suites ran. (3147 ms total) 58: [ PASSED ] 62 tests. 58/87 Test #58: ToolUnitTests ............................. Passed 3.19 sec test 59 Start 59: FileIOTests 59: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/fileio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/FileIOTests.xml" 59: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fileio/tests 59: Test timeout computed to be: 30 59: [==========] Running 413 tests from 15 test suites. 59: [----------] Global test environment set-up. 59: [----------] 4 tests from Checkpoint 59: [ RUN ] Checkpoint.ReadingThrowsWhenValueNotPresent 59: [ OK ] Checkpoint.ReadingThrowsWhenValueNotPresent (0 ms) 59: [ RUN ] Checkpoint.ReadingDoesNotThrowWhenValuePresent 59: [ OK ] Checkpoint.ReadingDoesNotThrowWhenValuePresent (0 ms) 59: [ RUN ] Checkpoint.KvtRoundTripInt64 59: [ OK ] Checkpoint.KvtRoundTripInt64 (0 ms) 59: [ RUN ] Checkpoint.KvtRoundTripReal 59: [ OK ] Checkpoint.KvtRoundTripReal (0 ms) 59: [----------] 4 tests from Checkpoint (0 ms total) 59: 59: [----------] 1 test from StructureIOTest 59: [ RUN ] StructureIOTest.ReadTpsConfRetainsChainids 59: [ OK ] StructureIOTest.ReadTpsConfRetainsChainids (0 ms) 59: [----------] 1 test from StructureIOTest (0 ms total) 59: 59: [----------] 2 tests from FileMD5Test 59: [ RUN ] FileMD5Test.CanComputeMD5 59: [ OK ] FileMD5Test.CanComputeMD5 (3 ms) 59: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 59: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 59: [----------] 2 tests from FileMD5Test (4 ms total) 59: 59: [----------] 4 tests from FileTypeTest 59: [ RUN ] FileTypeTest.CorrectValueForEmptyString 59: [ OK ] FileTypeTest.CorrectValueForEmptyString (0 ms) 59: [ RUN ] FileTypeTest.CorrectValueForNoExtension 59: [ OK ] FileTypeTest.CorrectValueForNoExtension (0 ms) 59: [ RUN ] FileTypeTest.CorrectValueForEmptyExtension 59: [ OK ] FileTypeTest.CorrectValueForEmptyExtension (0 ms) 59: [ RUN ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters 59: [ OK ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters (0 ms) 59: [----------] 4 tests from FileTypeTest (0 ms total) 59: 59: [----------] 3 tests from MrcSerializer 59: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet 59: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms) 59: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize 59: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms) 59: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip 59: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (0 ms) 59: [----------] 3 tests from MrcSerializer (0 ms total) 59: 59: [----------] 4 tests from MrcDensityMap 59: [ RUN ] MrcDensityMap.RoundTripIsIdempotent 59: [ OK ] MrcDensityMap.RoundTripIsIdempotent (0 ms) 59: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent 59: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (1 ms) 59: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile 59: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms) 59: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile 59: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (1 ms) 59: [----------] 4 tests from MrcDensityMap (3 ms total) 59: 59: [----------] 8 tests from MrcDensityMapHeaderTest 59: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader 59: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms) 59: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect 59: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms) 59: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid 59: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms) 59: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven 59: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms) 59: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined 59: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms) 59: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues 59: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms) 59: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents 59: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms) 59: [ RUN ] MrcDensityMapHeaderTest.IsSane 59: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms) 59: [----------] 8 tests from MrcDensityMapHeaderTest (0 ms total) 59: 59: [----------] 10 tests from ReadTest 59: [ RUN ] ReadTest.get_eint_ReadsInteger 59: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 59: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 59: 59: ERROR 1 [file unknown]: 59: Right hand side '0.8' for parameter 'test' in parameter file is not an 59: integer value 59: 59: 59: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 59: [ RUN ] ReadTest.get_eint_WarnsAboutString 59: 59: ERROR 1 [file unknown]: 59: Right hand side 'hello' for parameter 'test' in parameter file is not an 59: integer value 59: 59: 59: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 59: [ RUN ] ReadTest.get_eint64_ReadsInteger 59: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 59: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 59: 59: ERROR 1 [file unknown]: 59: Right hand side '0.8' for parameter 'test' in parameter file is not an 59: integer value 59: 59: 59: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 59: [ RUN ] ReadTest.get_eint64_WarnsAboutString 59: 59: ERROR 1 [file unknown]: 59: Right hand side 'hello' for parameter 'test' in parameter file is not an 59: integer value 59: 59: 59: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 59: [ RUN ] ReadTest.get_ereal_ReadsInteger 59: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 59: [ RUN ] ReadTest.get_ereal_ReadsFloat 59: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 59: [ RUN ] ReadTest.get_ereal_WarnsAboutString 59: 59: ERROR 1 [file unknown]: 59: Right hand side 'hello' for parameter 'test' in parameter file is not a 59: real value 59: 59: 59: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 59: [ RUN ] ReadTest.setStringEntry_ReturnsCorrectString 59: [ OK ] ReadTest.setStringEntry_ReturnsCorrectString (0 ms) 59: [----------] 10 tests from ReadTest (0 ms total) 59: 59: [----------] 3 tests from TimeControlTest 59: [ RUN ] TimeControlTest.UnSetHasNoValue 59: [ OK ] TimeControlTest.UnSetHasNoValue (0 ms) 59: [ RUN ] TimeControlTest.CanSetValue 59: [ OK ] TimeControlTest.CanSetValue (0 ms) 59: [ RUN ] TimeControlTest.CanUnsetValueAgain 59: [ OK ] TimeControlTest.CanUnsetValueAgain (0 ms) 59: [----------] 3 tests from TimeControlTest (0 ms total) 59: 59: [----------] 1 test from FileIOXdrSerializerTest 59: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect 59: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (0 ms) 59: [----------] 1 test from FileIOXdrSerializerTest (0 ms total) 59: 59: [----------] 1 test from TngTest 59: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 59: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 59: [----------] 1 test from TngTest (0 ms total) 59: 59: [----------] 4 tests from XvgioTest 59: [ RUN ] XvgioTest.readXvgIntWorks 59: [ OK ] XvgioTest.readXvgIntWorks (2 ms) 59: [ RUN ] XvgioTest.readXvgRealWorks 59: [ OK ] XvgioTest.readXvgRealWorks (0 ms) 59: [ RUN ] XvgioTest.readXvgIgnoreCommentLineWorks 59: [ OK ] XvgioTest.readXvgIgnoreCommentLineWorks (0 ms) 59: [ RUN ] XvgioTest.readXvgDeprecatedWorks 59: [ OK ] XvgioTest.readXvgDeprecatedWorks (0 ms) 59: [----------] 4 tests from XvgioTest (2 ms total) 59: 59: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 59: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 59: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (3 ms) 59: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 59: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (0 ms) 59: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 59: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (0 ms) 59: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 59: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (0 ms) 59: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (4 ms total) 59: 59: [----------] 360 tests from FileTypeMatch/FileTypeTest 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 (0 ms) 59: [----------] 360 tests from FileTypeMatch/FileTypeTest (1 ms total) 59: 59: [----------] 4 tests from XvgReadTimeSeries/XvgioTest 59: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 59: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 (5 ms) 59: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 59: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 (1 ms) 59: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 59: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 (0 ms) 59: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 59: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 (2 ms) 59: [----------] 4 tests from XvgReadTimeSeries/XvgioTest (10 ms total) 59: 59: [----------] Global test environment tear-down 59: [==========] 413 tests from 15 test suites ran. (27 ms total) 59: [ PASSED ] 413 tests. 59/87 Test #59: FileIOTests ............................... Passed 0.07 sec test 60 Start 60: SelectionUnitTests 60: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/selection-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/SelectionUnitTests.xml" 60: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/selection/tests 60: Test timeout computed to be: 30 60: [==========] Running 201 tests from 11 test suites. 60: [----------] Global test environment set-up. 60: [----------] 1 test from IndexGroupTest 60: [ RUN ] IndexGroupTest.RemovesDuplicates 60: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) 60: [----------] 1 test from IndexGroupTest (0 ms total) 60: 60: [----------] 15 tests from IndexBlockTest 60: [ RUN ] IndexBlockTest.CreatesUnknownBlock 60: [ OK ] IndexBlockTest.CreatesUnknownBlock (3 ms) 60: [ RUN ] IndexBlockTest.CreatesAtomBlock 60: [ OK ] IndexBlockTest.CreatesAtomBlock (0 ms) 60: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology 60: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (0 ms) 60: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology 60: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (0 ms) 60: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology 60: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms) 60: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology 60: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (0 ms) 60: [ RUN ] IndexBlockTest.CreatesSingleBlock 60: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms) 60: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive 60: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (1 ms) 60: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive 60: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) 60: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative 60: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) 60: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial 60: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) 60: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive 60: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) 60: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative 60: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) 60: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive 60: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) 60: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative 60: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) 60: [----------] 15 tests from IndexBlockTest (9 ms total) 60: 60: [----------] 11 tests from IndexMapTest 60: [ RUN ] IndexMapTest.InitializesAtomBlock 60: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms) 60: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom 60: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms) 60: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle 60: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms) 60: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue 60: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms) 60: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule 60: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (3 ms) 60: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll 60: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms) 60: [ RUN ] IndexMapTest.InitializesMoleculeBlock 60: [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms) 60: [ RUN ] IndexMapTest.MapsSingleBlock 60: [ OK ] IndexMapTest.MapsSingleBlock (0 ms) 60: [ RUN ] IndexMapTest.MapsResidueBlocks 60: [ OK ] IndexMapTest.MapsResidueBlocks (0 ms) 60: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask 60: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (0 ms) 60: [ RUN ] IndexMapTest.HandlesMultipleRequests 60: [ OK ] IndexMapTest.HandlesMultipleRequests (0 ms) 60: [----------] 11 tests from IndexMapTest (11 ms total) 60: 60: [----------] 3 tests from IndexGroupsAndNamesTest 60: [ RUN ] IndexGroupsAndNamesTest.containsNames 60: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms) 60: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing 60: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (1 ms) 60: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect 60: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms) 60: [----------] 3 tests from IndexGroupsAndNamesTest (1 ms total) 60: 60: [----------] 15 tests from NeighborhoodSearchTest 60: [ RUN ] NeighborhoodSearchTest.SimpleSearch 60: [ OK ] NeighborhoodSearchTest.SimpleSearch (20 ms) 60: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 60: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (33 ms) 60: [ RUN ] NeighborhoodSearchTest.GridSearchBox 60: [ OK ] NeighborhoodSearchTest.GridSearchBox (1 ms) 60: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 60: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (13 ms) 60: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 60: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (6 ms) 60: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 60: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (0 ms) 60: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 60: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (1 ms) 60: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 60: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (8 ms) 60: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 60: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (58 ms) 60: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches 60: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms) 60: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC 60: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) 60: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC 60: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) 60: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs 60: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) 60: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions 60: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (2 ms) 60: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 60: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (0 ms) 60: [----------] 15 tests from NeighborhoodSearchTest (152 ms total) 60: 60: [----------] 13 tests from PositionCalculationTest 60: [ RUN ] PositionCalculationTest.ComputesAtomPositions 60: [ OK ] PositionCalculationTest.ComputesAtomPositions (3 ms) 60: [ RUN ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex 60: [ OK ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex (1 ms) 60: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions 60: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (0 ms) 60: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions 60: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (0 ms) 60: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions 60: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms) 60: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions 60: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms) 60: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole 60: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms) 60: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax 60: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (0 ms) 60: [ RUN ] PositionCalculationTest.ComputesPositionMask 60: [ OK ] PositionCalculationTest.ComputesPositionMask (0 ms) 60: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms 60: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (0 ms) 60: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 60: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms) 60: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations 60: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (0 ms) 60: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations 60: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (0 ms) 60: [----------] 13 tests from PositionCalculationTest (16 ms total) 60: 60: [----------] 33 tests from SelectionCollectionTest 60: [ RUN ] SelectionCollectionTest.HandlesNoSelections 60: [ OK ] SelectionCollectionTest.HandlesNoSelections (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType 60: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (1 ms) 60: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests 60: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry 60: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (0 ms) 60: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile 60: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (1 ms) 60: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace 60: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions 60: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue 60: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 60: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 60: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 60: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 60: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (2 ms) 60: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 60: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 60: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference 60: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed 60: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup 60: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed 60: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 60: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (0 ms) 60: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo 60: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (0 ms) 60: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes 60: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (0 ms) 60: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo 60: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (0 ms) 60: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation 60: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (0 ms) 60: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 60: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (0 ms) 60: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 60: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets 60: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 60: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 60: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 60: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (0 ms) 60: [ RUN ] SelectionCollectionTest.RetrieveValidSelection 60: [ OK ] SelectionCollectionTest.RetrieveValidSelection (0 ms) 60: [ RUN ] SelectionCollectionTest.RetrieveInvalidSelection 60: [ OK ] SelectionCollectionTest.RetrieveInvalidSelection (0 ms) 60: [ RUN ] SelectionCollectionTest.CanCopyEmptyCollection 60: [ OK ] SelectionCollectionTest.CanCopyEmptyCollection (0 ms) 60: [ RUN ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately 60: [ OK ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately (0 ms) 60: [----------] 33 tests from SelectionCollectionTest (22 ms total) 60: 60: [----------] 14 tests from SelectionCollectionInteractiveTest 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput 60: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (2 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation 60: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (3 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput 60: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (3 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput 60: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (1 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups 60: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (0 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections 60: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (1 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus 60: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (10 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus 60: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (1 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus 60: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (6 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline 60: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (1 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections 60: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (0 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine 60: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (0 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput 60: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (0 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively 60: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (3 ms) 60: [----------] 14 tests from SelectionCollectionInteractiveTest (50 ms total) 60: 60: [----------] 70 tests from SelectionCollectionDataTest 60: [ RUN ] SelectionCollectionDataTest.HandlesAllNone 60: [ OK ] SelectionCollectionDataTest.HandlesAllNone (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr 60: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesResnr 60: [ OK ] SelectionCollectionDataTest.HandlesResnr (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesResIndex 60: [ OK ] SelectionCollectionDataTest.HandlesResIndex (1 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex 60: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (3 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesAtomname 60: [ OK ] SelectionCollectionDataTest.HandlesAtomname (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname 60: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype 60: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesChain 60: [ OK ] SelectionCollectionDataTest.HandlesChain (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesMass 60: [ OK ] SelectionCollectionDataTest.HandlesMass (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesCharge 60: [ OK ] SelectionCollectionDataTest.HandlesCharge (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc 60: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (6 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode 60: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy 60: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesBeta 60: [ OK ] SelectionCollectionDataTest.HandlesBeta (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesResname 60: [ OK ] SelectionCollectionDataTest.HandlesResname (1 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords 60: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (1 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue 60: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName 60: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords 60: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (1 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 60: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (1 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword 60: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (3 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword 60: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword 60: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (3 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 60: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (2 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 60: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (5 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 60: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (2 ms) 60: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 60: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (1 ms) 60: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 60: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 60: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (1 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 60: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 60: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (1 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 60: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (5 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 60: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (7 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed 60: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (1 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions 60: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers 60: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions 60: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges 60: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges 60: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (1 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode 60: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching 60: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching 60: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 60: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 60: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions 60: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame 60: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords 60: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods 60: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions 60: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic 60: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (1 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons 60: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (1 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 60: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (1 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 60: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 60: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (1 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 60: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (1 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 60: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 60: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (1 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 60: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (1 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis 60: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables 60: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (2 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables 60: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables 60: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups 60: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups 60: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 60: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (0 ms) 60: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation 60: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation (1 ms) 60: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation 60: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation (1 ms) 60: [ RUN ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent 60: [ OK ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent (1 ms) 60: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation 60: [ OK ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation (1 ms) 60: [----------] 70 tests from SelectionCollectionDataTest (155 ms total) 60: 60: [----------] 17 tests from SelectionOptionTest 60: [ RUN ] SelectionOptionTest.ParsesSimpleSelection 60: [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired 60: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired 60: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (0 ms) 60: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired 60: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (0 ms) 60: [ RUN ] SelectionOptionTest.ChecksEmptySelections 60: [ OK ] SelectionOptionTest.ChecksEmptySelections (0 ms) 60: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections 60: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesTooManySelections 60: [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesTooFewSelections 60: [ OK ] SelectionOptionTest.HandlesTooFewSelections (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText 60: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesAdjuster 60: [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster 60: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster 60: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster 60: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection 60: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections 60: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection 60: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster 60: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms) 60: [----------] 17 tests from SelectionOptionTest (11 ms total) 60: 60: [----------] 9 tests from SelectionFileOptionTest 60: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile 60: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (0 ms) 60: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions 60: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (0 ms) 60: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile 60: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms) 60: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile 60: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (0 ms) 60: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet 60: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (0 ms) 60: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile 60: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (0 ms) 60: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile 60: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms) 60: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile 60: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (0 ms) 60: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles 60: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (0 ms) 60: [----------] 9 tests from SelectionFileOptionTest (1 ms total) 60: 60: [----------] Global test environment tear-down 60: [==========] 201 tests from 11 test suites ran. (432 ms total) 60: [ PASSED ] 201 tests. 60/87 Test #60: SelectionUnitTests ........................ Passed 0.48 sec test 61 Start 61: MdrunOutputTests 61: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunOutputTests.xml" 61: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 61: Test timeout computed to be: 600 61: [==========] Running 12 tests from 5 test suites. 61: [----------] Global test environment set-up. 61: [----------] 1 test from MdrunTest 61: [ RUN ] MdrunTest.WritesHelp 61: [ OK ] MdrunTest.WritesHelp (48 ms) 61: [----------] 1 test from MdrunTest (48 ms total) 61: 61: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput 61: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 61: Generating 1-4 interactions: fudge = 0.5 61: Number of degrees of freedom in T-Coupling group rest is 9.00 61: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 61: NVE simulation: will use the initial temperature of 2573.591 K for 61: determining the Verlet buffer size 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 2 NOTEs 61: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc2' 61: 1 steps, 0.0 ps. 61: Setting the LD random seed to -805315078 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Generated 3 of the 3 1-4 parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 61: 61: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.104 0.052 199.7 61: (ns/day) (hour/ns) 61: Performance: 3.305 7.261 61: Reading frame 0 time 0.000 61: # Atoms 6 61: Reading frame 1 time 0.001 Last frame 1 time 0.001 61: 61: 61: Item #frames Timestep (ps) 61: Step 2 0.001 61: Time 2 0.001 61: Lambda 0 61: Coords 2 0.001 61: Velocities 0 61: Forces 0 61: Box 2 0.001 61: Checking file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc 61: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (60 ms) 61: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 61: Generating 1-4 interactions: fudge = 0.5 61: Number of degrees of freedom in T-Coupling group rest is 9.00 61: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 61: NVE simulation: will use the initial temperature of 2573.591 K for 61: determining the Verlet buffer size 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 2 NOTEs 61: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc2' 61: 1 steps, 0.0 ps. 61: Setting the LD random seed to -268930562 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Generated 3 of the 3 1-4 parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 61: 61: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.036 0.018 199.5 61: (ns/day) (hour/ns) 61: Performance: 9.507 2.524 61: Reading frame 0 time 0.000 61: # Atoms 6 61: Reading frame 1 time 0.001 Last frame 1 time 0.001 61: 61: 61: Item #frames Timestep (ps) 61: Step 2 0.001 61: Time 2 0.001 61: Lambda 0 61: Coords 2 0.001 61: Velocities 0 61: Forces 0 61: Box 2 0.001 61: Checking file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc 61: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (61 ms) 61: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 61: Generating 1-4 interactions: fudge = 0.5 61: Number of degrees of freedom in T-Coupling group rest is 9.00 61: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 61: NVE simulation: will use the initial temperature of 2573.591 K for 61: determining the Verlet buffer size 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 2 NOTEs 61: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc2' 61: 1 steps, 0.0 ps. 61: Setting the LD random seed to -269585417 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Generated 3 of the 3 1-4 parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 61: 61: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.044 0.022 199.6 61: (ns/day) (hour/ns) 61: Performance: 7.804 3.075 61: Reading frame 0 time 0.000 61: # Atoms 3 61: Reading frame 1 time 0.001 Last frame 1 time 0.001 61: 61: 61: Item #frames Timestep (ps) 61: Step 2 0.001 61: Time 2 0.001 61: Lambda 0 61: Coords 2 0.001 61: Velocities 0 61: Forces 0 61: Box 2 0.001 61: Checking file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc 61: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (25 ms) 61: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (148 ms total) 61: 61: [----------] 2 tests from Argon12/OutputFiles 61: [ RUN ] Argon12/OutputFiles.FilesArePresent/0 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Number of degrees of freedom in T-Coupling group System is 33.00 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 61: NVE simulation: will use the initial temperature of 68.810 K for 61: determining the Verlet buffer size 61: 61: 61: There were 3 NOTEs 61: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'Argon' 61: 16 steps, 0.0 ps. 61: Generated 1 of the 1 non-bonded parameter combinations 61: 61: Excluding 1 bonded neighbours molecule type 'Argon' 61: 61: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 61: 61: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.026 0.013 199.4 61: (ns/day) (hour/ns) 61: Performance: 111.518 0.215 61: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (25 ms) 61: [ RUN ] Argon12/OutputFiles.FilesArePresent/1 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Number of degrees of freedom in T-Coupling group System is 33.00 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 61: NVE simulation: will use the initial temperature of 68.810 K for 61: determining the Verlet buffer size 61: 61: 61: There were 3 NOTEs 61: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'Argon' 61: 16 steps, 0.0 ps. 61: Generated 1 of the 1 non-bonded parameter combinations 61: 61: Excluding 1 bonded neighbours molecule type 'Argon' 61: 61: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 61: 61: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.092 0.046 199.7 61: (ns/day) (hour/ns) 61: Performance: 32.011 0.750 61: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (71 ms) 61: [----------] 2 tests from Argon12/OutputFiles (96 ms total) 61: 61: [----------] 3 tests from MdrunCanWrite/Trajectories 61: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 61: Number of degrees of freedom in T-Coupling group System is 12.00 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There was 1 NOTE 61: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 61: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 61: 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc-and-methanol' 61: 6 steps, 0.0 ps. 61: Setting the LD random seed to -9700545 61: 61: Generated 8 of the 10 non-bonded parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'Methanol' 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 61: 61: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.048 0.024 199.6 61: (ns/day) (hour/ns) 61: Performance: 25.254 0.950 61: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (104 ms) 61: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 61: Number of degrees of freedom in T-Coupling group System is 12.00 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There was 1 NOTE 61: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 61: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 61: 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc-and-methanol' 61: 6 steps, 0.0 ps. 61: Setting the LD random seed to -873009154 61: 61: Generated 8 of the 10 non-bonded parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'Methanol' 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 61: 61: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.046 0.023 199.6 61: (ns/day) (hour/ns) 61: Performance: 26.238 0.915 61: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (44 ms) 61: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 61: Number of degrees of freedom in T-Coupling group System is 12.00 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There was 1 NOTE 61: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 61: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 61: 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc-and-methanol' 61: 6 steps, 0.0 ps. 61: Setting the LD random seed to -134349378 61: 61: Generated 8 of the 10 non-bonded parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'Methanol' 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 61: 61: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.104 0.052 199.8 61: (ns/day) (hour/ns) 61: Performance: 11.581 2.072 61: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (143 ms) 61: [----------] 3 tests from MdrunCanWrite/Trajectories (295 ms total) 61: 61: [----------] 3 tests from MdrunCanWrite/NptTrajectories 61: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 61: Number of degrees of freedom in T-Coupling group System is 12.00 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There was 1 NOTE 61: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 61: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 61: 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc-and-methanol' 61: 2 steps, 0.0 ps. 61: Setting the LD random seed to -43256837 61: 61: Generated 8 of the 10 non-bonded parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'Methanol' 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 61: 61: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.045 0.023 199.6 61: (ns/day) (hour/ns) 61: Performance: 11.464 2.093 61: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (44 ms) 61: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 61: 61: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 61: The Berendsen barostat does not generate any strictly correct ensemble, 61: and should not be used for new production simulations (in our opinion). 61: We recommend using the C-rescale barostat instead. 61: 61: Number of degrees of freedom in T-Coupling group System is 12.00 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There was 1 NOTE 61: 61: There was 1 WARNING 61: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 61: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 61: 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc-and-methanol' 61: 2 steps, 0.0 ps. 61: Setting the LD random seed to -641745153 61: 61: Generated 8 of the 10 non-bonded parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'Methanol' 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 61: 61: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.044 0.022 199.5 61: (ns/day) (hour/ns) 61: Performance: 11.674 2.056 61: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (39 ms) 61: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 61: Number of degrees of freedom in T-Coupling group System is 12.00 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There was 1 NOTE 61: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 61: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 61: 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc-and-methanol' 61: 2 steps, 0.0 ps. 61: Setting the LD random seed to -359678468 61: 61: Generated 8 of the 10 non-bonded parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'Methanol' 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 61: 61: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.078 0.039 199.6 61: (ns/day) (hour/ns) 61: Performance: 6.642 3.614 61: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (52 ms) 61: [----------] 3 tests from MdrunCanWrite/NptTrajectories (136 ms total) 61: 61: [----------] Global test environment tear-down 61: [==========] 12 tests from 5 test suites ran. (870 ms total) 61: [ PASSED ] 12 tests. 61/87 Test #61: MdrunOutputTests .......................... Passed 0.91 sec test 62 Start 62: MdrunModulesTests 62: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunModulesTests.xml" 62: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 62: Test timeout computed to be: 600 62: [==========] Running 15 tests from 3 test suites. 62: [----------] Global test environment set-up. 62: [----------] 9 tests from DensityFittingTest 62: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct 62: Number of degrees of freedom in T-Coupling group rest is 33.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: 62: Steepest Descents: 62: Tolerance (Fmax) = 1.00000e+01 62: Number of steps = 2 62: 62: Energy minimization reached the maximum number of steps before the forces 62: reached the requested precision Fmax < 10. 62: 62: writing lowest energy coordinates. 62: 62: Steepest Descents did not converge to Fmax < 10 in 3 steps. 62: Potential Energy = -3.85652562592421e+03 62: Maximum force = 4.50998690851897e+03 on atom 3 62: Norm of force = 1.68168494163492e+03 62: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as double precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -38316049 62: 62: Generated 1 of the 1 non-bonded parameter combinations 62: 62: Excluding 1 bonded neighbours molecule type 'Argon' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (194 ms) 62: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation 62: Number of degrees of freedom in T-Coupling group rest is 33.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: 62: Steepest Descents: 62: Tolerance (Fmax) = 1.00000e+01 62: Number of steps = 2 62: 62: Energy minimization reached the maximum number of steps before the forces 62: reached the requested precision Fmax < 10. 62: 62: writing lowest energy coordinates. 62: 62: Steepest Descents did not converge to Fmax < 10 in 3 steps. 62: Potential Energy = -9.82077921283928e+03 62: Maximum force = 7.39548334240075e+03 on atom 2 62: Norm of force = 2.78250777177324e+03 62: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.edr as double precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -395525 62: 62: Generated 1 of the 1 non-bonded parameter combinations 62: 62: Excluding 1 bonded neighbours molecule type 'Argon' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation (81 ms) 62: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff 62: 62: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 62: [ OK ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff (11 ms) 62: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix 62: Number of degrees of freedom in T-Coupling group rest is 33.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 62: Overriding nsteps with value passed on the command line: 4 steps 62: 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: 62: Steepest Descents: 62: Tolerance (Fmax) = 1.00000e+01 62: Number of steps = 4 62: 62: Energy minimization reached the maximum number of steps before the forces 62: reached the requested precision Fmax < 10. 62: 62: writing lowest energy coordinates. 62: 62: Steepest Descents did not converge to Fmax < 10 in 5 steps. 62: Potential Energy = -1.09549987768583e+04 62: Maximum force = 7.47247842297766e+03 on atom 2 62: Norm of force = 2.77579925913607e+03 62: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.edr as double precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Setting the LD random seed to -102047747 62: 62: Generated 1 of the 1 non-bonded parameter combinations 62: 62: Excluding 1 bonded neighbours molecule type 'Argon' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix (60 ms) 62: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff 62: 62: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 62: [ OK ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff (11 ms) 62: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix 62: Number of degrees of freedom in T-Coupling group rest is 33.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: 62: Steepest Descents: 62: Tolerance (Fmax) = 1.00000e+01 62: Number of steps = 2 62: 62: Energy minimization reached the maximum number of steps before the forces 62: reached the requested precision Fmax < 10. 62: 62: writing lowest energy coordinates. 62: 62: Steepest Descents did not converge to Fmax < 10 in 3 steps. 62: Potential Energy = -3.85652562592421e+03 62: Maximum force = 4.50998690851897e+03 on atom 3 62: Norm of force = 1.68168494163492e+03 62: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.edr as double precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to 2141118207 62: 62: Generated 1 of the 1 non-bonded parameter combinations 62: 62: Excluding 1 bonded neighbours molecule type 'Argon' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix (42 ms) 62: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy 62: Number of degrees of freedom in T-Coupling group rest is 33.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: 62: Steepest Descents: 62: Tolerance (Fmax) = 1.00000e+01 62: Number of steps = 2 62: 62: Energy minimization reached the maximum number of steps before the forces 62: reached the requested precision Fmax < 10. 62: 62: writing lowest energy coordinates. 62: 62: Steepest Descents did not converge to Fmax < 10 in 3 steps. 62: Potential Energy = -2.71386626041483e+04 62: Maximum force = 6.78276504921089e+03 on atom 2 62: Norm of force = 1.96088640980697e+03 62: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as double precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to 2028920765 62: 62: Generated 1 of the 1 non-bonded parameter combinations 62: 62: Excluding 1 bonded neighbours molecule type 'Argon' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (42 ms) 62: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch 62: 62: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 62: Setting the LD random seed to 1040121790 62: 62: Generated 1 of the 1 non-bonded parameter combinations 62: 62: Excluding 1 bonded neighbours molecule type 'Argon' 62: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (11 ms) 62: [ RUN ] DensityFittingTest.CheckpointWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstenergy (2) 62: 62: Number of degrees of freedom in T-Coupling group rest is 33.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 62: NVE simulation: will use the initial temperature of 68.810 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'Argon' 62: 2 steps, 0.0 ps. 62: Setting the LD random seed to -201736246 62: 62: Generated 1 of the 1 non-bonded parameter combinations 62: 62: Excluding 1 bonded neighbours molecule type 'Argon' 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.063 0.031 199.7 62: (ns/day) (hour/ns) 62: Performance: 8.234 2.915 62: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 62: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps 62: Can not increase nstlist because an NVE ensemble is used 62: 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'Argon' 62: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps). 62: 62: Writing final coordinates. 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.045 0.023 199.6 62: (ns/day) (hour/ns) 62: Performance: 19.129 1.255 62: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as double precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (75 ms) 62: [----------] 9 tests from DensityFittingTest (532 ms total) 62: 62: [----------] 4 tests from MimicTest 62: [ RUN ] MimicTest.OneQuantumMol 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 3 NOTEs 62: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/4water.gro' 62: 62: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: 62: NOTE: 18 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.000 0.000 182.4 62: (ns/day) (hour/ns) 62: Performance: 491.040 0.049 62: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file 62: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 1325258495 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] MimicTest.OneQuantumMol (28 ms) 62: [ RUN ] MimicTest.AllQuantumMol 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 3 NOTEs 62: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/4water.gro' 62: 62: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: 62: NOTE: 17 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.000 0.000 183.0 62: (ns/day) (hour/ns) 62: Performance: 481.259 0.050 62: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file 62: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -3410313 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] MimicTest.AllQuantumMol (29 ms) 62: [ RUN ] MimicTest.TwoQuantumMol 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 3 NOTEs 62: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/4water.gro' 62: 62: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.001 0.000 190.1 62: (ns/day) (hour/ns) 62: Performance: 250.268 0.096 62: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file 62: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -9734035 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] MimicTest.TwoQuantumMol (46 ms) 62: [ RUN ] MimicTest.BondCuts 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: Number of degrees of freedom in T-Coupling group rest is 66.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 62: NVE simulation: will use the initial temperature of 300.368 K for 62: determining the Verlet buffer size 62: 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 3 NOTEs 62: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/ala.gro' 62: 62: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: 62: NOTE: 15 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.001 0.000 189.8 62: (ns/day) (hour/ns) 62: Performance: 299.000 0.080 62: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file 62: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 2144944063 62: 62: Generated 2211 of the 2211 non-bonded parameter combinations 62: 62: Generated 2211 of the 2211 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] MimicTest.BondCuts (44 ms) 62: [----------] 4 tests from MimicTest (152 ms total) 62: 62: [----------] 2 tests from WithIntegrator/ImdTest 62: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0 62: Generating 1-4 interactions: fudge = 1 62: 62: NOTE 1 [file glycine_vacuo.top, line 12]: 62: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an 62: estimated oscillational period of 1.0e-02 ps, which is less than 10 times 62: the time step of 2.0e-03 ps. 62: Maybe you forgot to change the constraints mdp option. 62: 62: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 62: Number of degrees of freedom in T-Coupling group System is 27.00 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 2 NOTEs 62: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 62: Changing nstlist from 10 to 25, rlist from 1.077 to 1.248 62: 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: 62: IMD: Enabled. This simulation will accept incoming IMD connections. 62: IMD: Pulling from IMD remote is enabled (-imdpull). 62: IMD: Setting port for connection requests to 0. 62: IMD: Setting up incoming socket. 62: IMD: Listening for IMD connection on port 44127. 62: IMD: -imdwait not set, starting simulation. 62: starting mdrun 'Glycine' 62: 2 steps, 0.0 ps. 62: Setting the LD random seed to -1082690049 62: 62: Generated 20503 of the 20503 non-bonded parameter combinations 62: 62: Generated 17396 of the 20503 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Glycine' 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.071 nm, buffer size 0.071 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: Core t (s) Wall t (s) (%) 62: Time: 1.070 0.535 200.0 62: (ns/day) (hour/ns) 62: Performance: 0.968 24.782 62: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (731 ms) 62: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 62: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not 62: apply to steep. 62: 62: Generating 1-4 interactions: fudge = 1 62: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 62: Number of degrees of freedom in T-Coupling group System is 27.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 2 NOTEs 62: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: 62: IMD: Enabled. This simulation will accept incoming IMD connections. 62: IMD: Pulling from IMD remote is enabled (-imdpull). 62: IMD: Setting port for connection requests to 0. 62: IMD: Setting up incoming socket. 62: IMD: Listening for IMD connection on port 56081. 62: IMD: -imdwait not set, starting simulation. 62: 62: Steepest Descents: 62: Tolerance (Fmax) = 1.00000e+01 62: Number of steps = 2 62: 62: Energy minimization reached the maximum number of steps before the forces 62: reached the requested precision Fmax < 10. 62: 62: writing lowest energy coordinates. 62: 62: Steepest Descents did not converge to Fmax < 10 in 3 steps. 62: Potential Energy = 1.19770464690297e+03 62: Maximum force = 1.77948604657896e+04 on atom 9 62: Norm of force = 7.87328617833980e+03 62: Setting the LD random seed to -159507006 62: 62: Generated 20503 of the 20503 non-bonded parameter combinations 62: 62: Generated 17396 of the 20503 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Glycine' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (210 ms) 62: [----------] 2 tests from WithIntegrator/ImdTest (942 ms total) 62: 62: [----------] Global test environment tear-down 62: [==========] 15 tests from 3 test suites ran. (1748 ms total) 62: [ PASSED ] 15 tests. 62/87 Test #62: MdrunModulesTests ......................... Passed 1.83 sec test 63 Start 63: MdrunIOTests 63: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunIOTests.xml" 63: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 63: Test timeout computed to be: 600 63: [==========] Running 76 tests from 13 test suites. 63: [----------] Global test environment set-up. 63: [----------] 9 tests from GromppTest 63: [ RUN ] GromppTest.EmptyMdpFileWorks 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 63: NVE simulation: will use the initial temperature of 1046.791 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Setting the LD random seed to -554712969 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] GromppTest.EmptyMdpFileWorks (3 ms) 63: [ RUN ] GromppTest.SimulatedAnnealingWorks 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: Simulated annealing for group rest: Periodic, 4 timepoints 63: Time (ps) Temperature (K) 63: 0.0 298.0 63: 2.0 320.0 63: 4.0 320.0 63: 6.0 298.0 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 63: NVE simulation: will use the initial temperature of 1046.791 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Setting the LD random seed to -6361795 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] GromppTest.SimulatedAnnealingWorks (3 ms) 63: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: Simulated annealing for group Methanol: Single, 3 timepoints 63: Time (ps) Temperature (K) 63: 0.0 298.0 63: 3.0 280.0 63: 6.0- 270.0 63: Simulated annealing for group SOL: Periodic, 4 timepoints 63: Time (ps) Temperature (K) 63: 0.0 298.0 63: 2.0 320.0 63: 4.0 320.0 63: 6.0 298.0 63: Number of degrees of freedom in T-Coupling group Methanol is 7.20 63: Number of degrees of freedom in T-Coupling group SOL is 4.80 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 63: NVE simulation: will use the initial temperature of 1046.791 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Setting the LD random seed to -1191185058 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (2 ms) 63: [ RUN ] GromppTest.DeathTestHandlesNoMaxwarnError 63: Setting the LD random seed to 1607589587 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] GromppTest.DeathTestHandlesNoMaxwarnError (18 ms) 63: [ RUN ] GromppTest.HandlesMaxwarn 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: 63: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 63: The Berendsen thermostat does not generate the correct kinetic energy 63: distribution, and should not be used for new production simulations (in 63: our opinion). We would recommend the V-rescale thermostat. 63: 63: Number of degrees of freedom in T-Coupling group System is 12.00 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 2 NOTEs 63: 63: There was 1 WARNING 63: Setting the LD random seed to 1810857838 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] GromppTest.HandlesMaxwarn (2 ms) 63: [ RUN ] GromppTest.MaxwarnShouldBePositive 63: [ OK ] GromppTest.MaxwarnShouldBePositive (0 ms) 63: [ RUN ] GromppTest.ValidTransformationCoord 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: Pull group 1 'SOL' has 3 atoms 63: Pull group 2 'Methanol' has 3 atoms 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 63: NVE simulation: will use the initial temperature of 1046.791 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: Pull group natoms pbc atom distance at start reference at t=0 63: 1 3 5 63: 2 3 2 0.613 nm 0.000 nm 63: 1 3 5 63: 2 3 2 0.613 nm 0.000 nm 63: 63: There were 3 NOTEs 63: Setting the LD random seed to -352463361 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] GromppTest.ValidTransformationCoord (13 ms) 63: [ RUN ] GromppTest.InvalidTransformationCoord 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: Pull group 1 'SOL' has 3 atoms 63: Pull group 2 'Methanol' has 3 atoms 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 63: NVE simulation: will use the initial temperature of 1046.791 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: Pull group natoms pbc atom distance at start reference at t=0 63: 1 3 5 63: 2 3 2 0.613 nm 0.000 nm 63: 1 3 5 63: 2 3 2 Setting the LD random seed to -8687617 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: [ OK ] GromppTest.InvalidTransformationCoord (10 ms) 63: [ RUN ] GromppTest.RejectCRescaleAndAnisotropic 63: Setting the LD random seed to -19398657 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: [ OK ] GromppTest.RejectCRescaleAndAnisotropic (12 ms) 63: [----------] 9 tests from GromppTest (68 ms total) 63: 63: [----------] 6 tests from MdrunTerminationTest 63: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There was 1 NOTE 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 2 steps, 0.0 ps. 63: Setting the LD random seed to -33809725 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.842 0.421 200.0 63: (ns/day) (hour/ns) 63: Performance: 0.616 38.978 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Setting nsteps to 4 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 63: Input file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 2 63: Runtime for the run 0.002 ps 63: Run end step 2 63: Run end time 0.002 ps 63: 63: 63: Output file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 4 63: Runtime for the run 0.004 ps 63: Run end step 4 63: Run end time 0.004 ps 63: 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.186 0.093 199.9 63: (ns/day) (hour/ns) 63: Performance: 2.790 8.603 63: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (532 ms) 63: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There was 1 NOTE 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 10 to 1, rlist from 1.035 to 1 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 100 steps, 0.1 ps. 63: 63: Step 10: Run time exceeded 0.000 hours, will terminate the run within 200 steps 63: Setting the LD random seed to -37814913 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 12 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.284 0.142 199.9 63: (ns/day) (hour/ns) 63: Performance: 61.385 0.391 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Setting nsteps to 102 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). 63: Input file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 100 63: Runtime for the run 0.1 ps 63: Run end step 100 63: Run end time 0.1 ps 63: 63: 63: Output file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 102 63: Runtime for the run 0.102 ps 63: Run end step 102 63: Run end time 0.102 ps 63: 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.045 0.022 199.7 63: (ns/day) (hour/ns) 63: Performance: 11.574 2.074 63: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (180 ms) 63: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There was 1 NOTE 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 2 steps, 0.0 ps. 63: Setting the LD random seed to -1073807393 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.030 0.015 199.6 63: (ns/day) (hour/ns) 63: Performance: 17.069 1.406 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Setting nsteps to 4 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 63: Input file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 2 63: Runtime for the run 0.002 ps 63: Run end step 2 63: Run end time 0.002 ps 63: 63: 63: Output file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 4 63: Runtime for the run 0.004 ps 63: Run end step 4 63: Run end time 0.004 ps 63: 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.019 0.009 199.6 63: (ns/day) (hour/ns) 63: Performance: 27.559 0.871 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Setting nsteps to 6 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps). 63: Input file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 4 63: Runtime for the run 0.004 ps 63: Run end step 4 63: Run end time 0.004 ps 63: 63: 63: Output file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 6 63: Runtime for the run 0.006 ps 63: Run end step 6 63: Run end time 0.006 ps 63: 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.038 0.019 199.6 63: (ns/day) (hour/ns) 63: Performance: 13.629 1.761 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Setting nsteps to 8 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). 63: Input file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 6 63: Runtime for the run 0.006 ps 63: Run end step 6 63: Run end time 0.006 ps 63: 63: 63: Output file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 8 63: Runtime for the run 0.008 ps 63: Run end step 8 63: Run end time 0.008 ps 63: 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.023 0.011 199.6 63: (ns/day) (hour/ns) 63: Performance: 22.942 1.046 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: NOTE: 22 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.000 0.000 168.4 63: (ns/day) (hour/ns) 63: Performance: 922.107 0.026 63: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (81 ms) 63: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There was 1 NOTE 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 2 steps, 0.0 ps. 63: Setting the LD random seed to -1417937410 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.024 0.012 199.5 63: (ns/day) (hour/ns) 63: Performance: 21.147 1.135 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Setting nsteps to 4 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 4 steps, 0.0 ps. 63: Input file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 2 63: Runtime for the run 0.002 ps 63: Run end step 2 63: Run end time 0.002 ps 63: 63: 63: Output file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 4 63: Runtime for the run 0.004 ps 63: Run end step 4 63: Run end time 0.004 ps 63: 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.084 0.042 199.7 63: (ns/day) (hour/ns) 63: Performance: 10.315 2.327 63: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (69 ms) 63: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There was 1 NOTE 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 2 steps, 0.0 ps. 63: Setting the LD random seed to -310380814 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.111 0.056 199.8 63: (ns/day) (hour/ns) 63: Performance: 4.659 5.151 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Setting nsteps to 4 63: Input file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 2 63: Runtime for the run 0.002 ps 63: Run end step 2 63: Run end time 0.002 ps 63: 63: 63: Output file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 4 63: Runtime for the run 0.004 ps 63: Run end step 4 63: Run end time 0.004 ps 63: 63: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (80 ms) 63: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There was 1 NOTE 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 2 steps, 0.0 ps. 63: Setting the LD random seed to -1246925825 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 11 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.584 0.292 200.0 63: (ns/day) (hour/ns) 63: Performance: 0.887 27.048 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Setting nsteps to 4 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 63: Input file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 2 63: Runtime for the run 0.002 ps 63: Run end step 2 63: Run end time 0.002 ps 63: 63: 63: Output file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 4 63: Runtime for the run 0.004 ps 63: Run end step 4 63: Run end time 0.004 ps 63: 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.024 0.012 199.4 63: (ns/day) (hour/ns) 63: Performance: 21.569 1.113 63: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (412 ms) 63: [----------] 6 tests from MdrunTerminationTest (1356 ms total) 63: 63: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks 63: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.123 0.061 199.8 63: (ns/day) (hour/ns) 63: Performance: 23.944 1.002 63: trr version: GMX_trn_file (double precision) 63: 63: 63: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (84 ms) 63: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.343 0.172 200.0 63: (ns/day) (hour/ns) 63: Performance: 8.564 2.802 63: 63: 63: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (185 ms) 63: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (270 ms total) 63: 63: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.023 0.012 199.2 63: (ns/day) (hour/ns) 63: Performance: 125.335 0.191 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.042 0.021 199.5 63: (ns/day) (hour/ns) 63: Performance: 36.955 0.649 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.064 0.032 199.6 63: (ns/day) (hour/ns) 63: Performance: 24.366 0.985 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (92 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.083 0.042 196.9 63: (ns/day) (hour/ns) 63: Performance: 34.913 0.687 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.035 0.017 199.4 63: (ns/day) (hour/ns) 63: Performance: 44.769 0.536 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.224 0.112 199.9 63: (ns/day) (hour/ns) 63: Performance: 6.945 3.456 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (203 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 17 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.095 0.047 199.8 63: (ns/day) (hour/ns) 63: Performance: 30.959 0.775 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.051 0.025 199.6 63: (ns/day) (hour/ns) 63: Performance: 30.709 0.782 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 24 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.526 0.263 200.0 63: (ns/day) (hour/ns) 63: Performance: 2.955 8.121 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (418 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.041 0.021 199.8 63: (ns/day) (hour/ns) 63: Performance: 71.641 0.335 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.061 0.031 199.6 63: (ns/day) (hour/ns) 63: Performance: 25.282 0.949 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.070 0.035 199.4 63: (ns/day) (hour/ns) 63: Performance: 22.258 1.078 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (105 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.040 0.020 199.7 63: (ns/day) (hour/ns) 63: Performance: 73.310 0.327 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.047 0.023 199.6 63: (ns/day) (hour/ns) 63: Performance: 33.296 0.721 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.163 0.081 199.9 63: (ns/day) (hour/ns) 63: Performance: 9.548 2.514 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (158 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.709 to 0.735 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.024 0.012 199.5 63: (ns/day) (hour/ns) 63: Performance: 124.711 0.192 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.709 to 0.735 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.022 0.011 199.6 63: (ns/day) (hour/ns) 63: Performance: 69.860 0.344 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.709 to 0.735 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.046 0.023 199.8 63: (ns/day) (hour/ns) 63: Performance: 34.121 0.703 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (75 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.069 0.035 199.8 63: (ns/day) (hour/ns) 63: Performance: 42.251 0.568 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.065 0.033 199.7 63: (ns/day) (hour/ns) 63: Performance: 23.734 1.011 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.083 0.044 191.3 63: (ns/day) (hour/ns) 63: Performance: 17.832 1.346 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (131 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.032 0.016 199.7 63: (ns/day) (hour/ns) 63: Performance: 92.118 0.261 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.042 0.021 199.2 63: (ns/day) (hour/ns) 63: Performance: 36.585 0.656 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.087 0.043 199.7 63: (ns/day) (hour/ns) 63: Performance: 17.909 1.340 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (144 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.033 0.017 199.4 63: (ns/day) (hour/ns) 63: Performance: 88.544 0.271 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.054 0.027 199.6 63: (ns/day) (hour/ns) 63: Performance: 28.603 0.839 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.042 0.021 199.5 63: (ns/day) (hour/ns) 63: Performance: 37.296 0.644 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (99 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.159 0.080 199.8 63: (ns/day) (hour/ns) 63: Performance: 18.409 1.304 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: NOTE: 10 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.152 0.076 199.8 63: (ns/day) (hour/ns) 63: Performance: 10.254 2.340 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.043 0.022 199.6 63: (ns/day) (hour/ns) 63: Performance: 35.692 0.672 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (212 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.032 0.016 199.5 63: (ns/day) (hour/ns) 63: Performance: 91.469 0.262 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.032 0.016 199.6 63: (ns/day) (hour/ns) 63: Performance: 48.189 0.498 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.193 0.096 199.9 63: (ns/day) (hour/ns) 63: Performance: 8.060 2.978 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (152 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.032 0.016 199.5 63: (ns/day) (hour/ns) 63: Performance: 91.325 0.263 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: NOTE: 15 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.068 0.034 199.7 63: (ns/day) (hour/ns) 63: Performance: 22.971 1.045 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.094 0.047 199.6 63: (ns/day) (hour/ns) 63: Performance: 16.521 1.453 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (124 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.031 0.016 199.5 63: (ns/day) (hour/ns) 63: Performance: 94.153 0.255 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: NOTE: 16 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.392 0.196 199.9 63: (ns/day) (hour/ns) 63: Performance: 3.965 6.052 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.031 0.016 199.3 63: (ns/day) (hour/ns) 63: Performance: 49.408 0.486 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 (327 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.73 to 0.814 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.119 0.060 199.8 63: (ns/day) (hour/ns) 63: Performance: 24.631 0.974 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.73 to 0.814 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.150 0.075 199.7 63: (ns/day) (hour/ns) 63: Performance: 10.321 2.325 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.73 to 0.814 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.064 0.032 199.6 63: (ns/day) (hour/ns) 63: Performance: 24.241 0.990 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 (252 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.039 0.019 199.6 63: (ns/day) (hour/ns) 63: Performance: 75.945 0.316 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.035 0.018 199.6 63: (ns/day) (hour/ns) 63: Performance: 43.899 0.547 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.068 0.034 199.5 63: (ns/day) (hour/ns) 63: Performance: 22.838 1.051 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 (97 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 25, rlist from 0.753 to 0.895 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.036 0.018 199.6 63: (ns/day) (hour/ns) 63: Performance: 82.462 0.291 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 25, rlist from 0.753 to 0.895 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.061 0.030 199.7 63: (ns/day) (hour/ns) 63: Performance: 25.584 0.938 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 25, rlist from 0.753 to 0.895 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.056 0.028 199.5 63: (ns/day) (hour/ns) 63: Performance: 27.681 0.867 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 (102 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 63: NVE simulation: will use the initial temperature of 456.887 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 6 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 63: NVE simulation: will use the initial temperature of 456.887 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 6 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps. 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 1.005 0.503 200.0 63: (ns/day) (hour/ns) 63: Performance: 2.921 8.216 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.036 0.018 199.4 63: (ns/day) (hour/ns) 63: Performance: 43.100 0.557 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.029 0.015 199.3 63: (ns/day) (hour/ns) 63: Performance: 53.602 0.448 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 (975 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 63: NVE simulation: will use the initial temperature of 456.887 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 6 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 63: NVE simulation: will use the initial temperature of 456.887 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 6 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps. 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.037 0.019 199.3 63: (ns/day) (hour/ns) 63: Performance: 78.699 0.305 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.055 0.027 199.6 63: (ns/day) (hour/ns) 63: Performance: 28.372 0.846 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.029 0.015 198.6 63: (ns/day) (hour/ns) 63: Performance: 53.611 0.448 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 (108 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 63: NVE simulation: will use the initial temperature of 456.887 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 6 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 63: NVE simulation: will use the initial temperature of 456.887 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 6 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps. 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.031 0.015 199.3 63: (ns/day) (hour/ns) 63: Performance: 95.003 0.253 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.032 0.016 199.4 63: (ns/day) (hour/ns) 63: Performance: 49.089 0.489 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.040 0.020 199.4 63: (ns/day) (hour/ns) 63: Performance: 38.315 0.626 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 (109 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 63: NVE simulation: will use the initial temperature of 456.887 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 6 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 63: NVE simulation: will use the initial temperature of 456.887 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 6 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps. 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.032 0.016 199.4 63: (ns/day) (hour/ns) 63: Performance: 92.143 0.260 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.037 0.019 199.4 63: (ns/day) (hour/ns) 63: Performance: 41.763 0.575 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.032 0.016 199.5 63: (ns/day) (hour/ns) 63: Performance: 48.416 0.496 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 (187 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 5 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 5 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps. 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.064 0.032 199.7 63: (ns/day) (hour/ns) 63: Performance: 46.048 0.521 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.039 0.020 199.5 63: (ns/day) (hour/ns) 63: Performance: 39.272 0.611 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.057 0.029 199.6 63: (ns/day) (hour/ns) 63: Performance: 27.184 0.883 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 (215 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 5 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 5 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 80, rlist from 0.743 to 0.847 63: 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps. 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.059 0.030 199.7 63: (ns/day) (hour/ns) 63: Performance: 49.349 0.486 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 80, rlist from 0.743 to 0.847 63: 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.024 0.012 199.2 63: (ns/day) (hour/ns) 63: Performance: 63.921 0.375 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 80, rlist from 0.743 to 0.846 63: 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.063 0.032 199.7 63: (ns/day) (hour/ns) 63: Performance: 24.506 0.979 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 (508 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 5 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 5 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps. 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.094 0.047 199.8 63: (ns/day) (hour/ns) 63: Performance: 31.353 0.765 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.050 0.025 199.5 63: (ns/day) (hour/ns) 63: Performance: 31.307 0.767 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 48 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.165 0.083 199.9 63: (ns/day) (hour/ns) 63: Performance: 9.394 2.555 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 (334 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 5 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 5 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 25, rlist from 0.725 to 0.797 63: 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps. 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.030 0.015 199.5 63: (ns/day) (hour/ns) 63: Performance: 97.649 0.246 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 25, rlist from 0.725 to 0.797 63: 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.031 0.016 199.5 63: (ns/day) (hour/ns) 63: Performance: 50.144 0.479 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 25, rlist from 0.725 to 0.797 63: 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.144 0.072 199.8 63: (ns/day) (hour/ns) 63: Performance: 10.780 2.226 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 (222 ms) 63: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (5361 ms total) 63: 63: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact 63: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 293.480 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 293.480 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps. 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.096 0.048 199.6 63: (ns/day) (hour/ns) 63: Performance: 30.627 0.784 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.058 0.029 199.3 63: (ns/day) (hour/ns) 63: Performance: 26.844 0.894 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 32 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.248 0.124 199.9 63: (ns/day) (hour/ns) 63: Performance: 6.268 3.829 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (316 ms) 63: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 293.480 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 293.480 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps. 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 293.48 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 293.48 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 31 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.260 0.130 199.9 63: (ns/day) (hour/ns) 63: Performance: 11.287 2.126 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.096 0.048 199.6 63: (ns/day) (hour/ns) 63: Performance: 16.130 1.488 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.105 0.053 199.7 63: (ns/day) (hour/ns) 63: Performance: 14.749 1.627 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (383 ms) 63: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: NVE simulation: will use the initial temperature of 293.480 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: NVE simulation: will use the initial temperature of 293.480 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps. 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 24 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.136 0.068 199.9 63: (ns/day) (hour/ns) 63: Performance: 21.550 1.114 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.075 0.038 199.8 63: (ns/day) (hour/ns) 63: Performance: 20.623 1.164 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.102 0.051 199.5 63: (ns/day) (hour/ns) 63: Performance: 15.192 1.580 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (237 ms) 63: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: NVE simulation: will use the initial temperature of 293.480 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: NVE simulation: will use the initial temperature of 293.480 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps. 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 293.48 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 293.48 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 31 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.255 0.128 199.9 63: (ns/day) (hour/ns) 63: Performance: 11.502 2.087 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.101 0.050 199.8 63: (ns/day) (hour/ns) 63: Performance: 15.407 1.558 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.107 0.054 199.7 63: (ns/day) (hour/ns) 63: Performance: 14.510 1.654 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (283 ms) 63: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps. 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.053 0.027 199.4 63: (ns/day) (hour/ns) 63: Performance: 54.840 0.438 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.052 0.026 198.9 63: (ns/day) (hour/ns) 63: Performance: 29.912 0.802 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.116 0.058 199.8 63: (ns/day) (hour/ns) 63: Performance: 13.428 1.787 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (179 ms) 63: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.729 to 0.809 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps. 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.047 0.023 199.6 63: (ns/day) (hour/ns) 63: Performance: 62.514 0.384 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.729 to 0.809 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.063 0.032 199.4 63: (ns/day) (hour/ns) 63: Performance: 24.540 0.978 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.729 to 0.809 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.037 0.018 199.4 63: (ns/day) (hour/ns) 63: Performance: 42.444 0.565 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (207 ms) 63: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps. 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.067 0.034 199.4 63: (ns/day) (hour/ns) 63: Performance: 43.585 0.551 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.231 0.116 199.7 63: (ns/day) (hour/ns) 63: Performance: 6.732 3.565 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 1.137 0.568 200.0 63: (ns/day) (hour/ns) 63: Performance: 1.368 17.545 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (881 ms) 63: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 20, rlist from 0.751 to 0.848 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps. 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.043 0.022 197.7 63: (ns/day) (hour/ns) 63: Performance: 67.522 0.355 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 20, rlist from 0.751 to 0.848 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.043 0.021 199.1 63: (ns/day) (hour/ns) 63: Performance: 36.372 0.660 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 20, rlist from 0.751 to 0.848 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.047 0.024 199.5 63: (ns/day) (hour/ns) 63: Performance: 32.802 0.732 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (150 ms) 63: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (2640 ms total) 63: 63: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact 63: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 47 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.152 0.076 199.8 63: (ns/day) (hour/ns) 63: Performance: 19.334 1.241 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.026 0.013 199.4 63: (ns/day) (hour/ns) 63: Performance: 58.720 0.409 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 11 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 1.145 0.573 200.0 63: (ns/day) (hour/ns) 63: Performance: 1.358 17.671 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (785 ms) 63: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 19 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.336 0.168 199.9 63: (ns/day) (hour/ns) 63: Performance: 8.738 2.746 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.032 0.016 199.6 63: (ns/day) (hour/ns) 63: Performance: 47.898 0.501 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.028 0.014 199.6 63: (ns/day) (hour/ns) 63: Performance: 54.975 0.437 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (274 ms) 63: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 63: 1 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 63: 1 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 3.737 1.869 200.0 63: (ns/day) (hour/ns) 63: Performance: 0.786 30.533 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 1.287 0.643 200.0 63: (ns/day) (hour/ns) 63: Performance: 1.208 19.861 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.050 0.025 199.8 63: (ns/day) (hour/ns) 63: Performance: 31.186 0.770 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (2636 ms) 63: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 63: 1 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 63: 1 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.097 0.049 199.6 63: (ns/day) (hour/ns) 63: Performance: 30.202 0.795 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.047 0.024 199.6 63: (ns/day) (hour/ns) 63: Performance: 32.846 0.731 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 50 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.096 0.048 199.8 63: (ns/day) (hour/ns) 63: Performance: 16.190 1.482 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (168 ms) 63: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.059 0.030 199.5 63: (ns/day) (hour/ns) 63: Performance: 49.294 0.487 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.099 0.049 199.7 63: (ns/day) (hour/ns) 63: Performance: 15.761 1.523 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.078 0.039 199.5 63: (ns/day) (hour/ns) 63: Performance: 19.825 1.211 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (140 ms) 63: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.066 0.033 199.7 63: (ns/day) (hour/ns) 63: Performance: 44.697 0.537 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.069 0.035 199.8 63: (ns/day) (hour/ns) 63: Performance: 22.470 1.068 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.265 0.133 199.8 63: (ns/day) (hour/ns) 63: Performance: 5.861 4.095 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (267 ms) 63: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.056 0.028 199.5 63: (ns/day) (hour/ns) 63: Performance: 52.081 0.461 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.064 0.032 199.6 63: (ns/day) (hour/ns) 63: Performance: 24.303 0.988 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 37 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.153 0.077 199.8 63: (ns/day) (hour/ns) 63: Performance: 10.156 2.363 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (180 ms) 63: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 1.017 0.508 200.0 63: (ns/day) (hour/ns) 63: Performance: 2.889 8.307 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.125 0.063 199.8 63: (ns/day) (hour/ns) 63: Performance: 12.396 1.936 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.058 0.029 199.4 63: (ns/day) (hour/ns) 63: Performance: 26.681 0.900 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (643 ms) 63: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact (5097 ms total) 63: 63: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact 63: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.041 0.020 199.4 63: (ns/day) (hour/ns) 63: Performance: 71.656 0.335 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.049 0.025 199.2 63: (ns/day) (hour/ns) 63: Performance: 31.409 0.764 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.129 0.065 199.8 63: (ns/day) (hour/ns) 63: Performance: 11.996 2.001 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (136 ms) 63: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.055 0.028 199.6 63: (ns/day) (hour/ns) 63: Performance: 52.875 0.454 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: NOTE: 39 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.125 0.062 199.8 63: (ns/day) (hour/ns) 63: Performance: 12.471 1.924 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.094 0.047 199.7 63: (ns/day) (hour/ns) 63: Performance: 16.603 1.446 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (215 ms) 63: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact (354 ms total) 63: 63: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact 63: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 22 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.444 0.222 199.9 63: (ns/day) (hour/ns) 63: Performance: 6.621 3.625 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.034 0.017 199.5 63: (ns/day) (hour/ns) 63: Performance: 45.698 0.525 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.046 0.023 199.5 63: (ns/day) (hour/ns) 63: Performance: 33.387 0.719 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (372 ms) 63: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.048 0.024 199.7 63: (ns/day) (hour/ns) 63: Performance: 60.776 0.395 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.029 0.015 199.3 63: (ns/day) (hour/ns) 63: Performance: 52.979 0.453 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.038 0.019 199.3 63: (ns/day) (hour/ns) 63: Performance: 40.435 0.594 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (94 ms) 63: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 63: 1 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 63: 1 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 30 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.081 0.040 199.6 63: (ns/day) (hour/ns) 63: Performance: 36.304 0.661 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.069 0.034 199.8 63: (ns/day) (hour/ns) 63: Performance: 22.585 1.063 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.077 0.039 199.8 63: (ns/day) (hour/ns) 63: Performance: 20.124 1.193 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (159 ms) 63: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 63: 1 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 63: 1 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.169 0.085 199.8 63: (ns/day) (hour/ns) 63: Performance: 17.320 1.386 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 1.999 1.000 200.0 63: (ns/day) (hour/ns) 63: Performance: 0.778 30.857 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.024 0.012 199.5 63: (ns/day) (hour/ns) 63: Performance: 64.287 0.373 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (1180 ms) 63: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.051 0.025 199.7 63: (ns/day) (hour/ns) 63: Performance: 57.600 0.417 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: NOTE: 20 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.481 0.241 200.0 63: (ns/day) (hour/ns) 63: Performance: 3.232 7.426 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 46 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.210 0.105 199.9 63: (ns/day) (hour/ns) 63: Performance: 7.399 3.244 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (433 ms) 63: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.059 0.029 199.8 63: (ns/day) (hour/ns) 63: Performance: 49.811 0.482 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.308 0.154 199.9 63: (ns/day) (hour/ns) 63: Performance: 5.055 4.748 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 2.320 1.160 200.0 63: (ns/day) (hour/ns) 63: Performance: 0.670 35.803 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (1360 ms) 63: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 63: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (0 ms) 63: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.068 0.034 199.8 63: (ns/day) (hour/ns) 63: Performance: 43.329 0.554 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.051 0.025 199.7 63: (ns/day) (hour/ns) 63: Performance: 30.631 0.784 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 29 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.056 0.028 199.7 63: (ns/day) (hour/ns) 63: Performance: 27.829 0.862 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (104 ms) 63: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact (3709 ms total) 63: 63: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact 63: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 31 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.234 0.117 199.9 63: (ns/day) (hour/ns) 63: Performance: 12.560 1.911 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: NOTE: 22 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.110 0.055 199.8 63: (ns/day) (hour/ns) 63: Performance: 14.091 1.703 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.068 0.034 199.7 63: (ns/day) (hour/ns) 63: Performance: 22.791 1.053 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (260 ms) 63: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (260 ms total) 63: 63: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact 63: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Pull group 1 'FirstWaterMolecule' has 3 atoms 63: Pull group 2 'SecondWaterMolecule' has 3 atoms 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: Pull group natoms pbc atom distance at start reference at t=0 63: 1 3 2 63: 2 3 5 1.112 nm 1.000 nm 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Pull group 1 'FirstWaterMolecule' has 3 atoms 63: Pull group 2 'SecondWaterMolecule' has 3 atoms 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: Pull group natoms pbc atom distance at start reference at t=0 63: 1 3 2 63: 2 3 5 1.112 nm 1.000 nm 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.059 0.029 199.2 63: (ns/day) (hour/ns) 63: Performance: 49.916 0.481 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.088 0.044 199.8 63: (ns/day) (hour/ns) 63: Performance: 17.608 1.363 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.052 0.026 199.2 63: (ns/day) (hour/ns) 63: Performance: 29.852 0.804 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (149 ms) 63: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Pull group 1 'FirstWaterMolecule' has 3 atoms 63: Pull group 2 'SecondWaterMolecule' has 3 atoms 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: Pull group natoms pbc atom distance at start reference at t=0 63: 1 3 2 63: 2 3 5 1.112 nm 1.000 nm 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Pull group 1 'FirstWaterMolecule' has 3 atoms 63: Pull group 2 'SecondWaterMolecule' has 3 atoms 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: Pull group natoms pbc atom distance at start reference at t=0 63: 1 3 2 63: 2 3 5 1.112 nm 1.000 nm 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.096 0.048 199.6 63: (ns/day) (hour/ns) 63: Performance: 30.565 0.785 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.080 0.040 199.7 63: (ns/day) (hour/ns) 63: Performance: 19.389 1.238 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.089 0.045 199.6 63: (ns/day) (hour/ns) 63: Performance: 17.454 1.375 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (165 ms) 63: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact (314 ms total) 63: 63: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact 63: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 63: Setting the AWH bias MC random seed to 2092881917 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Pull group 1 'C_&_r_1' has 1 atoms 63: Pull group 2 'N_&_r_2' has 1 atoms 63: Pull group 3 'CA' has 1 atoms 63: Pull group 4 'C_&_r_2' has 1 atoms 63: Pull group 5 'N_&_r_3' has 1 atoms 63: Number of degrees of freedom in T-Coupling group System is 51.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: Pull group natoms pbc atom distance at start reference at t=0 63: 1 1 0 63: 2 1 0 179.098 deg 0.000 deg 63: 2 1 0 63: 3 1 0 158.667 deg 0.000 deg 63: 63: There were 3 NOTEs 63: Setting the AWH bias MC random seed to -1624273033 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Pull group 1 'C_&_r_1' has 1 atoms 63: Pull group 2 'N_&_r_2' has 1 atoms 63: Pull group 3 'CA' has 1 atoms 63: Pull group 4 'C_&_r_2' has 1 atoms 63: Pull group 5 'N_&_r_3' has 1 atoms 63: Number of degrees of freedom in T-Coupling group System is 51.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: Pull group natoms pbc atom distance at start reference at t=0 63: 1 1 0 63: 2 1 0 179.098 deg 0.000 deg 63: 2 1 0 63: 3 1 0 158.667 deg 0.000 deg 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine-dipeptide' 63: 16 steps, 0.0 ps. 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.094 0.047 199.5 63: (ns/day) (hour/ns) 63: Performance: 31.170 0.770 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine-dipeptide' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.062 0.031 199.3 63: (ns/day) (hour/ns) 63: Performance: 24.884 0.964 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine-dipeptide' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 1.140 0.570 200.0 63: (ns/day) (hour/ns) 63: Performance: 1.364 17.596 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (738 ms) 63: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 63: Setting the AWH bias MC random seed to 2025696839 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Pull group 1 'C_&_r_1' has 1 atoms 63: Pull group 2 'N_&_r_2' has 1 atoms 63: Pull group 3 'CA' has 1 atoms 63: Pull group 4 'C_&_r_2' has 1 atoms 63: Pull group 5 'N_&_r_3' has 1 atoms 63: Number of degrees of freedom in T-Coupling group System is 51.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: Pull group natoms pbc atom distance at start reference at t=0 63: 1 1 0 63: 2 1 0 179.098 deg 0.000 deg 63: 2 1 0 63: 3 1 0 158.667 deg 0.000 deg 63: 63: There were 3 NOTEs 63: Setting the AWH bias MC random seed to -348674 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Pull group 1 'C_&_r_1' has 1 atoms 63: Pull group 2 'N_&_r_2' has 1 atoms 63: Pull group 3 'CA' has 1 atoms 63: Pull group 4 'C_&_r_2' has 1 atoms 63: Pull group 5 'N_&_r_3' has 1 atoms 63: Number of degrees of freedom in T-Coupling group System is 51.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: Pull group natoms pbc atom distance at start reference at t=0 63: 1 1 0 63: 2 1 0 179.098 deg 0.000 deg 63: 2 1 0 63: 3 1 0 158.667 deg 0.000 deg 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine-dipeptide' 63: 16 steps, 0.0 ps. 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.104 0.052 199.6 63: (ns/day) (hour/ns) 63: Performance: 28.174 0.852 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine-dipeptide' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.674 0.337 199.9 63: (ns/day) (hour/ns) 63: Performance: 2.306 10.406 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine-dipeptide' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.056 0.028 199.5 63: (ns/day) (hour/ns) 63: Performance: 27.628 0.869 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (576 ms) 63: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact (1314 ms total) 63: 63: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact 63: [ RUN ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps. 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.124 0.062 199.8 63: (ns/day) (hour/ns) 63: Performance: 23.594 1.017 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: NOTE: 18 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.452 0.226 200.0 63: (ns/day) (hour/ns) 63: Performance: 3.442 6.972 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.826 0.413 199.9 63: (ns/day) (hour/ns) 63: Performance: 1.883 12.743 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (843 ms) 63: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact (843 ms total) 63: 63: [----------] 3 tests from Checking/InitialConstraintsTest 63: [ RUN ] Checking/InitialConstraintsTest.Works/0 63: Number of degrees of freedom in T-Coupling group rest is 11.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 1141.954 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc-and-methanol' 63: 1 steps, 0.0 ps. 63: Setting the LD random seed to 2147086079 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.109 0.054 199.8 63: (ns/day) (hour/ns) 63: Performance: 3.178 7.551 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (64 ms) 63: [ RUN ] Checking/InitialConstraintsTest.Works/1 63: Number of degrees of freedom in T-Coupling group rest is 11.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 1141.954 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc-and-methanol' 63: 1 steps, 0.0 ps. 63: Setting the LD random seed to -1057474 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.899 0.450 200.0 63: (ns/day) (hour/ns) 63: Performance: 0.384 62.466 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (496 ms) 63: [ RUN ] Checking/InitialConstraintsTest.Works/2 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 63: Integrator method md-vv-avek is implemented primarily for validation 63: purposes; for molecular dynamics, you should probably be using md or 63: md-vv 63: 63: Number of degrees of freedom in T-Coupling group rest is 11.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 63: NVE simulation: will use the initial temperature of 1141.954 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc-and-methanol' 63: 1 steps, 0.0 ps. 63: Setting the LD random seed to -805568577 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.980 0.490 200.0 63: (ns/day) (hour/ns) 63: Performance: 0.352 68.085 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (513 ms) 63: [----------] 3 tests from Checking/InitialConstraintsTest (1074 ms total) 63: 63: [----------] Global test environment tear-down 63: [==========] 76 tests from 13 test suites ran. (23341 ms total) 63: [ PASSED ] 76 tests. 63/87 Test #63: MdrunIOTests .............................. Passed 23.39 sec test 64 Start 64: MdrunTestsOneRank 64: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunTestsOneRank.xml" 64: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 64: Test timeout computed to be: 600 64: [==========] Running 28 tests from 7 test suites. 64: [----------] Global test environment set-up. 64: [----------] 1 test from CompelTest 64: [ RUN ] CompelTest.SwapCanRun 64: Generating 1-4 interactions: fudge = 0.5 64: Split0 group 'Ch0' contains 83 atoms. 64: Split1 group 'Ch1' contains 83 atoms. 64: Solvent group 'SOL' contains 11931 atoms. 64: Swap group 'NA+' contains 19 atoms. 64: Swap group 'CL-' contains 19 atoms. 64: Number of degrees of freedom in T-Coupling group System is 27869.00 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 64: Removing center of mass motion in the presence of position restraints 64: might cause artifacts. When you are using position restraints to 64: equilibrate a macro-molecule, the artifacts are usually negligible. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 2 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Update groups can not be used for this system because there are three or more consecutively coupled constraints 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: SWAP: Determining initial numbers of ions per compartment. 64: SWAP: Setting pointers for checkpoint writing 64: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 64: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 64: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 64: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 64: starting mdrun 'Channel_coco in octane membrane' 64: 2 steps, 0.0 ps. 64: Setting the LD random seed to -175260845 64: 64: Generated 330891 of the 330891 non-bonded parameter combinations 64: 64: Generated 330891 of the 330891 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Protein' 64: 64: turning all bonds into constraints... 64: 64: Excluding 3 bonded neighbours molecule type 'OCT' 64: 64: turning all bonds into constraints... 64: 64: Excluding 1 bonded neighbours molecule type 'NA' 64: 64: turning all bonds into constraints... 64: 64: Excluding 1 bonded neighbours molecule type 'CL' 64: 64: turning all bonds into constraints... 64: 64: Excluding 3 bonded neighbours molecule type 'Protein' 64: 64: Excluding 3 bonded neighbours molecule type 'OCT' 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning all bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.316 nm, buffer size 0.316 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.262 nm, buffer size 0.262 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 1 Mb of data 64: 64: Writing final coordinates. 64: 64: NOTE: 36 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.574 0.287 200.0 64: (ns/day) (hour/ns) 64: Performance: 4.512 5.319 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 64: 64: Update groups can not be used for this system because there are three or more consecutively coupled constraints 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: SWAP: Setting pointers for checkpoint writing 64: SWAP: Copying channel fluxes from checkpoint file data 64: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 64: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 64: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 64: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 64: starting mdrun 'Channel_coco in octane membrane' 64: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 64: 64: Writing final coordinates. 64: 64: NOTE: 14 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.735 0.367 200.0 64: (ns/day) (hour/ns) 64: Performance: 3.528 6.804 64: [ OK ] CompelTest.SwapCanRun (1875 ms) 64: [----------] 1 test from CompelTest (1875 ms total) 64: 64: [----------] 6 tests from BondedInteractionsTest 64: [ RUN ] BondedInteractionsTest.NormalBondWorks 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: 64: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 64: In moleculetype 'butane' 2 atoms are not bound by a potential or 64: constraint to any other atom in the same moleculetype. Although 64: technically this might not cause issues in a simulation, this often means 64: that the user forgot to add a bond/potential/constraint or put multiple 64: molecules in the same moleculetype definition by mistake. Run with -v to 64: get information for each atom. 64: 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 64: NVE simulation with an initial temperature of zero: will use a Verlet 64: buffer of 10%. Check your energy drift! 64: 64: 64: There were 3 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 64: 64: Reading frames from gro file 'A single butane', 4 atoms. 64: Reading frame 0 time 0.000 Last frame 0 time 0.000 64: 64: NOTE: 40 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.160 0.080 199.9 64: (ns/day) (hour/ns) 64: Performance: 1.078 22.258 64: Setting the LD random seed to -544740642 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'butane' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] BondedInteractionsTest.NormalBondWorks (129 ms) 64: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: 64: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 64: In moleculetype 'butane' 2 atoms are not bound by a potential or 64: constraint to any other atom in the same moleculetype. Although 64: technically this might not cause issues in a simulation, this often means 64: that the user forgot to add a bond/potential/constraint or put multiple 64: molecules in the same moleculetype definition by mistake. Run with -v to 64: get information for each atom. 64: 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 64: NVE simulation with an initial temperature of zero: will use a Verlet 64: buffer of 10%. Check your energy drift! 64: 64: 64: There were 3 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 64: 64: Reading frames from gro file 'A single butane', 4 atoms. 64: Reading frame 0 time 0.000 Last frame 0 time 0.000 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.008 0.004 198.3 64: (ns/day) (hour/ns) 64: Performance: 22.371 1.073 64: Setting the LD random seed to -605044833 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'butane' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] BondedInteractionsTest.TabulatedBondWorks (53 ms) 64: [ RUN ] BondedInteractionsTest.NormalAngleWorks 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: 64: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 64: In moleculetype 'butane' 4 atoms are not bound by a potential or 64: constraint to any other atom in the same moleculetype. Although 64: technically this might not cause issues in a simulation, this often means 64: that the user forgot to add a bond/potential/constraint or put multiple 64: molecules in the same moleculetype definition by mistake. Run with -v to 64: get information for each atom. 64: 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 64: NVE simulation with an initial temperature of zero: will use a Verlet 64: buffer of 10%. Check your energy drift! 64: 64: 64: There were 3 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 64: 64: Reading frames from gro file 'A single butane', 4 atoms. 64: Reading frame 0 time 0.000 Last frame 0 time 0.000 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.001 0.001 191.6 64: (ns/day) (hour/ns) 64: Performance: 160.847 0.149 64: Setting the LD random seed to -620792069 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'butane' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] BondedInteractionsTest.NormalAngleWorks (34 ms) 64: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: 64: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 64: In moleculetype 'butane' 4 atoms are not bound by a potential or 64: constraint to any other atom in the same moleculetype. Although 64: technically this might not cause issues in a simulation, this often means 64: that the user forgot to add a bond/potential/constraint or put multiple 64: molecules in the same moleculetype definition by mistake. Run with -v to 64: get information for each atom. 64: 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 64: NVE simulation with an initial temperature of zero: will use a Verlet 64: buffer of 10%. Check your energy drift! 64: 64: 64: There were 3 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 64: 64: Reading frames from gro file 'A single butane', 4 atoms. 64: Reading frame 0 time 0.000 Last frame 0 time 0.000 64: 64: NOTE: 18 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.000 0.000 184.2 64: (ns/day) (hour/ns) 64: Performance: 584.497 0.041 64: Setting the LD random seed to 2132795390 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'butane' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (10 ms) 64: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: 64: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 64: In moleculetype 'butane' 4 atoms are not bound by a potential or 64: constraint to any other atom in the same moleculetype. Although 64: technically this might not cause issues in a simulation, this often means 64: that the user forgot to add a bond/potential/constraint or put multiple 64: molecules in the same moleculetype definition by mistake. Run with -v to 64: get information for each atom. 64: 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 64: NVE simulation with an initial temperature of zero: will use a Verlet 64: buffer of 10%. Check your energy drift! 64: 64: 64: There were 3 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 64: 64: Reading frames from gro file 'A single butane', 4 atoms. 64: Reading frame 0 time 0.000 Last frame 0 time 0.000 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.007 0.003 199.0 64: (ns/day) (hour/ns) 64: Performance: 25.771 0.931 64: Setting the LD random seed to -939592068 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'butane' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] BondedInteractionsTest.NormalDihedralWorks (15 ms) 64: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: 64: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 64: In moleculetype 'butane' 4 atoms are not bound by a potential or 64: constraint to any other atom in the same moleculetype. Although 64: technically this might not cause issues in a simulation, this often means 64: that the user forgot to add a bond/potential/constraint or put multiple 64: molecules in the same moleculetype definition by mistake. Run with -v to 64: get information for each atom. 64: 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 64: NVE simulation with an initial temperature of zero: will use a Verlet 64: buffer of 10%. Check your energy drift! 64: 64: 64: There were 3 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 64: 64: Reading frames from gro file 'A single butane', 4 atoms. 64: Reading frame 0 time 0.000 Last frame 0 time 0.000 64: 64: NOTE: 11 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.000 0.000 189.6 64: (ns/day) (hour/ns) 64: Performance: 330.948 0.073 64: Setting the LD random seed to -84544163 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'butane' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (11 ms) 64: [----------] 6 tests from BondedInteractionsTest (256 ms total) 64: 64: [----------] 2 tests from BoxDeformationTest 64: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (10) 64: 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: Number of degrees of freedom in T-Coupling group rest is 33.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: There were 3 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Argon' 64: 0 steps, 0.0 ps. 64: 64: NOTE: 31 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.232 0.116 199.9 64: (ns/day) (hour/ns) 64: Performance: 1.488 16.127 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 1602156919 64: 64: Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: Setting gen_seed to 2012740351 64: 64: Velocities were taken from a Maxwell distribution at 0 K 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (197 ms) 64: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (10) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group rest is 1293.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: There were 2 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 20 steps, 0.0 ps. 64: Setting the LD random seed to -2113 64: 64: Generated 330891 of the 330891 non-bonded parameter combinations 64: 64: Generated 330891 of the 330891 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 64: Calculating fourier grid dimensions for X Y Z 64: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 64: 64: Estimate for the relative computational load of the PME mesh part: 0.15 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.317 0.159 199.9 64: (ns/day) (hour/ns) 64: Performance: 22.877 1.049 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (828 ms) 64: [----------] 2 tests from BoxDeformationTest (1026 ms total) 64: 64: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 64: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 2 [file ala.top, line 256]: 64: For energy conservation with LINCS, lincs_iter should be 2 or larger. 64: 64: 64: Number of degrees of freedom in T-Coupling group rest is 54.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 64: The optimal PME mesh load for parallel simulations is below 0.5 64: and for highly parallel simulations between 0.25 and 0.33, 64: for higher performance, increase the cut-off and the PME grid spacing. 64: 64: 64: 64: There were 3 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'UNNAMED in water' 64: 4 steps, 0.0 ps. 64: Setting the LD random seed to -272637977 64: 64: Generated 2211 of the 2211 non-bonded parameter combinations 64: 64: Generated 2211 of the 2211 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 64: 64: turning H bonds into constraints... 64: 64: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 64: Calculating fourier grid dimensions for X Y Z 64: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 64: 64: Estimate for the relative computational load of the PME mesh part: 0.94 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.471 0.236 199.9 64: (ns/day) (hour/ns) 64: Performance: 1.832 13.101 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 2 [file ala.top, line 256]: 64: For energy conservation with LINCS, lincs_iter should be 2 or larger. 64: 64: 64: Number of degrees of freedom in T-Coupling group rest is 54.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 64: The optimal PME mesh load for parallel simulations is below 0.5 64: and for highly parallel simulations between 0.25 and 0.33, 64: for higher performance, increase the cut-off and the PME grid spacing. 64: 64: 64: 64: There were 3 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'UNNAMED in water' 64: 4 steps, 0.0 ps. 64: Setting the LD random seed to 2147428351 64: 64: Generated 2211 of the 2211 non-bonded parameter combinations 64: 64: Generated 2211 of the 2211 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 64: 64: turning H bonds into constraints... 64: 64: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 64: Calculating fourier grid dimensions for X Y Z 64: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 64: 64: Estimate for the relative computational load of the PME mesh part: 0.94 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.753 0.376 199.9 64: (ns/day) (hour/ns) 64: Performance: 1.148 20.914 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (double precision) 64: 64: 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (1318 ms) 64: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 2 [file ala.top, line 256]: 64: For energy conservation with LINCS, lincs_iter should be 2 or larger. 64: 64: 64: Number of degrees of freedom in T-Coupling group rest is 54.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 64: The optimal PME mesh load for parallel simulations is below 0.5 64: and for highly parallel simulations between 0.25 and 0.33, 64: for higher performance, increase the cut-off and the PME grid spacing. 64: 64: 64: 64: There were 3 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'UNNAMED in water' 64: 4 steps, 0.0 ps. 64: Setting the LD random seed to -1744846854 64: 64: Generated 2211 of the 2211 non-bonded parameter combinations 64: 64: Generated 2211 of the 2211 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 64: 64: turning H bonds into constraints... 64: 64: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 64: Calculating fourier grid dimensions for X Y Z 64: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 64: 64: Estimate for the relative computational load of the PME mesh part: 0.94 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.418 0.209 199.9 64: (ns/day) (hour/ns) 64: Performance: 2.065 11.620 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 2 [file ala.top, line 256]: 64: For energy conservation with LINCS, lincs_iter should be 2 or larger. 64: 64: 64: Number of degrees of freedom in T-Coupling group rest is 54.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 64: The optimal PME mesh load for parallel simulations is below 0.5 64: and for highly parallel simulations between 0.25 and 0.33, 64: for higher performance, increase the cut-off and the PME grid spacing. 64: 64: 64: 64: There were 3 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 64: Can not increase nstlist because an NVE ensemble is used 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'UNNAMED in water' 64: 4 steps, 0.0 ps. 64: Setting the LD random seed to 1442226167 64: 64: Generated 2211 of the 2211 non-bonded parameter combinations 64: 64: Generated 2211 of the 2211 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 64: 64: turning H bonds into constraints... 64: 64: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 64: Calculating fourier grid dimensions for X Y Z 64: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 64: 64: Estimate for the relative computational load of the PME mesh part: 0.94 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.165 0.083 199.8 64: (ns/day) (hour/ns) 64: Performance: 5.225 4.593 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 64: 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (569 ms) 64: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (1888 ms total) 64: 64: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 64: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Pull group 1 'FirstWaterMolecule' has 3 atoms 64: Pull group 2 'SecondWaterMolecule' has 3 atoms 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: Pull group natoms pbc atom distance at start reference at t=0 64: 1 3 2 64: 2 3 5 1.112 nm 1.000 nm 64: 64: There was 1 NOTE 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 4 steps, 0.0 ps. 64: Setting the LD random seed to 2147413613 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Generated 3 of the 3 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.103 0.052 199.8 64: (ns/day) (hour/ns) 64: Performance: 8.348 2.875 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Pull group 1 'FirstWaterMolecule' has 3 atoms 64: Pull group 2 'SecondWaterMolecule' has 3 atoms 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: Pull group natoms pbc atom distance at start reference at t=0 64: 1 3 2 64: 2 3 5 1.112 nm 1.000 nm 64: 64: There was 1 NOTE 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 64: Can not increase nstlist because an NVE ensemble is used 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 4 steps, 0.0 ps. 64: Setting the LD random seed to -34808133 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Generated 3 of the 3 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.069 0.034 199.7 64: (ns/day) (hour/ns) 64: Performance: 12.579 1.908 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 64: 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (120 ms) 64: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (120 ms total) 64: 64: [----------] 12 tests from FreezeWorks/FreezeGroupTest 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 64: NVE simulation: will use the initial temperature of 318.937 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 5 NOTEs 64: 64: There was 1 WARNING 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.041 0.020 199.4 64: (ns/day) (hour/ns) 64: Performance: 38.053 0.631 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (58 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 64: NVE simulation: will use the initial temperature of 318.937 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 5 NOTEs 64: 64: There was 1 WARNING 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: NOTE: 45 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.193 0.096 199.9 64: (ns/day) (hour/ns) 64: Performance: 8.073 2.973 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (234 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 64: NVE simulation: will use the initial temperature of 318.937 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 5 NOTEs 64: 64: There was 1 WARNING 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.526 0.263 200.0 64: (ns/day) (hour/ns) 64: Performance: 2.955 8.122 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (279 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 64: NVE simulation: will use the initial temperature of 318.937 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 5 NOTEs 64: 64: There was 1 WARNING 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.060 0.030 199.6 64: (ns/day) (hour/ns) 64: Performance: 25.677 0.935 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (107 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 64: NVE simulation: will use the initial temperature of 318.937 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 5 NOTEs 64: 64: There was 1 WARNING 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: NOTE: 22 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.294 0.147 199.9 64: (ns/day) (hour/ns) 64: Performance: 5.289 4.538 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (232 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 64: ./src/programs/mdrun/tests/freezegroups.cpp:194: Skipped 64: Parrinello-Rahman is not implemented in md-vv. 64: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 NOTEs 64: 64: There was 1 WARNING 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.149 0.074 199.8 64: (ns/day) (hour/ns) 64: Performance: 10.462 2.294 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (99 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 NOTEs 64: 64: There was 1 WARNING 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.071 0.036 199.7 64: (ns/day) (hour/ns) 64: Performance: 21.802 1.101 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (76 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 NOTEs 64: 64: There was 1 WARNING 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.025 0.012 199.1 64: (ns/day) (hour/ns) 64: Performance: 62.490 0.384 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (92 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 NOTEs 64: 64: There was 1 WARNING 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.087 0.044 199.7 64: (ns/day) (hour/ns) 64: Performance: 17.818 1.347 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (111 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 NOTEs 64: 64: There was 1 WARNING 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.035 0.018 199.5 64: (ns/day) (hour/ns) 64: Performance: 44.258 0.542 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (93 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 NOTEs 64: 64: There was 1 WARNING 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.061 0.031 199.6 64: (ns/day) (hour/ns) 64: Performance: 25.462 0.943 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (252 ms) 64: [----------] 12 tests from FreezeWorks/FreezeGroupTest (1638 ms total) 64: 64: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 64: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 64: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: Net Acceleration in X direction, will not be corrected 64: Net Acceleration in Y direction, will not be corrected 64: Net Acceleration in Z direction, will not be corrected 64: 64: There were 3 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 8 steps, 0.0 ps. 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Generated 3 of the 3 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Setting gen_seed to 798881215 64: 64: Velocities were taken from a Maxwell distribution at 0 K 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: NOTE: 42 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.152 0.076 199.8 64: (ns/day) (hour/ns) 64: Performance: 20.501 1.171 64: 64: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (133 ms) 64: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 64: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 64: Net Acceleration in X direction, will not be corrected 64: Net Acceleration in Y direction, will not be corrected 64: Net Acceleration in Z direction, will not be corrected 64: 64: There were 3 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because verlet-buffer-tolerance is not set or used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 8 steps, 0.0 ps. 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Generated 3 of the 3 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Setting gen_seed to -35787014 64: 64: Velocities were taken from a Maxwell distribution at 0 K 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.054 0.027 199.5 64: (ns/day) (hour/ns) 64: Performance: 57.121 0.420 64: 64: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (74 ms) 64: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 64: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: Net Acceleration in X direction, will not be corrected 64: Net Acceleration in Y direction, will not be corrected 64: Net Acceleration in Z direction, will not be corrected 64: 64: There were 3 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 8 steps, 0.0 ps. 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Generated 3 of the 3 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Setting gen_seed to -1358995777 64: 64: Velocities were taken from a Maxwell distribution at 0 K 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.140 0.070 199.8 64: (ns/day) (hour/ns) 64: Performance: 22.169 1.083 64: 64: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (74 ms) 64: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 64: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 64: Net Acceleration in X direction, will not be corrected 64: Net Acceleration in Y direction, will not be corrected 64: Net Acceleration in Z direction, will not be corrected 64: 64: There were 3 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because verlet-buffer-tolerance is not set or used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 8 steps, 0.0 ps. 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Generated 3 of the 3 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Setting gen_seed to -23201031 64: 64: Velocities were taken from a Maxwell distribution at 0 K 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.113 0.057 199.3 64: (ns/day) (hour/ns) 64: Performance: 27.413 0.875 64: 64: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (79 ms) 64: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (361 ms total) 64: 64: [----------] Global test environment tear-down 64: [==========] 28 tests from 7 test suites ran. (7601 ms total) 64: [ PASSED ] 27 tests. 64: [ SKIPPED ] 1 test, listed below: 64: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 64/87 Test #64: MdrunTestsOneRank ......................... Passed 7.70 sec test 65 Start 65: MdrunTestsTwoRanks 65: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunTestsTwoRanks.xml" 65: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 65: Test timeout computed to be: 600 65: [==========] Running 28 tests from 7 test suites. 65: [----------] Global test environment set-up. 65: [----------] 1 test from CompelTest 65: [ RUN ] CompelTest.SwapCanRun 65: Generating 1-4 interactions: fudge = 0.5 65: Split0 group 'Ch0' contains 83 atoms. 65: Split1 group 'Ch1' contains 83 atoms. 65: Solvent group 'SOL' contains 11931 atoms. 65: Swap group 'NA+' contains 19 atoms. 65: Swap group 'CL-' contains 19 atoms. 65: Number of degrees of freedom in T-Coupling group System is 27869.00 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 65: Removing center of mass motion in the presence of position restraints 65: might cause artifacts. When you are using position restraints to 65: equilibrate a macro-molecule, the artifacts are usually negligible. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 2 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Update groups can not be used for this system because there are three or more consecutively coupled constraints 65: 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: SWAP: Determining initial numbers of ions per compartment. 65: SWAP: Setting pointers for checkpoint writing 65: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 65: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 65: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 65: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 65: starting mdrun 'Channel_coco in octane membrane' 65: 2 steps, 0.0 ps. 65: Setting the LD random seed to 2067689445 65: 65: Generated 330891 of the 330891 non-bonded parameter combinations 65: 65: Generated 330891 of the 330891 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Protein' 65: 65: turning all bonds into constraints... 65: 65: Excluding 3 bonded neighbours molecule type 'OCT' 65: 65: turning all bonds into constraints... 65: 65: Excluding 1 bonded neighbours molecule type 'NA' 65: 65: turning all bonds into constraints... 65: 65: Excluding 1 bonded neighbours molecule type 'CL' 65: 65: turning all bonds into constraints... 65: 65: Excluding 3 bonded neighbours molecule type 'Protein' 65: 65: Excluding 3 bonded neighbours molecule type 'OCT' 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning all bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.316 nm, buffer size 0.316 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.262 nm, buffer size 0.262 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 1 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 4.9%. 65: The balanceable part of the MD step is 23%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 1.1%. 65: 65: 65: NOTE: 33 % of the run time was spent in domain decomposition, 65: 6 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 3.587 0.897 399.9 65: (ns/day) (hour/ns) 65: Performance: 1.445 16.608 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 65: 65: Update groups can not be used for this system because there are three or more consecutively coupled constraints 65: 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: SWAP: Setting pointers for checkpoint writing 65: SWAP: Copying channel fluxes from checkpoint file data 65: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 65: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 65: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 65: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 65: starting mdrun 'Channel_coco in octane membrane' 65: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 2.407 0.602 399.9 65: (ns/day) (hour/ns) 65: Performance: 2.153 11.146 65: [ OK ] CompelTest.SwapCanRun (2526 ms) 65: [----------] 1 test from CompelTest (2531 ms total) 65: 65: [----------] 6 tests from BondedInteractionsTest 65: [ RUN ] BondedInteractionsTest.NormalBondWorks 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: 65: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 65: In moleculetype 'butane' 2 atoms are not bound by a potential or 65: constraint to any other atom in the same moleculetype. Although 65: technically this might not cause issues in a simulation, this often means 65: that the user forgot to add a bond/potential/constraint or put multiple 65: molecules in the same moleculetype definition by mistake. Run with -v to 65: get information for each atom. 65: 65: Number of degrees of freedom in T-Coupling group rest is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 65: NVE simulation with an initial temperature of zero: will use a Verlet 65: buffer of 10%. Check your energy drift! 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 65: 65: Reading frames from gro file 'A single butane', 4 atoms. 65: Reading frame 0 time 0.000 Last frame 0 time 0.000 65: 65: NOTE: 81 % of the run time was spent in domain decomposition, 65: 0 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 6 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.628 0.157 399.9 65: (ns/day) (hour/ns) 65: Performance: 0.551 43.589 65: Setting the LD random seed to 1810480894 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'butane' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] BondedInteractionsTest.NormalBondWorks (249 ms) 65: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: 65: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 65: In moleculetype 'butane' 2 atoms are not bound by a potential or 65: constraint to any other atom in the same moleculetype. Although 65: technically this might not cause issues in a simulation, this often means 65: that the user forgot to add a bond/potential/constraint or put multiple 65: molecules in the same moleculetype definition by mistake. Run with -v to 65: get information for each atom. 65: 65: Number of degrees of freedom in T-Coupling group rest is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 65: NVE simulation with an initial temperature of zero: will use a Verlet 65: buffer of 10%. Check your energy drift! 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 65: 65: Reading frames from gro file 'A single butane', 4 atoms. 65: Reading frame 0 time 0.000 Last frame 0 time 0.000 65: 65: NOTE: 77 % of the run time was spent in domain decomposition, 65: 0 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.248 0.062 399.8 65: (ns/day) (hour/ns) 65: Performance: 1.390 17.261 65: Setting the LD random seed to -270488578 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'butane' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] BondedInteractionsTest.TabulatedBondWorks (154 ms) 65: [ RUN ] BondedInteractionsTest.NormalAngleWorks 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: 65: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 65: In moleculetype 'butane' 4 atoms are not bound by a potential or 65: constraint to any other atom in the same moleculetype. Although 65: technically this might not cause issues in a simulation, this often means 65: that the user forgot to add a bond/potential/constraint or put multiple 65: molecules in the same moleculetype definition by mistake. Run with -v to 65: get information for each atom. 65: 65: Number of degrees of freedom in T-Coupling group rest is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 65: NVE simulation with an initial temperature of zero: will use a Verlet 65: buffer of 10%. Check your energy drift! 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 65: 65: Reading frames from gro file 'A single butane', 4 atoms. 65: Reading frame 0 time 0.000 Last frame 0 time 0.000 65: 65: NOTE: 40 % of the run time was spent in domain decomposition, 65: 29 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.881 0.220 399.9 65: (ns/day) (hour/ns) 65: Performance: 0.392 61.197 65: Setting the LD random seed to -1665450161 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'butane' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] BondedInteractionsTest.NormalAngleWorks (939 ms) 65: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: 65: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 65: In moleculetype 'butane' 4 atoms are not bound by a potential or 65: constraint to any other atom in the same moleculetype. Although 65: technically this might not cause issues in a simulation, this often means 65: that the user forgot to add a bond/potential/constraint or put multiple 65: molecules in the same moleculetype definition by mistake. Run with -v to 65: get information for each atom. 65: 65: Number of degrees of freedom in T-Coupling group rest is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 65: NVE simulation with an initial temperature of zero: will use a Verlet 65: buffer of 10%. Check your energy drift! 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 65: 65: Reading frames from gro file 'A single butane', 4 atoms. 65: Reading frame 0 time 0.000 Last frame 0 time 0.000 65: 65: NOTE: 55 % of the run time was spent in domain decomposition, 65: 0 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.073 0.018 399.3 65: (ns/day) (hour/ns) 65: Performance: 4.747 5.056 65: Setting the LD random seed to 515374822 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'butane' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (97 ms) 65: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: 65: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 65: In moleculetype 'butane' 4 atoms are not bound by a potential or 65: constraint to any other atom in the same moleculetype. Although 65: technically this might not cause issues in a simulation, this often means 65: that the user forgot to add a bond/potential/constraint or put multiple 65: molecules in the same moleculetype definition by mistake. Run with -v to 65: get information for each atom. 65: 65: Number of degrees of freedom in T-Coupling group rest is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 65: NVE simulation with an initial temperature of zero: will use a Verlet 65: buffer of 10%. Check your energy drift! 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 65: 65: Reading frames from gro file 'A single butane', 4 atoms. 65: Reading frame 0 time 0.000 Last frame 0 time 0.000 65: 65: NOTE: 39 % of the run time was spent in domain decomposition, 65: 23 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 6 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.932 0.233 399.9 65: (ns/day) (hour/ns) 65: Performance: 0.371 64.719 65: Setting the LD random seed to -537022481 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'butane' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] BondedInteractionsTest.NormalDihedralWorks (604 ms) 65: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: 65: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 65: In moleculetype 'butane' 4 atoms are not bound by a potential or 65: constraint to any other atom in the same moleculetype. Although 65: technically this might not cause issues in a simulation, this often means 65: that the user forgot to add a bond/potential/constraint or put multiple 65: molecules in the same moleculetype definition by mistake. Run with -v to 65: get information for each atom. 65: 65: Number of degrees of freedom in T-Coupling group rest is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 65: NVE simulation with an initial temperature of zero: will use a Verlet 65: buffer of 10%. Check your energy drift! 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 65: 65: Reading frames from gro file 'A single butane', 4 atoms. 65: Reading frame 0 time 0.000 Last frame 0 time 0.000 65: 65: NOTE: 67 % of the run time was spent in domain decomposition, 65: 0 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 7 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.112 0.028 399.6 65: (ns/day) (hour/ns) 65: Performance: 3.082 7.786 65: Setting the LD random seed to -4358665 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'butane' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (178 ms) 65: [----------] 6 tests from BondedInteractionsTest (2224 ms total) 65: 65: [----------] 2 tests from BoxDeformationTest 65: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (10) 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: Number of degrees of freedom in T-Coupling group rest is 33.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 0 steps, 0.0 ps. 65: 65: NOTE: 29 % of the run time was spent in domain decomposition, 65: 12 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 7 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 1.232 0.318 387.5 65: (ns/day) (hour/ns) 65: Performance: 0.544 44.148 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as double precision energy file 65: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -33595461 65: 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Setting gen_seed to -540549298 65: 65: Velocities were taken from a Maxwell distribution at 0 K 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (560 ms) 65: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (10) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group rest is 1293.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: There were 2 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 20 steps, 0.0 ps. 65: Setting the LD random seed to -273947601 65: 65: Generated 330891 of the 330891 non-bonded parameter combinations 65: 65: Generated 330891 of the 330891 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 65: Calculating fourier grid dimensions for X Y Z 65: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 65: 65: Estimate for the relative computational load of the PME mesh part: 0.15 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB got disabled because it was unsuitable to use. 65: Average load imbalance: 25.6%. 65: The balanceable part of the MD step is 9%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 2.3%. 65: 65: 65: Core t (s) Wall t (s) (%) 65: Time: 5.368 1.344 399.4 65: (ns/day) (hour/ns) 65: Performance: 2.700 8.890 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as double precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (2420 ms) 65: [----------] 2 tests from BoxDeformationTest (2981 ms total) 65: 65: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 65: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 2 [file ala.top, line 256]: 65: For energy conservation with LINCS, lincs_iter should be 2 or larger. 65: 65: 65: Number of degrees of freedom in T-Coupling group rest is 54.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 65: The optimal PME mesh load for parallel simulations is below 0.5 65: and for highly parallel simulations between 0.25 and 0.33, 65: for higher performance, increase the cut-off and the PME grid spacing. 65: 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'UNNAMED in water' 65: 4 steps, 0.0 ps. 65: Setting the LD random seed to 1994281693 65: 65: Generated 2211 of the 2211 non-bonded parameter combinations 65: 65: Generated 2211 of the 2211 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 65: 65: turning H bonds into constraints... 65: 65: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 65: Calculating fourier grid dimensions for X Y Z 65: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 65: 65: Estimate for the relative computational load of the PME mesh part: 0.94 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 12 % of the run time was spent in domain decomposition, 65: 0 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 3.664 0.916 400.0 65: (ns/day) (hour/ns) 65: Performance: 0.472 50.895 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 2 [file ala.top, line 256]: 65: For energy conservation with LINCS, lincs_iter should be 2 or larger. 65: 65: 65: Number of degrees of freedom in T-Coupling group rest is 54.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 65: The optimal PME mesh load for parallel simulations is below 0.5 65: and for highly parallel simulations between 0.25 and 0.33, 65: for higher performance, increase the cut-off and the PME grid spacing. 65: 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'UNNAMED in water' 65: 4 steps, 0.0 ps. 65: Setting the LD random seed to -70733 65: 65: Generated 2211 of the 2211 non-bonded parameter combinations 65: 65: Generated 2211 of the 2211 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 65: 65: turning H bonds into constraints... 65: 65: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 65: Calculating fourier grid dimensions for X Y Z 65: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 65: 65: Estimate for the relative computational load of the PME mesh part: 0.94 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 20 % of the run time was spent in domain decomposition, 65: 2 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 4.827 1.223 394.8 65: (ns/day) (hour/ns) 65: Performance: 0.353 67.927 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (double precision) 65: 65: 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (3622 ms) 65: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 2 [file ala.top, line 256]: 65: For energy conservation with LINCS, lincs_iter should be 2 or larger. 65: 65: 65: Number of degrees of freedom in T-Coupling group rest is 54.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 65: The optimal PME mesh load for parallel simulations is below 0.5 65: and for highly parallel simulations between 0.25 and 0.33, 65: for higher performance, increase the cut-off and the PME grid spacing. 65: 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'UNNAMED in water' 65: 4 steps, 0.0 ps. 65: Setting the LD random seed to -285246658 65: 65: Generated 2211 of the 2211 non-bonded parameter combinations 65: 65: Generated 2211 of the 2211 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 65: 65: turning H bonds into constraints... 65: 65: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 65: Calculating fourier grid dimensions for X Y Z 65: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 65: 65: Estimate for the relative computational load of the PME mesh part: 0.94 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 67 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.172 0.047 365.8 65: (ns/day) (hour/ns) 65: Performance: 9.174 2.616 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 2 [file ala.top, line 256]: 65: For energy conservation with LINCS, lincs_iter should be 2 or larger. 65: 65: 65: Number of degrees of freedom in T-Coupling group rest is 54.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 65: The optimal PME mesh load for parallel simulations is below 0.5 65: and for highly parallel simulations between 0.25 and 0.33, 65: for higher performance, increase the cut-off and the PME grid spacing. 65: 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 65: Can not increase nstlist because an NVE ensemble is used 65: 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'UNNAMED in water' 65: 4 steps, 0.0 ps. 65: Setting the LD random seed to -493371907 65: 65: Generated 2211 of the 2211 non-bonded parameter combinations 65: 65: Generated 2211 of the 2211 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 65: 65: turning H bonds into constraints... 65: 65: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 65: Calculating fourier grid dimensions for X Y Z 65: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 65: 65: Estimate for the relative computational load of the PME mesh part: 0.94 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 60 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.219 0.055 399.2 65: (ns/day) (hour/ns) 65: Performance: 7.884 3.044 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 65: 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (724 ms) 65: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (4346 ms total) 65: 65: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 65: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Pull group 1 'FirstWaterMolecule' has 3 atoms 65: Pull group 2 'SecondWaterMolecule' has 3 atoms 65: Number of degrees of freedom in T-Coupling group rest is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: Pull group natoms pbc atom distance at start reference at t=0 65: 1 3 2 65: 2 3 5 1.112 nm 1.000 nm 65: 65: There was 1 NOTE 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 4 steps, 0.0 ps. 65: Setting the LD random seed to -135333011 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 22 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 1.453 0.379 383.1 65: (ns/day) (hour/ns) 65: Performance: 1.139 21.069 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Pull group 1 'FirstWaterMolecule' has 3 atoms 65: Pull group 2 'SecondWaterMolecule' has 3 atoms 65: Number of degrees of freedom in T-Coupling group rest is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: Pull group natoms pbc atom distance at start reference at t=0 65: 1 3 2 65: 2 3 5 1.112 nm 1.000 nm 65: 65: There was 1 NOTE 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 65: Can not increase nstlist because an NVE ensemble is used 65: 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 4 steps, 0.0 ps. 65: Setting the LD random seed to 1877930459 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 42 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 4.080 1.020 399.9 65: (ns/day) (hour/ns) 65: Performance: 0.424 56.669 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 65: 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (2535 ms) 65: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (2535 ms total) 65: 65: [----------] 12 tests from FreezeWorks/FreezeGroupTest 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 65: NVE simulation: will use the initial temperature of 318.937 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 5 NOTEs 65: 65: There was 1 WARNING 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 23.8%. 65: The balanceable part of the MD step is 0%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 0.1%. 65: 65: 65: NOTE: 48 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 2.094 0.528 396.5 65: (ns/day) (hour/ns) 65: Performance: 1.473 16.294 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (704 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 65: NVE simulation: will use the initial temperature of 318.937 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 5 NOTEs 65: 65: There was 1 WARNING 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 83.9%. 65: The balanceable part of the MD step is 8%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 6.3%. 65: 65: NOTE: 6.3 % of the available CPU time was lost due to load imbalance 65: in the domain decomposition. 65: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 65: You can also consider manually changing the decomposition (option -dd); 65: e.g. by using fewer domains along the box dimension in which there is 65: considerable inhomogeneity in the simulated system. 65: 65: NOTE: 40 % of the run time was spent in domain decomposition, 65: 24 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.806 0.202 399.9 65: (ns/day) (hour/ns) 65: Performance: 3.856 6.224 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (605 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 65: NVE simulation: will use the initial temperature of 318.937 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 5 NOTEs 65: 65: There was 1 WARNING 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 33.7%. 65: The balanceable part of the MD step is 28%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 9.4%. 65: 65: NOTE: 9.4 % of the available CPU time was lost due to load imbalance 65: in the domain decomposition. 65: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 65: You can also consider manually changing the decomposition (option -dd); 65: e.g. by using fewer domains along the box dimension in which there is 65: considerable inhomogeneity in the simulated system. 65: 65: NOTE: 18 % of the run time was spent in domain decomposition, 65: 4 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 6 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 2.056 0.524 392.4 65: (ns/day) (hour/ns) 65: Performance: 1.484 16.170 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (765 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 65: NVE simulation: will use the initial temperature of 318.937 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 5 NOTEs 65: 65: There was 1 WARNING 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 11.4%. 65: The balanceable part of the MD step is 56%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 6.4%. 65: 65: NOTE: 6.4 % of the available CPU time was lost due to load imbalance 65: in the domain decomposition. 65: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 65: You can also consider manually changing the decomposition (option -dd); 65: e.g. by using fewer domains along the box dimension in which there is 65: considerable inhomogeneity in the simulated system. 65: 65: NOTE: 18 % of the run time was spent in domain decomposition, 65: 3 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 9 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 5.292 1.323 400.0 65: (ns/day) (hour/ns) 65: Performance: 0.588 40.836 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (1747 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 65: NVE simulation: will use the initial temperature of 318.937 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 5 NOTEs 65: 65: There was 1 WARNING 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 12.8%. 65: The balanceable part of the MD step is 60%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 7.7%. 65: 65: NOTE: 7.7 % of the available CPU time was lost due to load imbalance 65: in the domain decomposition. 65: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 65: You can also consider manually changing the decomposition (option -dd); 65: e.g. by using fewer domains along the box dimension in which there is 65: considerable inhomogeneity in the simulated system. 65: 65: NOTE: 10 % of the run time was spent in domain decomposition, 65: 1 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 11 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 6.472 1.620 399.5 65: (ns/day) (hour/ns) 65: Performance: 0.480 50.000 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (2334 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 65: ./src/programs/mdrun/tests/freezegroups.cpp:194: Skipped 65: Parrinello-Rahman is not implemented in md-vv. 65: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: 65: There was 1 WARNING 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 65: 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 48 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.202 0.072 281.3 65: (ns/day) (hour/ns) 65: Performance: 10.831 2.216 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (162 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: 65: There was 1 WARNING 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 65: 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 8 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 4.796 1.214 395.1 65: (ns/day) (hour/ns) 65: Performance: 0.641 37.464 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (2107 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: 65: There was 1 WARNING 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 65: 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 44 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.269 0.068 393.3 65: (ns/day) (hour/ns) 65: Performance: 11.376 2.110 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (183 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: 65: There was 1 WARNING 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 65: 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 31 % of the run time was spent in domain decomposition, 65: 0 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 13 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.688 0.176 390.9 65: (ns/day) (hour/ns) 65: Performance: 4.419 5.431 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (824 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: 65: There was 1 WARNING 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 65: 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 13 % of the run time was spent in domain decomposition, 65: 5 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 2.973 0.754 394.3 65: (ns/day) (hour/ns) 65: Performance: 1.031 23.270 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (1091 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: 65: There was 1 WARNING 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 65: 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 49 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.109 0.028 390.2 65: (ns/day) (hour/ns) 65: Performance: 27.941 0.859 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (301 ms) 65: [----------] 12 tests from FreezeWorks/FreezeGroupTest (10829 ms total) 65: 65: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 65: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 65: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: Net Acceleration in X direction, will not be corrected 65: Net Acceleration in Y direction, will not be corrected 65: Net Acceleration in Z direction, will not be corrected 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 8 steps, 0.0 ps. 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Setting gen_seed to 1475079327 65: 65: Velocities were taken from a Maxwell distribution at 0 K 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 2.4%. 65: The balanceable part of the MD step is 0%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 0.0%. 65: 65: 65: NOTE: 24 % of the run time was spent in domain decomposition, 65: 0 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 30 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.425 0.111 384.1 65: (ns/day) (hour/ns) 65: Performance: 14.057 1.707 65: 65: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (200 ms) 65: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 65: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 65: Net Acceleration in X direction, will not be corrected 65: Net Acceleration in Y direction, will not be corrected 65: Net Acceleration in Z direction, will not be corrected 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because verlet-buffer-tolerance is not set or used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 8 steps, 0.0 ps. 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Setting gen_seed to -268569857 65: 65: Velocities were taken from a Maxwell distribution at 0 K 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 22.5%. 65: The balanceable part of the MD step is 42%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 9.5%. 65: 65: NOTE: 9.5 % of the available CPU time was lost due to load imbalance 65: in the domain decomposition. 65: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 65: You can also consider manually changing the decomposition (option -dd); 65: e.g. by using fewer domains along the box dimension in which there is 65: considerable inhomogeneity in the simulated system. 65: 65: NOTE: 14 % of the run time was spent in domain decomposition, 65: 4 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 2.217 0.554 400.0 65: (ns/day) (hour/ns) 65: Performance: 2.806 8.552 65: 65: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (801 ms) 65: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 65: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: Net Acceleration in X direction, will not be corrected 65: Net Acceleration in Y direction, will not be corrected 65: Net Acceleration in Z direction, will not be corrected 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 8 steps, 0.0 ps. 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Setting gen_seed to 2012335871 65: 65: Velocities were taken from a Maxwell distribution at 0 K 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 1.8%. 65: The balanceable part of the MD step is 16%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 0.3%. 65: 65: 65: NOTE: 52 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.084 0.021 398.5 65: (ns/day) (hour/ns) 65: Performance: 73.546 0.326 65: 65: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (99 ms) 65: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 65: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 65: Net Acceleration in X direction, will not be corrected 65: Net Acceleration in Y direction, will not be corrected 65: Net Acceleration in Z direction, will not be corrected 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because verlet-buffer-tolerance is not set or used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 8 steps, 0.0 ps. 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Setting gen_seed to -624707 65: 65: Velocities were taken from a Maxwell distribution at 0 K 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 1.4%. 65: The balanceable part of the MD step is 38%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 0.5%. 65: 65: 65: NOTE: 54 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.191 0.048 399.4 65: (ns/day) (hour/ns) 65: Performance: 32.494 0.739 65: 65: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (175 ms) 65: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (1277 ms total) 65: 65: [----------] Global test environment tear-down 65: [==========] 28 tests from 7 test suites ran. (27057 ms total) 65: [ PASSED ] 27 tests. 65: [ SKIPPED ] 1 test, listed below: 65: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 65/87 Test #65: MdrunTestsTwoRanks ........................ Passed 27.12 sec test 66 Start 66: MdrunSingleRankAlgorithmsTests 66: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-single-rank-algorithms-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunSingleRankAlgorithmsTests.xml" 66: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 66: Test timeout computed to be: 600 66: [==========] Running 5 tests from 3 test suites. 66: [----------] Global test environment set-up. 66: [----------] 1 test from DispersionCorrectionTest 66: [ RUN ] DispersionCorrectionTest.DispersionCorrectionCanRun 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 30.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 66: Changing nstlist from 10 to 40, rlist from 1.027 to 1.175 66: 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 200 steps, 0.4 ps. 66: Setting the LD random seed to -70488887 66: 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning H bonds into constraints... 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Converted 3 Bonds with virtual sites to connections, 7 left 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 12 Constraints with virtual sites to connections, 0 left 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.038 nm, buffer size 0.038 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.023 nm, buffer size 0.023 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.093 0.047 199.8 66: (ns/day) (hour/ns) 66: Performance: 745.654 0.032 66: [ OK ] DispersionCorrectionTest.DispersionCorrectionCanRun (151 ms) 66: [----------] 1 test from DispersionCorrectionTest (152 ms total) 66: 66: [----------] 1 test from OriresTest 66: [ RUN ] OriresTest.OriresCanRun 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 518.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 66: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank. 66: Changing nstlist from 10 to 25, rlist from 1.076 to 1.219 66: 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1' 66: 10 steps, 0.0 ps. 66: Setting the LD random seed to 2111827727 66: 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.070 nm, buffer size 0.070 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 33 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.243 0.122 199.9 66: (ns/day) (hour/ns) 66: Performance: 15.606 1.538 66: [ OK ] OriresTest.OriresCanRun (605 ms) 66: [----------] 1 test from OriresTest (605 ms total) 66: 66: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest 66: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 66: Number of degrees of freedom in T-Coupling group rest is 10.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 66: NVE simulation with an initial temperature of zero: will use a Verlet 66: buffer of 10%. Check your energy drift! 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 66: The optimal PME mesh load for parallel simulations is below 0.5 66: and for highly parallel simulations between 0.25 and 0.33, 66: for higher performance, increase the cut-off and the PME grid spacing. 66: 66: 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Dipoles' 66: 20 steps, 0.1 ps. 66: Setting the LD random seed to 2079717871 66: 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Dipole' 66: 66: Searching the wall atom type(s) 66: 66: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 66: Calculating fourier grid dimensions for X Y Z 66: Using a fourier grid of 20x20x40, spacing 0.200 0.200 0.200 66: 66: Estimate for the relative computational load of the PME mesh part: 1.00 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.064 0.032 199.5 66: (ns/day) (hour/ns) 66: Performance: 142.271 0.169 66: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 trr version: GMX_trn_file (double precision) 66: 66: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 (831 ms) 66: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 66: Test system 'epsilon-surface-constraint' cannot run with 1 ranks. 66: The supported numbers are > 1. 66: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 (0 ms) 66: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 66: With epsilon_surface > 0 all molecules should be neutral. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 66: With epsilon_surface > 0 you can only use domain decomposition when there 66: are only small molecules with all bonds constrained (mdrun will check for 66: this). 66: 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 66: NVE simulation with an initial temperature of zero: will use a Verlet 66: buffer of 10%. Check your energy drift! 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 66: The optimal PME mesh load for parallel simulations is below 0.5 66: and for highly parallel simulations between 0.25 and 0.33, 66: for higher performance, increase the cut-off and the PME grid spacing. 66: 66: 66: 66: There were 4 NOTEs 66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Dipoles' 66: 20 steps, 0.1 ps. 66: Setting the LD random seed to -1346897670 66: 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Dipole' 66: 66: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 66: Calculating fourier grid dimensions for X Y Z 66: Using a fourier grid of 20x20x20, spacing 0.200 0.200 0.200 66: 66: Estimate for the relative computational load of the PME mesh part: 1.00 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.093 0.046 199.8 66: (ns/day) (hour/ns) 66: Performance: 97.551 0.246 66: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 66: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 (258 ms) 66: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest (1095 ms total) 66: 66: [----------] Global test environment tear-down 66: [==========] 5 tests from 3 test suites ran. (2013 ms total) 66: [ PASSED ] 5 tests. 66/87 Test #66: MdrunSingleRankAlgorithmsTests ............ Passed 2.08 sec test 67 Start 67: Minimize1RankTests 67: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/minimize-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/Minimize1RankTests.xml" 67: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 67: Test timeout computed to be: 600 67: [==========] Running 12 tests from 2 test suites. 67: [----------] Global test environment set-up. 67: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 67: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group System is 27.00 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 4 NOTEs 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 5 steps. 67: Potential Energy = -4.79910463671093e+01 67: Maximum force = 1.86297359432254e+02 on atom 13 67: Norm of force = 8.77219865482271e+01 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 67: 67: Generated 330891 of the 330891 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (507 ms) 67: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group System is 27.00 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 4 NOTEs 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Polak-Ribiere Conjugate Gradients: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: F-max = 3.02331e+02 on atom 3 67: F-Norm = 1.18024e+02 67: 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 67: Potential Energy = -5.58622538633290e+01 67: Maximum force = 4.27274822366542e+02 on atom 13 67: Norm of force = 1.84530029253835e+02 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 67: 67: Generated 330891 of the 330891 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (524 ms) 67: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: Generating 1-4 interactions: fudge = 1 67: Number of degrees of freedom in T-Coupling group System is 22.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 4 NOTEs 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 5 steps. 67: Potential Energy = 3.19376899751523e+02 67: Maximum force = 9.99884921009767e+03 on atom 9 67: Norm of force = 4.61669565054298e+03 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 67: 67: Generated 17396 of the 20503 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Glycine' 67: 67: turning H bonds into constraints... 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (83 ms) 67: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: Generating 1-4 interactions: fudge = 1 67: 67: NOTE 3 [file glycine_vacuo.top, line 12]: 67: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 67: 67: Number of degrees of freedom in T-Coupling group System is 22.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 5 NOTEs 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Polak-Ribiere Conjugate Gradients: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: F-max = 2.41575e+04 on atom 10 67: F-Norm = 1.18451e+04 67: 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 67: Potential Energy = 1.51743018140929e+02 67: Maximum force = 7.42089573409108e+03 on atom 9 67: Norm of force = 3.56929298615740e+03 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 67: 67: Generated 17396 of the 20503 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Glycine' 67: 67: turning H bonds into constraints... 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (84 ms) 67: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file unknown]: 67: You are using constraints on all bonds, whereas the forcefield has been 67: parametrized only with constraints involving hydrogen atoms. We suggest 67: using constraints = h-bonds instead, this will also improve performance. 67: 67: Number of degrees of freedom in T-Coupling group System is 23.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 5 NOTEs 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 67: Update groups can not be used for this system because an incompatible virtual site type is used 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 5 steps. 67: Potential Energy = -1.56984193848274e+02 67: Maximum force = 4.56923624626366e+02 on atom 17 67: Norm of force = 1.83258377168339e+02 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 67: 67: turning all bonds into constraints... 67: 67: Cleaning up constraints and constant bonded interactions with virtual sites 67: 67: Removed 18 Angles with virtual sites, 21 left 67: 67: Removed 10 Proper Dih.s with virtual sites, 44 left 67: 67: Converted 15 Constraints with virtual sites to connections, 7 left 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (15 ms) 67: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file unknown]: 67: You are using constraints on all bonds, whereas the forcefield has been 67: parametrized only with constraints involving hydrogen atoms. We suggest 67: using constraints = h-bonds instead, this will also improve performance. 67: 67: 67: NOTE 4 [file unknown]: 67: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 67: 67: Number of degrees of freedom in T-Coupling group System is 23.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 6 NOTEs 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 67: Update groups can not be used for this system because an incompatible virtual site type is used 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Polak-Ribiere Conjugate Gradients: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: F-max = 1.06800e+03 on atom 28 67: F-Norm = 4.26922e+02 67: 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 67: Potential Energy = -1.69410778678182e+02 67: Maximum force = 2.18225948474083e+02 on atom 17 67: Norm of force = 7.92068036537875e+01 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 67: 67: turning all bonds into constraints... 67: 67: Cleaning up constraints and constant bonded interactions with virtual sites 67: 67: Removed 18 Angles with virtual sites, 21 left 67: 67: Removed 10 Proper Dih.s with virtual sites, 44 left 67: 67: Converted 15 Constraints with virtual sites to connections, 7 left 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (46 ms) 67: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (1265 ms total) 67: 67: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 67: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents converged to Fmax < 10 in 1 steps 67: Potential Energy = -9.74257075835447e-01 67: Maximum force = 4.01322929015133e+00 on atom 1 67: Norm of force = 1.63839399694378e+00 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (90 ms) 67: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Polak-Ribiere Conjugate Gradients: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: F-max = 4.01323e+00 on atom 1 67: F-Norm = 1.63839e+00 67: 67: 67: writing lowest energy coordinates. 67: 67: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 67: Potential Energy = -9.90642313893957e-01 67: Maximum force = 2.57812909491104e+00 on atom 1 67: Norm of force = 1.05251679559258e+00 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (40 ms) 67: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 67: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 3 NOTEs 67: 67: There was 1 WARNING 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 67: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Low-Memory BFGS Minimizer: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: Using 10 BFGS correction steps. 67: 67: F-max = 4.01323e+00 on atom 1 67: F-Norm = 1.63839e+00 67: 67: 67: writing lowest energy coordinates. 67: 67: Low-Memory BFGS Minimizer converged to Fmax < 10 in -1 steps 67: Potential Energy = -9.90642313893957e-01 67: Maximum force = 2.57812909491104e+00 on atom 1 67: Norm of force = 1.05251679559258e+00 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (42 ms) 67: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: Generating 1-4 interactions: fudge = 1 67: Number of degrees of freedom in T-Coupling group System is 27.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 4 NOTEs 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 5 steps. 67: Potential Energy = 3.19395484891518e+02 67: Maximum force = 9.97041707197910e+03 on atom 9 67: Norm of force = 4.62274878665467e+03 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 67: 67: Generated 17396 of the 20503 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Glycine' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (93 ms) 67: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: Generating 1-4 interactions: fudge = 1 67: Number of degrees of freedom in T-Coupling group System is 27.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 4 NOTEs 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Polak-Ribiere Conjugate Gradients: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: F-max = 2.41672e+04 on atom 10 67: F-Norm = 1.19357e+04 67: 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 67: Potential Energy = 1.56258793899481e+02 67: Maximum force = 7.50181017480396e+03 on atom 9 67: Norm of force = 3.61390332564874e+03 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 67: 67: Generated 17396 of the 20503 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Glycine' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (72 ms) 67: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 67: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 67: 67: Generating 1-4 interactions: fudge = 1 67: Number of degrees of freedom in T-Coupling group System is 27.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 67: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Low-Memory BFGS Minimizer: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: Using 10 BFGS correction steps. 67: 67: F-max = 2.41672e+04 on atom 10 67: F-Norm = 1.19357e+04 67: 67: 67: Energy minimization has stopped, but the forces have not converged to the 67: requested precision Fmax < 10 (which may not be possible for your system). It 67: stopped because the algorithm tried to make a new step whose size was too 67: small, or there was no change in the energy since last step. Either way, we 67: regard the minimization as converged to within the available machine 67: precision, given your starting configuration and EM parameters. 67: 67: writing lowest energy coordinates. 67: 67: Low-Memory BFGS Minimizer converged to machine precision in 0 steps, 67: but did not reach the requested Fmax < 10. 67: Potential Energy = 5.61116097794204e+02 67: Maximum force = 1.26854826291223e+04 on atom 10 67: Norm of force = 6.06436286976271e+03 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 67: 67: Generated 17396 of the 20503 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Glycine' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (79 ms) 67: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (420 ms total) 67: 67: [----------] Global test environment tear-down 67: [==========] 12 tests from 2 test suites ran. (1949 ms total) 67: [ PASSED ] 12 tests. 67/87 Test #67: Minimize1RankTests ........................ Passed 2.01 sec test 68 Start 68: Minimize2RankTests 68: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/minimize-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/Minimize2RankTests.xml" 68: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 68: Test timeout computed to be: 600 68: [==========] Running 12 tests from 2 test suites. 68: [----------] Global test environment set-up. 68: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 68: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 27.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 4 NOTEs 68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: Steepest Descents: 68: Tolerance (Fmax) = 1.00000e+01 68: Number of steps = 4 68: 68: Energy minimization reached the maximum number of steps before the forces 68: reached the requested precision Fmax < 10. 68: 68: writing lowest energy coordinates. 68: 68: Steepest Descents did not converge to Fmax < 10 in 5 steps. 68: Potential Energy = -4.79910463671096e+01 68: Maximum force = 1.86297359432255e+02 on atom 13 68: Norm of force = 8.77219865482272e+01 68: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 68: 68: Generated 330891 of the 330891 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (447 ms) 68: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 27.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 4 NOTEs 68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: Polak-Ribiere Conjugate Gradients: 68: Tolerance (Fmax) = 1.00000e+01 68: Number of steps = 4 68: F-max = 3.02331e+02 on atom 3 68: F-Norm = 1.18024e+02 68: 68: 68: Energy minimization reached the maximum number of steps before the forces 68: reached the requested precision Fmax < 10. 68: 68: writing lowest energy coordinates. 68: 68: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 68: Potential Energy = -5.58622538633294e+01 68: Maximum force = 4.27274822366532e+02 on atom 13 68: Norm of force = 1.84530029253832e+02 68: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 68: 68: Generated 330891 of the 330891 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (1049 ms) 68: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: Generating 1-4 interactions: fudge = 1 68: Number of degrees of freedom in T-Coupling group System is 22.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 4 NOTEs 68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: Steepest Descents: 68: Tolerance (Fmax) = 1.00000e+01 68: Number of steps = 4 68: 68: Energy minimization reached the maximum number of steps before the forces 68: reached the requested precision Fmax < 10. 68: 68: writing lowest energy coordinates. 68: 68: Steepest Descents did not converge to Fmax < 10 in 5 steps. 68: Potential Energy = 3.19376899751523e+02 68: Maximum force = 9.99884921009767e+03 on atom 9 68: Norm of force = 4.61669565054298e+03 68: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 68: 68: Generated 17396 of the 20503 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Glycine' 68: 68: turning H bonds into constraints... 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (133 ms) 68: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: Generating 1-4 interactions: fudge = 1 68: 68: NOTE 3 [file glycine_vacuo.top, line 12]: 68: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 68: 68: Number of degrees of freedom in T-Coupling group System is 22.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 5 NOTEs 68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: Polak-Ribiere Conjugate Gradients: 68: Tolerance (Fmax) = 1.00000e+01 68: Number of steps = 4 68: F-max = 2.41575e+04 on atom 10 68: F-Norm = 1.18451e+04 68: 68: 68: Energy minimization reached the maximum number of steps before the forces 68: reached the requested precision Fmax < 10. 68: 68: writing lowest energy coordinates. 68: 68: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 68: Potential Energy = 1.51743018140928e+02 68: Maximum force = 7.42089573409111e+03 on atom 9 68: Norm of force = 3.56929298615739e+03 68: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 68: 68: Generated 17396 of the 20503 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Glycine' 68: 68: turning H bonds into constraints... 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (775 ms) 68: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 5 NOTEs 68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: Steepest Descents: 68: Tolerance (Fmax) = 1.00000e+01 68: Number of steps = 4 68: 68: Energy minimization reached the maximum number of steps before the forces 68: reached the requested precision Fmax < 10. 68: 68: writing lowest energy coordinates. 68: 68: Steepest Descents did not converge to Fmax < 10 in 5 steps. 68: Potential Energy = -1.56984193848274e+02 68: Maximum force = 4.56923624626366e+02 on atom 17 68: Norm of force = 1.83258377168339e+02 68: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (734 ms) 68: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: 68: NOTE 4 [file unknown]: 68: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 6 NOTEs 68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: Polak-Ribiere Conjugate Gradients: 68: Tolerance (Fmax) = 1.00000e+01 68: Number of steps = 4 68: F-max = 1.06800e+03 on atom 28 68: F-Norm = 4.26922e+02 68: 68: 68: Energy minimization reached the maximum number of steps before the forces 68: reached the requested precision Fmax < 10. 68: 68: writing lowest energy coordinates. 68: 68: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 68: Potential Energy = -1.69410778678181e+02 68: Maximum force = 2.18225948474083e+02 on atom 17 68: Norm of force = 7.92068036537875e+01 68: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (134 ms) 68: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (3282 ms total) 68: 68: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 68: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: Steepest Descents: 68: Tolerance (Fmax) = 1.00000e+01 68: Number of steps = 4 68: 68: writing lowest energy coordinates. 68: 68: Steepest Descents converged to Fmax < 10 in 1 steps 68: Potential Energy = -9.74257075835447e-01 68: Maximum force = 4.01322929015133e+00 on atom 3 68: Norm of force = 1.63839399694378e+00 68: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (270 ms) 68: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: Polak-Ribiere Conjugate Gradients: 68: Tolerance (Fmax) = 1.00000e+01 68: Number of steps = 4 68: F-max = 4.01323e+00 on atom 3 68: F-Norm = 1.63839e+00 68: 68: 68: writing lowest energy coordinates. 68: 68: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 68: Potential Energy = -9.90642313893957e-01 68: Maximum force = 2.57812909491104e+00 on atom 3 68: Norm of force = 1.05251679559258e+00 68: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (141 ms) 68: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 68: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 3 NOTEs 68: 68: There was 1 WARNING 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (3 ms) 68: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: Generating 1-4 interactions: fudge = 1 68: Number of degrees of freedom in T-Coupling group System is 27.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 4 NOTEs 68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: Steepest Descents: 68: Tolerance (Fmax) = 1.00000e+01 68: Number of steps = 4 68: 68: Energy minimization reached the maximum number of steps before the forces 68: reached the requested precision Fmax < 10. 68: 68: writing lowest energy coordinates. 68: 68: Steepest Descents did not converge to Fmax < 10 in 5 steps. 68: Potential Energy = 3.19395484891518e+02 68: Maximum force = 9.97041707197910e+03 on atom 9 68: Norm of force = 4.62274878665467e+03 68: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 68: 68: Generated 17396 of the 20503 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Glycine' 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (140 ms) 68: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: Generating 1-4 interactions: fudge = 1 68: Number of degrees of freedom in T-Coupling group System is 27.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 4 NOTEs 68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: Polak-Ribiere Conjugate Gradients: 68: Tolerance (Fmax) = 1.00000e+01 68: Number of steps = 4 68: F-max = 2.41672e+04 on atom 10 68: F-Norm = 1.19357e+04 68: 68: 68: Energy minimization reached the maximum number of steps before the forces 68: reached the requested precision Fmax < 10. 68: 68: writing lowest energy coordinates. 68: 68: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 68: Potential Energy = 1.56258793899481e+02 68: Maximum force = 7.50181017480396e+03 on atom 9 68: Norm of force = 3.61390332564874e+03 68: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 68: 68: Generated 17396 of the 20503 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Glycine' 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (371 ms) 68: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 68: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 68: 68: Generating 1-4 interactions: fudge = 1 68: Number of degrees of freedom in T-Coupling group System is 27.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 4 NOTEs 68: 68: There was 1 WARNING 68: Generated 20503 of the 20503 non-bonded parameter combinations 68: 68: Generated 17396 of the 20503 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Glycine' 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (48 ms) 68: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (977 ms total) 68: 68: [----------] Global test environment tear-down 68: [==========] 12 tests from 2 test suites ran. (4369 ms total) 68: [ PASSED ] 12 tests. 68/87 Test #68: Minimize2RankTests ........................ Passed 4.40 sec test 69 Start 69: MdrunNonIntegratorTests 69: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunNonIntegratorTests.xml" 69: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 69: Test timeout computed to be: 600 69: [==========] Running 53 tests from 5 test suites. 69: [----------] Global test environment set-up. 69: [----------] 1 test from NonbondedBenchTest 69: [ RUN ] NonbondedBenchTest.BasicEndToEndTest 69: SIMD width: 2 69: System size: 3000 atoms 69: Cut-off radius: 1 nm 69: Number of threads: 1 69: Number of iterations: 1 69: Compute energies: no 69: Ewald excl. corr.: analytical 69: 69: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle 69: total useful 69: Ewald all geom. 4xM 51.704 51.7044 0.0205 0.0122 69: [ OK ] NonbondedBenchTest.BasicEndToEndTest (70 ms) 69: [----------] 1 test from NonbondedBenchTest (70 ms total) 69: 69: [----------] 5 tests from NormalModesWorks/NormalModesTest 69: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/0 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 69: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 69: setting nstcomm equal to nstcalcenergy for less overhead 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 15.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 69: COM removal frequency is set to (4). 69: Other settings require a global communication frequency of 100. 69: Note that this will require additional global communication steps, 69: which will reduce performance when using multiple ranks. 69: Consider setting nstcomm to a multiple of 100. 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: Small system size (N=6), using full Hessian format. 69: Allocating Hessian memory... 69: 69: starting normal mode calculation '2 scaled waters' 69: 12 steps. 69: 69: Maximum force: 9.96989e-06 69: 69: 69: Writing Hessian... 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Reading double precision matrix generated by GROMACS 2024.4-Debian_2024.4_1 69: 69: Diagonalizing to find vectors 7 through 18... 69: Writing eigenvalues... 69: 69: Writing average structure & eigenvectors 7--18 to eigenvec.trr 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Generated 3 of the 3 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: This run will generate roughly 0 Mb of data 69: There are: 6 Atoms 69: Using begin = 7 and end = 18 69: Full matrix storage format, nrow=18, ncols=18 69: Writing eigenfrequencies - negative eigenvalues will be set to zero. 69: Cannot compute entropy when -first = 7 69: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/0 (29 ms) 69: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/1 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 69: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 69: setting nstcomm equal to nstcalcenergy for less overhead 69: 69: Generating 1-4 interactions: fudge = 1 69: 69: NOTE 3 [file villin.top, line 2452]: 69: System has non-zero total charge: -2.000000 69: Total charge should normally be an integer. See 69: https://manual.gromacs.org/current/user-guide/floating-point.html 69: for discussion on how close it should be to an integer. 69: 69: 69: 69: Number of degrees of freedom in T-Coupling group System is 765.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 69: COM removal frequency is set to (4). 69: Other settings require a global communication frequency of 100. 69: Note that this will require additional global communication steps, 69: which will reduce performance when using multiple ranks. 69: Consider setting nstcomm to a multiple of 100. 69: 69: 69: There were 5 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: Small system size (N=256), using full Hessian format. 69: Allocating Hessian memory... 69: 69: starting normal mode calculation 'AMYLOID BETA A4 PROTEIN' 69: 512 steps. 69: 69: Maximum force: 6.97568e-04 69: 69: 69: Writing Hessian... 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Reading double precision matrix generated by GROMACS 2024.4-Debian_2024.4_1 69: 69: Diagonalizing to find vectors 7 through 50... 69: Writing eigenvalues... 69: 69: Writing average structure & eigenvectors 7--50 to eigenvec.trr 69: Generated 20503 of the 20503 non-bonded parameter combinations 69: 69: Generated 17396 of the 20503 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 69: 69: This run will generate roughly 0 Mb of data 69: There are: 256 Atoms 69: Using begin = 7 and end = 50 69: Full matrix storage format, nrow=768, ncols=768 69: Writing eigenfrequencies - negative eigenvalues will be set to zero. 69: Cannot compute entropy when -first = 7 69: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/1 (1077 ms) 69: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/2 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 69: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 69: setting nstcomm equal to nstcalcenergy for less overhead 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 15.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 69: COM removal frequency is set to (4). 69: Other settings require a global communication frequency of 100. 69: Note that this will require additional global communication steps, 69: which will reduce performance when using multiple ranks. 69: Consider setting nstcomm to a multiple of 100. 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: Small system size (N=6), using full Hessian format. 69: Allocating Hessian memory... 69: 69: starting normal mode calculation 'flex spc dimer' 69: 12 steps. 69: 69: Maximum force: 3.36401e-04 69: 69: 69: Writing Hessian... 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Reading double precision matrix generated by GROMACS 2024.4-Debian_2024.4_1 69: 69: Diagonalizing to find vectors 7 through 18... 69: Writing eigenvalues... 69: 69: Writing average structure & eigenvectors 7--18 to eigenvec.trr 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: This run will generate roughly 0 Mb of data 69: There are: 6 Atoms 69: Using begin = 7 and end = 18 69: Full matrix storage format, nrow=18, ncols=18 69: Writing eigenfrequencies - negative eigenvalues will be set to zero. 69: Cannot compute entropy when -first = 7 69: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/2 (422 ms) 69: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/3 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 69: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 69: setting nstcomm equal to nstcalcenergy for less overhead 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 6.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 69: COM removal frequency is set to (4). 69: Other settings require a global communication frequency of 100. 69: Note that this will require additional global communication steps, 69: which will reduce performance when using multiple ranks. 69: Consider setting nstcomm to a multiple of 100. 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: Small system size (N=3), using full Hessian format. 69: Allocating Hessian memory... 69: 69: starting normal mode calculation '1 TIP5P' 69: 6 steps. 69: 69: Maximum force: 2.42882e-04 69: 69: 69: Writing Hessian... 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Reading double precision matrix generated by GROMACS 2024.4-Debian_2024.4_1 69: 69: Diagonalizing to find vectors 7 through 9... 69: Writing eigenvalues... 69: 69: Writing average structure & eigenvectors 7--9 to eigenvec.trr 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: This run will generate roughly 0 Mb of data 69: There are: 3 Atoms 69: There are: 2 VSites 69: Using begin = 7 and end = 9 69: Full matrix storage format, nrow=9, ncols=9 69: Writing eigenfrequencies - negative eigenvalues will be set to zero. 69: Cannot compute entropy when -first = 7 69: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/3 (371 ms) 69: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/4 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: Number of degrees of freedom in T-Coupling group System is 15.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 2 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Update groups can not be used for this system because the construction atoms of a virtual site are only partly with a group of constrained atoms 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: Small system size (N=6), using full Hessian format. 69: Allocating Hessian memory... 69: 69: starting normal mode calculation 'sw dimer' 69: 12 steps. 69: 69: Maximum force: 1.07599e-03 69: The force is probably not small enough to ensure that you are at a minimum. 69: Be aware that negative eigenvalues may occur 69: when the resulting matrix is diagonalized. 69: 69: 69: Writing Hessian... 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Reading double precision matrix generated by GROMACS 2024.4-Debian_2024.4_1 69: 69: Diagonalizing to find vectors 7 through 18... 69: Writing eigenvalues... 69: 69: Writing average structure & eigenvectors 7--18 to eigenvec.trr 69: Generated 6 of the 10 non-bonded parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SW' 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: This run will generate roughly 0 Mb of data 69: There are: 6 Atoms 69: There are: 2 Shells 69: There are: 2 VSites 69: 69: NOTE: in the current version shell prediction during the crun is disabled 69: 69: Using begin = 7 and end = 18 69: Full matrix storage format, nrow=18, ncols=18 69: Writing eigenfrequencies - negative eigenvalues will be set to zero. 69: Cannot compute entropy when -first = 7 69: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/4 (25 ms) 69: [----------] 5 tests from NormalModesWorks/NormalModesTest (1929 ms total) 69: 69: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 69: NVE simulation: will use the initial temperature of 68.810 K for 69: determining the Verlet buffer size 69: 69: 69: There were 3 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Argon' 69: 16 steps, 0.0 ps. 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Argon' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 39 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.154 0.077 199.8 69: (ns/day) (hour/ns) 69: Performance: 19.090 1.257 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr' 69: 69: trr version: GMX_trn_file (double precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 34 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 192.7 69: (ns/day) (hour/ns) 69: Performance: 1213.432 0.020 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (155 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 69: NVE simulation: will use the initial temperature of 68.810 K for 69: determining the Verlet buffer size 69: 69: 69: There were 3 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Argon' 69: 16 steps, 0.0 ps. 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Argon' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 22 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.127 0.064 199.8 69: (ns/day) (hour/ns) 69: Performance: 23.112 1.038 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 20 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.001 193.1 69: (ns/day) (hour/ns) 69: Performance: 2201.785 0.011 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (102 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: There were 2 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 100, rlist from 0.712 to 0.746 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Argon' 69: 16 steps, 0.0 ps. 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Argon' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.056 0.028 199.5 69: (ns/day) (hour/ns) 69: Performance: 52.615 0.456 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 100, rlist from 0.712 to 0.746 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 30 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.000 193.8 69: (ns/day) (hour/ns) 69: Performance: 3428.266 0.007 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (53 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: There were 2 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Argon' 69: 16 steps, 0.0 ps. 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Argon' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.050 0.025 199.6 69: (ns/day) (hour/ns) 69: Performance: 59.046 0.406 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.009 0.005 199.3 69: (ns/day) (hour/ns) 69: Performance: 312.578 0.077 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (40 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 69: NVE simulation: will use the initial temperature of 398.997 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.029 0.015 199.3 69: (ns/day) (hour/ns) 69: Performance: 100.726 0.238 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 18 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.000 192.0 69: (ns/day) (hour/ns) 69: Performance: 3695.617 0.006 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (471 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 69: NVE simulation: will use the initial temperature of 398.997 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.053 0.027 199.4 69: (ns/day) (hour/ns) 69: Performance: 55.160 0.435 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 25 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.000 192.1 69: (ns/day) (hour/ns) 69: Performance: 3626.012 0.007 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (435 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 100, rlist from 0.736 to 0.834 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.738 nm, buffer size 0.038 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.071 0.036 199.7 69: (ns/day) (hour/ns) 69: Performance: 41.239 0.582 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 100, rlist from 0.736 to 0.834 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 21 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.000 191.5 69: (ns/day) (hour/ns) 69: Performance: 4952.246 0.005 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (432 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.075 0.037 199.6 69: (ns/day) (hour/ns) 69: Performance: 39.309 0.611 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 21 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.001 189.9 69: (ns/day) (hour/ns) 69: Performance: 1881.672 0.013 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (436 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file unknown]: 69: You are using constraints on all bonds, whereas the forcefield has been 69: parametrized only with constraints involving hydrogen atoms. We suggest 69: using constraints = h-bonds instead, this will also improve performance. 69: 69: Number of degrees of freedom in T-Coupling group System is 23.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 69: NVE simulation: will use the initial temperature of 456.887 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 69: There are 9 non-linear virtual site constructions. Their contribution to 69: the energy error is approximated. In most cases this does not affect the 69: error significantly. 69: 69: 69: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 6 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine dipeptide in vacuo' 69: 16 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: turning all bonds into constraints... 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Converted 15 Constraints with virtual sites to connections, 7 left 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.072 0.036 199.5 69: (ns/day) (hour/ns) 69: Performance: 40.572 0.592 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 26 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 194.8 69: (ns/day) (hour/ns) 69: Performance: 1477.006 0.016 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (63 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file unknown]: 69: You are using constraints on all bonds, whereas the forcefield has been 69: parametrized only with constraints involving hydrogen atoms. We suggest 69: using constraints = h-bonds instead, this will also improve performance. 69: 69: Number of degrees of freedom in T-Coupling group System is 23.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 69: NVE simulation: will use the initial temperature of 456.887 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 69: There are 9 non-linear virtual site constructions. Their contribution to 69: the energy error is approximated. In most cases this does not affect the 69: error significantly. 69: 69: 69: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 6 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine dipeptide in vacuo' 69: 16 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: turning all bonds into constraints... 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Converted 15 Constraints with virtual sites to connections, 7 left 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.101 0.050 199.7 69: (ns/day) (hour/ns) 69: Performance: 29.118 0.824 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 24 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 194.9 69: (ns/day) (hour/ns) 69: Performance: 1500.754 0.016 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (83 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file unknown]: 69: You are using constraints on all bonds, whereas the forcefield has been 69: parametrized only with constraints involving hydrogen atoms. We suggest 69: using constraints = h-bonds instead, this will also improve performance. 69: 69: Number of degrees of freedom in T-Coupling group System is 23.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 69: There are 9 non-linear virtual site constructions. Their contribution to 69: the energy error is approximated. In most cases this does not affect the 69: error significantly. 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 80, rlist from 0.75 to 0.871 69: 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine dipeptide in vacuo' 69: 16 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: turning all bonds into constraints... 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Converted 15 Constraints with virtual sites to connections, 7 left 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.080 0.040 199.7 69: (ns/day) (hour/ns) 69: Performance: 36.730 0.653 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 80, rlist from 0.75 to 0.871 69: 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 19 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 193.7 69: (ns/day) (hour/ns) 69: Performance: 1776.411 0.014 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (179 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file unknown]: 69: You are using constraints on all bonds, whereas the forcefield has been 69: parametrized only with constraints involving hydrogen atoms. We suggest 69: using constraints = h-bonds instead, this will also improve performance. 69: 69: Number of degrees of freedom in T-Coupling group System is 23.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 69: There are 9 non-linear virtual site constructions. Their contribution to 69: the energy error is approximated. In most cases this does not affect the 69: error significantly. 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 25, rlist from 0.73 to 0.814 69: 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine dipeptide in vacuo' 69: 16 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: turning all bonds into constraints... 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Converted 15 Constraints with virtual sites to connections, 7 left 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.090 0.045 199.6 69: (ns/day) (hour/ns) 69: Performance: 32.511 0.738 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 25, rlist from 0.73 to 0.814 69: 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 21 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 194.7 69: (ns/day) (hour/ns) 69: Performance: 1628.494 0.015 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (115 ms) 69: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (2571 ms total) 69: 69: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.092 0.046 199.7 69: (ns/day) (hour/ns) 69: Performance: 31.970 0.751 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.008 0.004 196.4 69: (ns/day) (hour/ns) 69: Performance: 340.421 0.071 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (99 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.102 0.051 199.7 69: (ns/day) (hour/ns) 69: Performance: 28.757 0.835 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 19 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 183.2 69: (ns/day) (hour/ns) 69: Performance: 1699.943 0.014 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (81 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.124 0.062 199.6 69: (ns/day) (hour/ns) 69: Performance: 23.644 1.015 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 17 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 171.9 69: (ns/day) (hour/ns) 69: Performance: 1400.772 0.017 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (98 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.140 0.070 199.7 69: (ns/day) (hour/ns) 69: Performance: 20.963 1.145 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 18 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 183.7 69: (ns/day) (hour/ns) 69: Performance: 1403.324 0.017 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (122 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.055 0.028 199.5 69: (ns/day) (hour/ns) 69: Performance: 53.389 0.450 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.018 0.009 197.9 69: (ns/day) (hour/ns) 69: Performance: 157.310 0.153 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (75 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.062 0.031 199.6 69: (ns/day) (hour/ns) 69: Performance: 46.941 0.511 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 20 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 183.6 69: (ns/day) (hour/ns) 69: Performance: 1288.827 0.019 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (54 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.051 0.026 199.5 69: (ns/day) (hour/ns) 69: Performance: 57.210 0.420 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 19 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 184.0 69: (ns/day) (hour/ns) 69: Performance: 1580.450 0.015 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (61 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.051 0.026 199.5 69: (ns/day) (hour/ns) 69: Performance: 57.250 0.419 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 18 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 183.6 69: (ns/day) (hour/ns) 69: Performance: 1507.732 0.016 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (48 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.042 0.021 199.4 69: (ns/day) (hour/ns) 69: Performance: 69.376 0.346 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 20 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 185.2 69: (ns/day) (hour/ns) 69: Performance: 1438.719 0.017 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (47 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.042 0.021 199.3 69: (ns/day) (hour/ns) 69: Performance: 70.379 0.341 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 13 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 183.3 69: (ns/day) (hour/ns) 69: Performance: 1758.160 0.014 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (43 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.100 0.050 199.7 69: (ns/day) (hour/ns) 69: Performance: 29.395 0.816 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 18 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 184.5 69: (ns/day) (hour/ns) 69: Performance: 1500.023 0.016 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (72 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.072 0.036 199.6 69: (ns/day) (hour/ns) 69: Performance: 40.868 0.587 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.010 0.005 196.1 69: (ns/day) (hour/ns) 69: Performance: 283.990 0.085 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (62 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.057 0.028 199.8 69: (ns/day) (hour/ns) 69: Performance: 51.734 0.464 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 18 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 186.5 69: (ns/day) (hour/ns) 69: Performance: 1216.547 0.020 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (64 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.061 0.031 199.2 69: (ns/day) (hour/ns) 69: Performance: 47.838 0.502 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 22 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.005 0.002 190.4 69: (ns/day) (hour/ns) 69: Performance: 609.598 0.039 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (60 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.080 0.040 199.4 69: (ns/day) (hour/ns) 69: Performance: 36.602 0.656 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 19 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 186.0 69: (ns/day) (hour/ns) 69: Performance: 1255.982 0.019 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (100 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.056 0.028 199.1 69: (ns/day) (hour/ns) 69: Performance: 52.642 0.456 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 17 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 173.4 69: (ns/day) (hour/ns) 69: Performance: 1270.487 0.019 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (51 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.095 0.048 199.7 69: (ns/day) (hour/ns) 69: Performance: 30.878 0.777 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.010 0.005 194.2 69: (ns/day) (hour/ns) 69: Performance: 293.390 0.082 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (81 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.050 0.025 199.6 69: (ns/day) (hour/ns) 69: Performance: 59.186 0.405 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.018 0.009 198.0 69: (ns/day) (hour/ns) 69: Performance: 160.822 0.149 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (55 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.048 0.024 199.4 69: (ns/day) (hour/ns) 69: Performance: 61.417 0.391 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 19 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 179.2 69: (ns/day) (hour/ns) 69: Performance: 1704.647 0.014 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (46 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.050 0.025 199.6 69: (ns/day) (hour/ns) 69: Performance: 58.740 0.409 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 18 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 184.1 69: (ns/day) (hour/ns) 69: Performance: 1716.043 0.014 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (41 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.056 0.028 199.8 69: (ns/day) (hour/ns) 69: Performance: 52.851 0.454 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 19 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 182.2 69: (ns/day) (hour/ns) 69: Performance: 1696.666 0.014 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (51 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.051 0.026 199.4 69: (ns/day) (hour/ns) 69: Performance: 57.383 0.418 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 18 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 185.2 69: (ns/day) (hour/ns) 69: Performance: 1126.869 0.021 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (51 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.039 0.019 199.3 69: (ns/day) (hour/ns) 69: Performance: 75.528 0.318 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 20 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.003 0.001 187.9 69: (ns/day) (hour/ns) 69: Performance: 984.435 0.024 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (45 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.048 0.024 199.3 69: (ns/day) (hour/ns) 69: Performance: 60.611 0.396 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 23 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.003 0.001 184.5 69: (ns/day) (hour/ns) 69: Performance: 999.610 0.024 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (85 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.061 0.031 199.4 69: (ns/day) (hour/ns) 69: Performance: 48.055 0.499 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 18 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 186.5 69: (ns/day) (hour/ns) 69: Performance: 1462.282 0.016 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (72 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.048 0.024 199.1 69: (ns/day) (hour/ns) 69: Performance: 61.309 0.391 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 22 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.003 0.001 186.2 69: (ns/day) (hour/ns) 69: Performance: 997.021 0.024 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (53 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.064 0.032 199.4 69: (ns/day) (hour/ns) 69: Performance: 45.707 0.525 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 16 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 183.0 69: (ns/day) (hour/ns) 69: Performance: 1280.522 0.019 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (69 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.059 0.030 199.4 69: (ns/day) (hour/ns) 69: Performance: 49.465 0.485 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.003 91.1 69: (ns/day) (hour/ns) 69: Performance: 545.813 0.044 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (75 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.052 0.026 199.4 69: (ns/day) (hour/ns) 69: Performance: 56.745 0.423 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.008 0.004 194.9 69: (ns/day) (hour/ns) 69: Performance: 371.321 0.065 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (64 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.092 0.046 199.7 69: (ns/day) (hour/ns) 69: Performance: 31.877 0.753 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.015 0.007 197.0 69: (ns/day) (hour/ns) 69: Performance: 197.829 0.121 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (93 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.093 0.047 199.7 69: (ns/day) (hour/ns) 69: Performance: 31.426 0.764 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.005 34.5 69: (ns/day) (hour/ns) 69: Performance: 289.352 0.083 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (95 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.101 0.051 199.5 69: (ns/day) (hour/ns) 69: Performance: 28.938 0.829 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.003 0.002 191.0 69: (ns/day) (hour/ns) 69: Performance: 916.755 0.026 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (119 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.139 0.070 199.7 69: (ns/day) (hour/ns) 69: Performance: 21.102 1.137 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 19 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.002 0.001 180.8 69: (ns/day) (hour/ns) 69: Performance: 1619.079 0.015 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (125 ms) 69: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (2387 ms total) 69: 69: [----------] 2 tests from Angles1/SimpleMdrunTest 69: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/0 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file angles1.top, line 72]: 69: In moleculetype 'butane' 4 atoms are not bound by a potential or 69: constraint to any other atom in the same moleculetype. Although 69: technically this might not cause issues in a simulation, this often means 69: that the user forgot to add a bond/potential/constraint or put multiple 69: molecules in the same moleculetype definition by mistake. Run with -v to 69: get information for each atom. 69: 69: Number of degrees of freedom in T-Coupling group System is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0_input.mdp]: 69: NVE simulation: will use the initial temperature of 238.919 K for 69: determining the Verlet buffer size 69: 69: 69: There were 3 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'This_incredible_box_of_butane' 69: 50 steps, 0.1 ps. 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'butane' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.104 0.052 199.7 69: (ns/day) (hour/ns) 69: Performance: 84.792 0.283 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 5 time 0.020 Reading energy frame 6 time 0.024 Reading energy frame 7 time 0.028 Reading energy frame 8 time 0.032 Reading energy frame 9 time 0.036 Reading energy frame 10 time 0.040 Reading energy frame 11 time 0.044 Reading energy frame 12 time 0.048 Reading energy frame 13 time 0.050 Last energy frame read 13 time 0.050 69: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/0 (72 ms) 69: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/1 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file angles1.top, line 72]: 69: In moleculetype 'butane' 4 atoms are not bound by a potential or 69: constraint to any other atom in the same moleculetype. Although 69: technically this might not cause issues in a simulation, this often means 69: that the user forgot to add a bond/potential/constraint or put multiple 69: molecules in the same moleculetype definition by mistake. Run with -v to 69: get information for each atom. 69: 69: Number of degrees of freedom in T-Coupling group System is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1_input.mdp]: 69: NVE simulation: will use the initial temperature of 238.919 K for 69: determining the Verlet buffer size 69: 69: 69: There were 3 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'This_incredible_box_of_butane' 69: 50 steps, 0.1 ps. 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'butane' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.059 0.030 199.5 69: (ns/day) (hour/ns) 69: Performance: 147.755 0.162 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 5 time 0.020 Reading energy frame 6 time 0.024 Reading energy frame 7 time 0.028 Reading energy frame 8 time 0.032 Reading energy frame 9 time 0.036 Reading energy frame 10 time 0.040 Reading energy frame 11 time 0.044 Reading energy frame 12 time 0.048 Reading energy frame 13 time 0.050 Last energy frame read 13 time 0.050 69: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/1 (58 ms) 69: [----------] 2 tests from Angles1/SimpleMdrunTest (131 ms total) 69: 69: [----------] Global test environment tear-down 69: [==========] 53 tests from 5 test suites ran. (7268 ms total) 69: [ PASSED ] 53 tests. 69/87 Test #69: MdrunNonIntegratorTests ................... Passed 7.33 sec test 70 Start 70: MdrunTpiTests 70: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-tpi-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunTpiTests.xml" 70: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 70: Test timeout computed to be: 600 70: [==========] Running 2 tests from 1 test suite. 70: [----------] Global test environment set-up. 70: [----------] 2 tests from Simple/TpiTest 70: [ RUN ] Simple/TpiTest.ReproducesOutput/0 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 1308.00 70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 70: TPI is not implemented for GPUs. 70: 70: Using 1 MPI thread 70: Using 1 OpenMP thread 70: 70: 70: NOTE: Thread affinity was not set. 70: Reading frames from gro file '216 water molecules', 648 atoms. 70: Reading frame 0 time 0.000 mu 6.291e+01 6.291e+01 70: Last frame 0 time 0.000 70: Generated 331705 of the 331705 non-bonded parameter combinations 70: 70: Generated 331705 of the 331705 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Excluding 3 bonded neighbours molecule type 'methane' 70: Analysing residue names: 70: There are: 216 Water residues 70: There are: 1 Other residues 70: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] Simple/TpiTest.ReproducesOutput/0 (544 ms) 70: [ RUN ] Simple/TpiTest.ReproducesOutput/1 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 1308.00 70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 70: TPI is not implemented for GPUs. 70: 70: Using 1 MPI thread 70: Using 1 OpenMP thread 70: 70: 70: NOTE: Thread affinity was not set. 70: Reading frames from gro file '216 water molecules', 648 atoms. 70: Reading frame 0 time 0.000 mu 4.535e+01 4.535e+01 70: Last frame 0 time 0.000 70: Generated 331705 of the 331705 non-bonded parameter combinations 70: 70: Generated 331705 of the 331705 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Excluding 3 bonded neighbours molecule type 'methane' 70: Analysing residue names: 70: There are: 216 Water residues 70: There are: 1 Other residues 70: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] Simple/TpiTest.ReproducesOutput/1 (534 ms) 70: [----------] 2 tests from Simple/TpiTest (1078 ms total) 70: 70: [----------] Global test environment tear-down 70: [==========] 2 tests from 1 test suite ran. (1120 ms total) 70: [ PASSED ] 2 tests. 70/87 Test #70: MdrunTpiTests ............................. Passed 1.15 sec test 71 Start 71: MdrunMpiTests 71: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunMpiTests.xml" 71: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 71: Test timeout computed to be: 600 71: [==========] Running 16 tests from 2 test suites. 71: [----------] Global test environment set-up. 71: [----------] 4 tests from MimicTest 71: [ RUN ] MimicTest.OneQuantumMol 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 71: For a correct single-point energy evaluation with nsteps = 0, use 71: continuation = yes to avoid constraining the input coordinates. 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group rest is 21.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/4water.gro' 71: 71: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 71: Reading frame 0 time 0.000 Last frame 0 time 0.000 71: 71: NOTE: 86 % of the run time was spent in domain decomposition, 71: 3 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.249 0.062 399.7 71: (ns/day) (hour/ns) 71: Performance: 1.385 17.333 71: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file 71: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -269591047 71: 71: Generated 10 of the 10 non-bonded parameter combinations 71: 71: Generated 10 of the 10 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MimicTest.OneQuantumMol (152 ms) 71: [ RUN ] MimicTest.AllQuantumMol 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 71: For a correct single-point energy evaluation with nsteps = 0, use 71: continuation = yes to avoid constraining the input coordinates. 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group rest is 21.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/4water.gro' 71: 71: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 71: Reading frame 0 time 0.000 Last frame 0 time 0.000 71: 71: NOTE: 64 % of the run time was spent in domain decomposition, 71: 1 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.025 0.006 398.5 71: (ns/day) (hour/ns) 71: Performance: 13.698 1.752 71: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file 71: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1707425793 71: 71: Generated 10 of the 10 non-bonded parameter combinations 71: 71: Generated 10 of the 10 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MimicTest.AllQuantumMol (112 ms) 71: [ RUN ] MimicTest.TwoQuantumMol 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 71: For a correct single-point energy evaluation with nsteps = 0, use 71: continuation = yes to avoid constraining the input coordinates. 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group rest is 21.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/4water.gro' 71: 71: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 71: Reading frame 0 time 0.000 Last frame 0 time 0.000 71: 71: NOTE: 13 % of the run time was spent in domain decomposition, 71: 7 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.002 0.000 384.4 71: (ns/day) (hour/ns) 71: Performance: 205.261 0.117 71: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file 71: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -907719937 71: 71: Generated 10 of the 10 non-bonded parameter combinations 71: 71: Generated 10 of the 10 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MimicTest.TwoQuantumMol (6 ms) 71: [ RUN ] MimicTest.BondCuts 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 71: For a correct single-point energy evaluation with nsteps = 0, use 71: continuation = yes to avoid constraining the input coordinates. 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group rest is 66.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 71: NVE simulation: will use the initial temperature of 300.368 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/ala.gro' 71: 71: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 71: Reading frame 0 time 0.000 Last frame 0 time 0.000 71: 71: NOTE: 13 % of the run time was spent in domain decomposition, 71: 7 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.002 0.001 386.7 71: (ns/day) (hour/ns) 71: Performance: 134.044 0.179 71: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file 71: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -625285122 71: 71: Generated 2211 of the 2211 non-bonded parameter combinations 71: 71: Generated 2211 of the 2211 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 71: 71: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 71: 71: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MimicTest.BondCuts (81 ms) 71: [----------] 4 tests from MimicTest (352 ms total) 71: 71: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group rest is 9.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: There was 1 NOTE 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 9.00 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group rest is 9.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 71: The optimal PME mesh load for parallel simulations is below 0.5 71: and for highly parallel simulations between 0.25 and 0.33, 71: for higher performance, increase the cut-off and the PME grid spacing. 71: 71: 71: 71: There were 2 NOTEs 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 9.00 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 71: The optimal PME mesh load for parallel simulations is below 0.5 71: and for highly parallel simulations between 0.25 and 0.33, 71: for higher performance, increase the cut-off and the PME grid spacing. 71: 71: 71: 71: There was 1 NOTE 71: Setting the LD random seed to -67934337 71: 71: Generated 3 of the 3 non-bonded parameter combinations 71: 71: Generated 3 of the 3 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: This run will generate roughly 0 Mb of data 71: Setting the LD random seed to 1333262199 71: 71: Generated 3 of the 3 non-bonded parameter combinations 71: 71: Generated 3 of the 3 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 1.017 nm, buffer size 0.017 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 1.005 nm, buffer size 0.005 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: Setting the LD random seed to 2134302711 71: 71: Generated 3 of the 3 non-bonded parameter combinations 71: 71: Generated 3 of the 3 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 71: Calculating fourier grid dimensions for X Y Z 71: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 71: 71: Estimate for the relative computational load of the PME mesh part: 1.00 71: 71: This run will generate roughly 0 Mb of data 71: Setting the LD random seed to -3305638 71: 71: Generated 3 of the 3 non-bonded parameter combinations 71: 71: Generated 3 of the 3 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 71: 71: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: Calculating fourier grid dimensions for X Y Z 71: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 71: 71: Estimate for the relative computational load of the PME mesh part: 1.00 71: 71: This run will generate roughly 0 Mb of data 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_No.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc2' 71: 20 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: 71: Dynamic load balancing report: 71: DLB was off during the run due to low measured imbalance. 71: Average load imbalance: 2.6%. 71: The balanceable part of the MD step is 48%, load imbalance is computed from this. 71: Part of the total run time spent waiting due to load imbalance: 1.2%. 71: 71: 71: NOTE: 50 % of the run time was spent communicating energies, 71: you might want to increase some nst* mdp options 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.941 0.235 399.8 71: (ns/day) (hour/ns) 71: Performance: 7.711 3.112 71: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (238 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 71: ./src/programs/mdrun/tests/domain_decomposition.cpp:372: Skipped 71: Test configuration is invalid: 71: Cannot have separate PME ranks when PME is not used 71: 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 71: ./src/programs/mdrun/tests/domain_decomposition.cpp:372: Skipped 71: Test configuration is invalid: 71: Cannot have separate PME ranks when PME is not used 71: Cannot use two separate PME ranks when there are only two ranks total 71: 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_TemperatureAndPressure.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 71: Changing nstlist from 10 to 50, rlist from 1.009 to 1.15 71: 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc2' 71: 20 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: NOTE: 48 % of the run time was spent communicating energies, 71: you might want to increase some nst* mdp options 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.074 0.019 398.1 71: (ns/day) (hour/ns) 71: Performance: 97.532 0.246 71: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (22 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 71: ./src/programs/mdrun/tests/domain_decomposition.cpp:372: Skipped 71: Test configuration is invalid: 71: Cannot have separate PME ranks when PME is not used 71: 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 71: ./src/programs/mdrun/tests/domain_decomposition.cpp:372: Skipped 71: Test configuration is invalid: 71: Cannot have separate PME ranks when PME is not used 71: Cannot use two separate PME ranks when there are only two ranks total 71: 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc2' 71: 20 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: 71: Dynamic load balancing report: 71: DLB was off during the run due to low measured imbalance. 71: Average load imbalance: 2.8%. 71: The balanceable part of the MD step is 4%, load imbalance is computed from this. 71: Part of the total run time spent waiting due to load imbalance: 0.1%. 71: 71: 71: NOTE: 6 % of the run time was spent communicating energies, 71: you might want to increase some nst* mdp options 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.631 0.158 399.6 71: (ns/day) (hour/ns) 71: Performance: 11.497 2.087 71: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (313 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc2' 71: 20 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.265 0.066 398.8 71: (ns/day) (hour/ns) 71: Performance: 27.338 0.878 71: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (224 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 71: ./src/programs/mdrun/tests/domain_decomposition.cpp:372: Skipped 71: Test configuration is invalid: 71: Cannot use two separate PME ranks when there are only two ranks total 71: 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 71: Changing nstlist from 10 to 100, rlist from 1 to 1 71: 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc2' 71: 20 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: NOTE: 41 % of the run time was spent communicating energies, 71: you might want to increase some nst* mdp options 71: 71: Core t (s) Wall t (s) (%) 71: Time: 1.904 0.496 383.7 71: (ns/day) (hour/ns) 71: Performance: 3.657 6.564 71: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (643 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 71: Changing nstlist from 10 to 100, rlist from 1 to 1 71: 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc2' 71: 20 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.114 0.029 398.6 71: (ns/day) (hour/ns) 71: Performance: 63.398 0.379 71: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (97 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 71: ./src/programs/mdrun/tests/domain_decomposition.cpp:372: Skipped 71: Test configuration is invalid: 71: Cannot use two separate PME ranks when there are only two ranks total 71: 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 71: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest (1541 ms total) 71: 71: [----------] Global test environment tear-down 71: [==========] 16 tests from 2 test suites ran. (2727 ms total) 71: [ PASSED ] 10 tests. 71: [ SKIPPED ] 6 tests, listed below: 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 71/87 Test #71: MdrunMpiTests ............................. Passed 2.78 sec test 72 Start 72: MdrunMultiSimTests 72: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-multisim-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunMultiSimTests.xml" 72: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 72: Test timeout computed to be: 600 72: [==========] Running 2 tests from 1 test suite. 72: [----------] Global test environment set-up. 72: [----------] 2 tests from InNvt/MultiSimTerminationTest 72: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 72: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) 72: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 72: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 (0 ms) 72: [----------] 2 tests from InNvt/MultiSimTerminationTest (0 ms total) 72: 72: [----------] Global test environment tear-down 72: [==========] 2 tests from 1 test suite ran. (36 ms total) 72: [ PASSED ] 2 tests. 72: 72: YOU HAVE 4 DISABLED TESTS 72: 72/87 Test #72: MdrunMultiSimTests ........................ Passed 0.06 sec test 73 Start 73: MdrunMultiSimReplexTests 73: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-multisim-replex-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunMultiSimReplexTests.xml" 73: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 73: Test timeout computed to be: 600 73: [==========] Running 1 test from 1 test suite. 73: [----------] Global test environment set-up. 73: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest 73: [ RUN ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 73: [ OK ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) 73: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest (0 ms total) 73: 73: [----------] Global test environment tear-down 73: [==========] 1 test from 1 test suite ran. (38 ms total) 73: [ PASSED ] 1 test. 73: 73: YOU HAVE 4 DISABLED TESTS 73: 73/87 Test #73: MdrunMultiSimReplexTests .................. Passed 0.08 sec test 74 Start 74: MdrunMultiSimReplexEquivalenceTests 74: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-multisim-replex-equivalence-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunMultiSimReplexEquivalenceTests.xml" 74: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 74: Test timeout computed to be: 600 74: [==========] Running 0 tests from 0 test suites. 74: [==========] 0 tests from 0 test suites ran. (0 ms total) 74: [ PASSED ] 0 tests. 74: 74: YOU HAVE 10 DISABLED TESTS 74: 74/87 Test #74: MdrunMultiSimReplexEquivalenceTests ....... Passed 0.03 sec test 75 Start 75: MdrunMpi1RankPmeTests 75: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunMpi1RankPmeTests.xml" 75: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 75: Test timeout computed to be: 600 75: [==========] Running 19 tests from 1 test suite. 75: [----------] Global test environment set-up. 75: [----------] 19 tests from ReproducesEnergies/PmeTest 75: Number of degrees of freedom in T-Coupling group rest is 12.00 75: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 75: NVE simulation: will use the initial temperature of 1046.791 K for 75: determining the Verlet buffer size 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 75: The optimal PME mesh load for parallel simulations is below 0.5 75: and for highly parallel simulations between 0.25 and 0.33, 75: for higher performance, increase the cut-off and the PME grid spacing. 75: 75: 75: 75: There were 2 NOTEs 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 75: For a correct single-point energy evaluation with nsteps = 0, use 75: continuation = yes to avoid constraining the input coordinates. 75: 75: Number of degrees of freedom in T-Coupling group rest is 13.00 75: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 75: NVE simulation: will use the initial temperature of 966.268 K for 75: determining the Verlet buffer size 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 75: The optimal PME mesh load for parallel simulations is below 0.5 75: and for highly parallel simulations between 0.25 and 0.33, 75: for higher performance, increase the cut-off and the PME grid spacing. 75: 75: 75: 75: There were 3 NOTEs 75: Setting the LD random seed to -37816866 75: 75: Generated 8 of the 10 non-bonded parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'Methanol' 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 75: 75: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 75: 75: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: Calculating fourier grid dimensions for X Y Z 75: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 75: 75: Estimate for the relative computational load of the PME mesh part: 1.00 75: 75: This run will generate roughly 0 Mb of data 75: Setting the LD random seed to 1338674559 75: 75: Generated 8 of the 10 non-bonded parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'Methanol' 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Searching the wall atom type(s) 75: 75: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 75: 75: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 75: 75: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: Calculating fourier grid dimensions for X Y Z 75: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118 75: 75: Estimate for the relative computational load of the PME mesh part: 1.00 75: 75: This run will generate roughly 0 Mb of data 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu 75: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 75: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 1 MPI thread 75: Using 2 OpenMP threads 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'spc-and-methanol' 75: 20 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 25 % of the run time was spent in domain decomposition, 75: 8 % of the run time was spent in pair search, 75: you might want to increase nstlist (this has no effect on accuracy) 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.383 0.192 199.9 75: (ns/day) (hour/ns) 75: Performance: 9.461 2.537 75: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_0_pme_cpu.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu (552 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto 75: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 75: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 1 MPI thread 75: Using 2 OpenMP threads 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'spc-and-methanol' 75: 20 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.074 0.037 199.8 75: (ns/day) (hour/ns) 75: Performance: 49.188 0.488 75: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_0_pme_auto.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto (45 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Double-precision build of GROMACS. 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Double-precision build of GROMACS. 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Double-precision build of GROMACS. 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu 75: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 75: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 1 MPI thread 75: Using 2 OpenMP threads 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'spc-and-methanol' 75: 0 steps, 0.0 ps. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.003 0.002 194.3 75: (ns/day) (hour/ns) 75: Performance: 51.134 0.469 75: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls_mdrun_notunepme_npme_0_pme_cpu.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu (490 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Double-precision build of GROMACS. 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Double-precision build of GROMACS. 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets using PME rank(s) but the simulation is using only one rank 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets using PME rank(s) but the simulation is using only one rank 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets using PME rank(s) but the simulation is using only one rank 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Double-precision build of GROMACS. 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets using PME rank(s) but the simulation is using only one rank 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Double-precision build of GROMACS. 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets using PME rank(s) but the simulation is using only one rank 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Double-precision build of GROMACS. 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets using PME rank(s) but the simulation is using only one rank 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets using PME rank(s) but the simulation is using only one rank 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Double-precision build of GROMACS. 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets using PME rank(s) but the simulation is using only one rank 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Double-precision build of GROMACS. 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu 75: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 75: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 1 MPI thread 75: Using 2 OpenMP threads 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'spc-and-methanol' 75: 20 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.082 0.041 199.8 75: (ns/day) (hour/ns) 75: Performance: 44.286 0.542 75: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_tunepme_npme_0_pme_cpu.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu (51 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Double-precision build of GROMACS. 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Double-precision build of GROMACS. 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 75: [----------] 19 tests from ReproducesEnergies/PmeTest (1141 ms total) 75: 75: [----------] Global test environment tear-down 75: [==========] 19 tests from 1 test suite ran. (1191 ms total) 75: [ PASSED ] 4 tests. 75: [ SKIPPED ] 15 tests, listed below: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu 75/87 Test #75: MdrunMpi1RankPmeTests ..................... Passed 1.22 sec test 76 Start 76: MdrunMpi2RankPmeTests 76: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunMpi2RankPmeTests.xml" 76: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 76: Test timeout computed to be: 600 76: [==========] Running 19 tests from 1 test suite. 76: [----------] Global test environment set-up. 76: [----------] 19 tests from ReproducesEnergies/PmeTest 76: Number of degrees of freedom in T-Coupling group rest is 12.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 76: NVE simulation: will use the initial temperature of 1046.791 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 76: The optimal PME mesh load for parallel simulations is below 0.5 76: and for highly parallel simulations between 0.25 and 0.33, 76: for higher performance, increase the cut-off and the PME grid spacing. 76: 76: 76: 76: There were 2 NOTEs 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 76: For a correct single-point energy evaluation with nsteps = 0, use 76: continuation = yes to avoid constraining the input coordinates. 76: 76: Number of degrees of freedom in T-Coupling group rest is 13.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 76: NVE simulation: will use the initial temperature of 966.268 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 76: The optimal PME mesh load for parallel simulations is below 0.5 76: and for highly parallel simulations between 0.25 and 0.33, 76: for higher performance, increase the cut-off and the PME grid spacing. 76: 76: 76: 76: There were 3 NOTEs 76: Setting the LD random seed to -139511939 76: 76: Generated 8 of the 10 non-bonded parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'Methanol' 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: Calculating fourier grid dimensions for X Y Z 76: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 76: 76: Estimate for the relative computational load of the PME mesh part: 1.00 76: 76: This run will generate roughly 0 Mb of data 76: Setting the LD random seed to -6652939 76: 76: Generated 8 of the 10 non-bonded parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'Methanol' 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Searching the wall atom type(s) 76: 76: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: Calculating fourier grid dimensions for X Y Z 76: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118 76: 76: Estimate for the relative computational load of the PME mesh part: 1.00 76: 76: This run will generate roughly 0 Mb of data 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu 76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 76: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc-and-methanol' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: 76: Dynamic load balancing report: 76: DLB was off during the run due to low measured imbalance. 76: Average load imbalance: 11.2%. 76: The balanceable part of the MD step is 2%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 0.2%. 76: 76: 76: NOTE: 27 % of the run time was spent in domain decomposition, 76: 0 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: NOTE: 32 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.272 0.068 399.4 76: (ns/day) (hour/ns) 76: Performance: 26.628 0.901 76: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_0_pme_cpu.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu (369 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto 76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 76: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc-and-methanol' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: 76: Dynamic load balancing report: 76: DLB was off during the run due to low measured imbalance. 76: Average load imbalance: 3.4%. 76: The balanceable part of the MD step is 11%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 0.4%. 76: 76: 76: NOTE: 7 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: 76: Core t (s) Wall t (s) (%) 76: Time: 1.326 0.332 399.9 76: (ns/day) (hour/ns) 76: Performance: 5.473 4.385 76: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_0_pme_auto.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto (505 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: it targets PME decomposition, but that is not supported 76: PME GPU does not support: 76: Double-precision build of GROMACS. 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: it targets PME decomposition, but that is not supported 76: PME GPU does not support: 76: Double-precision build of GROMACS. 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: it targets PME decomposition, but that is not supported 76: PME GPU does not support: 76: Double-precision build of GROMACS. 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu 76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 76: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc-and-methanol' 76: 0 steps, 0.0 ps. 76: 76: NOTE: 15 % of the run time was spent in domain decomposition, 76: 0 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: NOTE: 15 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.434 0.109 399.4 76: (ns/day) (hour/ns) 76: Performance: 0.796 30.164 76: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls_mdrun_notunepme_npme_0_pme_cpu.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu (692 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: it targets PME decomposition, but that is not supported 76: PME GPU does not support: 76: Double-precision build of GROMACS. 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: it targets PME decomposition, but that is not supported 76: PME GPU does not support: 76: Double-precision build of GROMACS. 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu 76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 76: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc-and-methanol' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.465 0.116 399.6 76: (ns/day) (hour/ns) 76: Performance: 15.586 1.540 76: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_1_pme_cpu.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu (290 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto 76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 76: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc-and-methanol' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.451 0.113 399.4 76: (ns/day) (hour/ns) 76: Performance: 16.070 1.493 76: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_1_pme_auto.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto (144 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: PME GPU does not support: 76: Double-precision build of GROMACS. 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: PME GPU does not support: 76: Double-precision build of GROMACS. 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: PME GPU does not support: 76: Double-precision build of GROMACS. 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu 76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 76: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc-and-methanol' 76: 0 steps, 0.0 ps. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.337 0.084 399.3 76: (ns/day) (hour/ns) 76: Performance: 1.024 23.439 76: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls_mdrun_notunepme_npme_1_pme_cpu.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu (525 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: PME GPU does not support: 76: Double-precision build of GROMACS. 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: PME GPU does not support: 76: Double-precision build of GROMACS. 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu 76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 76: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc-and-methanol' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: 76: Dynamic load balancing report: 76: DLB was turned on during the run due to measured imbalance. 76: Average load imbalance: 23.7%. 76: The balanceable part of the MD step is 14%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 3.3%. 76: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 76: 76: 76: NOTE: 9 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: 76: Core t (s) Wall t (s) (%) 76: Time: 2.024 0.506 399.9 76: (ns/day) (hour/ns) 76: Performance: 3.585 6.695 76: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_tunepme_npme_0_pme_cpu.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu (588 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: it targets PME decomposition, but that is not supported 76: PME GPU does not support: 76: Double-precision build of GROMACS. 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: it targets PME decomposition, but that is not supported 76: PME GPU does not support: 76: Double-precision build of GROMACS. 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 76: [----------] 19 tests from ReproducesEnergies/PmeTest (3119 ms total) 76: 76: [----------] Global test environment tear-down 76: [==========] 19 tests from 1 test suite ran. (3185 ms total) 76: [ PASSED ] 7 tests. 76: [ SKIPPED ] 12 tests, listed below: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu 76/87 Test #76: MdrunMpi2RankPmeTests ..................... Passed 3.20 sec test 77 Start 77: MdrunCoordinationBasicTests1Rank 77: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-coordination-basic-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunCoordinationBasicTests1Rank.xml" 77: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 77: Test timeout computed to be: 1920 77: [==========] Running 1 test from 1 test suite. 77: [----------] Global test environment set-up. 77: [----------] 1 test from BasicPropagators/PeriodicActionsTest 77: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Number of degrees of freedom in T-Coupling group System is 33.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 68.810 K for 77: determining the Verlet buffer size 77: 77: 77: There were 3 NOTEs 77: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 1 OpenMP thread 77: 77: 77: NOTE: Thread affinity was not set. 77: starting mdrun 'Argon' 77: 16 steps, 0.0 ps. 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.021 0.021 99.9 77: (ns/day) (hour/ns) 77: Performance: 69.140 0.347 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Number of degrees of freedom in T-Coupling group System is 33.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 68.810 K for 77: determining the Verlet buffer size 77: 77: 77: There were 3 NOTEs 77: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 1 OpenMP thread 77: 77: 77: NOTE: Thread affinity was not set. 77: starting mdrun 'Argon' 77: 16 steps, 0.0 ps. 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.027 0.027 99.9 77: (ns/day) (hour/ns) 77: Performance: 53.853 0.446 77: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Number of degrees of freedom in T-Coupling group System is 33.00 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 68.810 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: COM removal frequency is set to (1). 77: Other settings require a global communication frequency of 4. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 4. 77: 77: 77: There were 5 NOTEs 77: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 1 OpenMP thread 77: 77: 77: NOTE: Thread affinity was not set. 77: starting mdrun 'Argon' 77: 16 steps, 0.0 ps. 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.007 0.007 99.6 77: (ns/day) (hour/ns) 77: Performance: 218.476 0.110 77: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Number of degrees of freedom in T-Coupling group System is 33.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 68.810 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: COM removal frequency is set to (1). 77: Other settings require a global communication frequency of 100. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 100. 77: 77: 77: There were 4 NOTEs 77: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 1 OpenMP thread 77: 77: 77: NOTE: Thread affinity was not set. 77: starting mdrun 'Argon' 77: 16 steps, 0.0 ps. 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.011 0.011 99.7 77: (ns/day) (hour/ns) 77: Performance: 135.383 0.177 77: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Number of degrees of freedom in T-Coupling group System is 33.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 68.810 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: COM removal frequency is set to (1). 77: Other settings require a global communication frequency of 100. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 100. 77: 77: 77: There were 4 NOTEs 77: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 1 OpenMP thread 77: 77: 77: NOTE: Thread affinity was not set. 77: starting mdrun 'Argon' 77: 16 steps, 0.0 ps. 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.017 0.017 99.8 77: (ns/day) (hour/ns) 77: Performance: 86.330 0.278 77: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Number of degrees of freedom in T-Coupling group System is 33.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 68.810 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: COM removal frequency is set to (1). 77: Other settings require a global communication frequency of 100. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 100. 77: 77: 77: There were 4 NOTEs 77: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 1 OpenMP thread 77: 77: 77: NOTE: Thread affinity was not set. 77: starting mdrun 'Argon' 77: 16 steps, 0.0 ps. 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.015 0.015 99.6 77: (ns/day) (hour/ns) 77: Performance: 97.452 0.246 77: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 77: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (137 ms) 77: [----------] 1 test from BasicPropagators/PeriodicActionsTest (137 ms total) 77: 77: [----------] Global test environment tear-down 77: [==========] 1 test from 1 test suite ran. (172 ms total) 77: [ PASSED ] 1 test. 77/87 Test #77: MdrunCoordinationBasicTests1Rank .......... Passed 0.24 sec test 78 Start 78: MdrunCoordinationBasicTests2Ranks 78: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-coordination-basic-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunCoordinationBasicTests2Ranks.xml" 78: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 78: Test timeout computed to be: 1920 78: [==========] Running 1 test from 1 test suite. 78: [----------] Global test environment set-up. 78: [----------] 1 test from BasicPropagators/PeriodicActionsTest 78: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 78: that with the Verlet scheme, nstlist has no effect on the accuracy of 78: your simulation. 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (1) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: There were 3 NOTEs 78: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI threads 78: Using 1 OpenMP thread per tMPI thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: 78: Dynamic load balancing report: 78: DLB was off during the run due to low measured imbalance. 78: Average load imbalance: 1.2%. 78: The balanceable part of the MD step is 52%, load imbalance is computed from this. 78: Part of the total run time spent waiting due to load imbalance: 0.6%. 78: 78: 78: NOTE: 53 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.047 0.023 199.5 78: (ns/day) (hour/ns) 78: Performance: 62.627 0.383 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 78: that with the Verlet scheme, nstlist has no effect on the accuracy of 78: your simulation. 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (1) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: There were 3 NOTEs 78: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI threads 78: Using 1 OpenMP thread per tMPI thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: 78: Dynamic load balancing report: 78: DLB was off during the run due to low measured imbalance. 78: Average load imbalance: 1.8%. 78: The balanceable part of the MD step is 49%, load imbalance is computed from this. 78: Part of the total run time spent waiting due to load imbalance: 0.9%. 78: 78: 78: NOTE: 71 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.053 0.031 173.8 78: (ns/day) (hour/ns) 78: Performance: 47.939 0.501 78: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 78: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 78: that with the Verlet scheme, nstlist has no effect on the accuracy of 78: your simulation. 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 78: setting nstcomm equal to nstcalcenergy for less overhead 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: COM removal frequency is set to (1). 78: Other settings require a global communication frequency of 4. 78: Note that this will require additional global communication steps, 78: which will reduce performance when using multiple ranks. 78: Consider setting nstcomm to a multiple of 4. 78: 78: 78: There were 5 NOTEs 78: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI threads 78: Using 1 OpenMP thread per tMPI thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: 78: Dynamic load balancing report: 78: DLB was turned on during the run due to measured imbalance. 78: Average load imbalance: 4.9%. 78: The balanceable part of the MD step is 44%, load imbalance is computed from this. 78: Part of the total run time spent waiting due to load imbalance: 2.2%. 78: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 78: 78: 78: NOTE: 56 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.025 0.013 199.1 78: (ns/day) (hour/ns) 78: Performance: 117.335 0.205 78: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 78: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 78: that with the Verlet scheme, nstlist has no effect on the accuracy of 78: your simulation. 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 78: setting nstcomm equal to nstcalcenergy for less overhead 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: COM removal frequency is set to (1). 78: Other settings require a global communication frequency of 100. 78: Note that this will require additional global communication steps, 78: which will reduce performance when using multiple ranks. 78: Consider setting nstcomm to a multiple of 100. 78: 78: 78: There were 4 NOTEs 78: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI threads 78: Using 1 OpenMP thread per tMPI thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: 78: Dynamic load balancing report: 78: DLB was off during the run due to low measured imbalance. 78: Average load imbalance: 3.3%. 78: The balanceable part of the MD step is 40%, load imbalance is computed from this. 78: Part of the total run time spent waiting due to load imbalance: 1.4%. 78: 78: 78: NOTE: 50 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.215 0.108 199.9 78: (ns/day) (hour/ns) 78: Performance: 13.641 1.759 78: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 78: that with the Verlet scheme, nstlist has no effect on the accuracy of 78: your simulation. 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 78: setting nstcomm equal to nstcalcenergy for less overhead 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: COM removal frequency is set to (1). 78: Other settings require a global communication frequency of 100. 78: Note that this will require additional global communication steps, 78: which will reduce performance when using multiple ranks. 78: Consider setting nstcomm to a multiple of 100. 78: 78: 78: There were 4 NOTEs 78: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI threads 78: Using 1 OpenMP thread per tMPI thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: 78: Dynamic load balancing report: 78: DLB was turned on during the run due to measured imbalance. 78: Average load imbalance: 9.0%. 78: The balanceable part of the MD step is 37%, load imbalance is computed from this. 78: Part of the total run time spent waiting due to load imbalance: 3.3%. 78: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 78: 78: 78: NOTE: 48 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.039 0.020 199.3 78: (ns/day) (hour/ns) 78: Performance: 74.499 0.322 78: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 78: that with the Verlet scheme, nstlist has no effect on the accuracy of 78: your simulation. 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 78: setting nstcomm equal to nstcalcenergy for less overhead 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: COM removal frequency is set to (1). 78: Other settings require a global communication frequency of 100. 78: Note that this will require additional global communication steps, 78: which will reduce performance when using multiple ranks. 78: Consider setting nstcomm to a multiple of 100. 78: 78: 78: There were 4 NOTEs 78: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI threads 78: Using 1 OpenMP thread per tMPI thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: 78: Dynamic load balancing report: 78: DLB was off during the run due to low measured imbalance. 78: Average load imbalance: 1.3%. 78: The balanceable part of the MD step is 38%, load imbalance is computed from this. 78: Part of the total run time spent waiting due to load imbalance: 0.5%. 78: 78: 78: NOTE: 48 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.036 0.018 199.4 78: (ns/day) (hour/ns) 78: Performance: 80.600 0.298 78: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 78: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (471 ms) 78: [----------] 1 test from BasicPropagators/PeriodicActionsTest (472 ms total) 78: 78: [----------] Global test environment tear-down 78: [==========] 1 test from 1 test suite ran. (507 ms total) 78: [ PASSED ] 1 test. 78/87 Test #78: MdrunCoordinationBasicTests2Ranks ......... Passed 0.53 sec test 79 Start 79: MdrunCoordinationCouplingTests1Rank 79: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-coordination-coupling-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunCoordinationCouplingTests1Rank.xml" 79: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 79: Test timeout computed to be: 1920 79: [==========] Running 25 tests from 1 test suite. 79: [----------] Global test environment set-up. 79: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.017 99.7 79: (ns/day) (hour/ns) 79: Performance: 88.516 0.271 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.012 0.012 99.6 79: (ns/day) (hour/ns) 79: Performance: 126.800 0.189 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 4. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 4. 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.009 0.009 99.4 79: (ns/day) (hour/ns) 79: Performance: 155.003 0.155 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.028 0.028 99.8 79: (ns/day) (hour/ns) 79: Performance: 52.404 0.458 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.011 0.011 99.6 79: (ns/day) (hour/ns) 79: Performance: 137.532 0.175 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.019 0.019 99.7 79: (ns/day) (hour/ns) 79: Performance: 77.078 0.311 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (128 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.014 99.8 79: (ns/day) (hour/ns) 79: Performance: 105.264 0.228 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.014 99.7 79: (ns/day) (hour/ns) 79: Performance: 106.265 0.226 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.013 0.013 99.7 79: (ns/day) (hour/ns) 79: Performance: 109.742 0.219 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.037 0.037 99.9 79: (ns/day) (hour/ns) 79: Performance: 39.850 0.602 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.043 0.043 99.9 79: (ns/day) (hour/ns) 79: Performance: 34.209 0.702 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.020 0.020 99.7 79: (ns/day) (hour/ns) 79: Performance: 73.660 0.326 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (176 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.022 0.022 99.8 79: (ns/day) (hour/ns) 79: Performance: 67.801 0.354 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.016 99.8 79: (ns/day) (hour/ns) 79: Performance: 92.345 0.260 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.017 99.8 79: (ns/day) (hour/ns) 79: Performance: 88.351 0.272 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.020 0.020 99.7 79: (ns/day) (hour/ns) 79: Performance: 73.285 0.327 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.018 0.018 99.8 79: (ns/day) (hour/ns) 79: Performance: 81.960 0.293 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.026 0.026 99.9 79: (ns/day) (hour/ns) 79: Performance: 57.390 0.418 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (167 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.016 99.8 79: (ns/day) (hour/ns) 79: Performance: 94.560 0.254 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.013 0.013 99.8 79: (ns/day) (hour/ns) 79: Performance: 114.316 0.210 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.010 99.7 79: (ns/day) (hour/ns) 79: Performance: 142.116 0.169 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.011 0.011 99.6 79: (ns/day) (hour/ns) 79: Performance: 127.946 0.188 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.014 99.8 79: (ns/day) (hour/ns) 79: Performance: 108.276 0.222 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.014 99.8 79: (ns/day) (hour/ns) 79: Performance: 103.042 0.233 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (102 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.015 99.8 79: (ns/day) (hour/ns) 79: Performance: 97.913 0.245 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.027 0.027 99.9 79: (ns/day) (hour/ns) 79: Performance: 55.271 0.434 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.026 0.026 99.8 79: (ns/day) (hour/ns) 79: Performance: 57.059 0.421 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.019 0.019 99.8 79: (ns/day) (hour/ns) 79: Performance: 78.315 0.306 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.022 0.022 99.9 79: (ns/day) (hour/ns) 79: Performance: 67.197 0.357 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.023 0.023 99.9 79: (ns/day) (hour/ns) 79: Performance: 63.254 0.379 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (156 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.025 0.025 99.8 79: (ns/day) (hour/ns) 79: Performance: 57.902 0.414 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.024 0.024 99.8 79: (ns/day) (hour/ns) 79: Performance: 61.579 0.390 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.016 99.7 79: (ns/day) (hour/ns) 79: Performance: 92.969 0.258 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.029 0.029 99.9 79: (ns/day) (hour/ns) 79: Performance: 51.359 0.467 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.012 0.012 99.8 79: (ns/day) (hour/ns) 79: Performance: 119.547 0.201 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.022 0.022 99.9 79: (ns/day) (hour/ns) 79: Performance: 68.114 0.352 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (167 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.017 99.9 79: (ns/day) (hour/ns) 79: Performance: 86.719 0.277 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.025 0.025 99.7 79: (ns/day) (hour/ns) 79: Performance: 58.384 0.411 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.017 99.8 79: (ns/day) (hour/ns) 79: Performance: 85.077 0.282 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.023 0.023 99.8 79: (ns/day) (hour/ns) 79: Performance: 64.950 0.370 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.024 0.024 99.9 79: (ns/day) (hour/ns) 79: Performance: 61.935 0.388 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.019 0.019 99.8 79: (ns/day) (hour/ns) 79: Performance: 77.606 0.309 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (174 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.015 99.8 79: (ns/day) (hour/ns) 79: Performance: 99.541 0.241 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.009 0.009 99.7 79: (ns/day) (hour/ns) 79: Performance: 160.253 0.150 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.017 99.8 79: (ns/day) (hour/ns) 79: Performance: 85.497 0.281 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.024 0.024 99.6 79: (ns/day) (hour/ns) 79: Performance: 60.921 0.394 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.038 0.039 99.8 79: (ns/day) (hour/ns) 79: Performance: 38.133 0.629 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.022 0.022 99.7 79: (ns/day) (hour/ns) 79: Performance: 66.427 0.361 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (186 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.020 0.020 99.7 79: (ns/day) (hour/ns) 79: Performance: 72.330 0.332 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.009 0.009 99.6 79: (ns/day) (hour/ns) 79: Performance: 156.150 0.154 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.009 0.009 99.6 79: (ns/day) (hour/ns) 79: Performance: 165.177 0.145 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.011 0.011 99.7 79: (ns/day) (hour/ns) 79: Performance: 131.118 0.183 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.024 0.024 99.8 79: (ns/day) (hour/ns) 79: Performance: 61.673 0.389 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.024 0.024 99.8 79: (ns/day) (hour/ns) 79: Performance: 62.358 0.385 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (162 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.016 99.6 79: (ns/day) (hour/ns) 79: Performance: 94.279 0.255 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.019 0.019 99.8 79: (ns/day) (hour/ns) 79: Performance: 77.593 0.309 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.018 0.018 99.7 79: (ns/day) (hour/ns) 79: Performance: 83.539 0.287 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.024 0.024 99.8 79: (ns/day) (hour/ns) 79: Performance: 60.415 0.397 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.022 0.022 99.8 79: (ns/day) (hour/ns) 79: Performance: 66.923 0.359 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.028 0.028 99.8 79: (ns/day) (hour/ns) 79: Performance: 52.227 0.460 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (174 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.019 0.019 99.8 79: (ns/day) (hour/ns) 79: Performance: 76.728 0.313 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.011 0.011 99.7 79: (ns/day) (hour/ns) 79: Performance: 129.364 0.186 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.020 0.020 99.8 79: (ns/day) (hour/ns) 79: Performance: 74.104 0.324 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.022 0.022 99.8 79: (ns/day) (hour/ns) 79: Performance: 66.048 0.363 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.032 0.032 99.9 79: (ns/day) (hour/ns) 79: Performance: 46.539 0.516 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.022 0.022 99.7 79: (ns/day) (hour/ns) 79: Performance: 67.423 0.356 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (174 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.018 0.018 99.5 79: (ns/day) (hour/ns) 79: Performance: 80.027 0.300 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.013 0.014 99.7 79: (ns/day) (hour/ns) 79: Performance: 108.538 0.221 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.007 0.007 99.7 79: (ns/day) (hour/ns) 79: Performance: 197.912 0.121 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.029 0.029 99.9 79: (ns/day) (hour/ns) 79: Performance: 50.392 0.476 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.023 0.023 99.9 79: (ns/day) (hour/ns) 79: Performance: 65.076 0.369 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.022 0.022 99.8 79: (ns/day) (hour/ns) 79: Performance: 66.087 0.363 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (172 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.015 99.7 79: (ns/day) (hour/ns) 79: Performance: 96.647 0.248 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.017 99.7 79: (ns/day) (hour/ns) 79: Performance: 85.814 0.280 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 4. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 4. 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.017 99.8 79: (ns/day) (hour/ns) 79: Performance: 86.859 0.276 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.022 0.022 99.8 79: (ns/day) (hour/ns) 79: Performance: 66.258 0.362 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.014 99.8 79: (ns/day) (hour/ns) 79: Performance: 105.674 0.227 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.019 0.019 99.9 79: (ns/day) (hour/ns) 79: Performance: 79.236 0.303 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (151 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.024 0.024 99.9 79: (ns/day) (hour/ns) 79: Performance: 61.584 0.390 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.012 0.012 99.6 79: (ns/day) (hour/ns) 79: Performance: 118.046 0.203 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.010 99.6 79: (ns/day) (hour/ns) 79: Performance: 147.295 0.163 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.027 0.027 99.8 79: (ns/day) (hour/ns) 79: Performance: 53.865 0.446 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.021 99.8 79: (ns/day) (hour/ns) 79: Performance: 71.323 0.336 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.036 0.036 99.9 79: (ns/day) (hour/ns) 79: Performance: 41.135 0.583 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (180 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.013 0.013 99.6 79: (ns/day) (hour/ns) 79: Performance: 116.391 0.206 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.020 0.020 99.8 79: (ns/day) (hour/ns) 79: Performance: 72.944 0.329 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.011 0.012 99.7 79: (ns/day) (hour/ns) 79: Performance: 127.646 0.188 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.021 99.8 79: (ns/day) (hour/ns) 79: Performance: 68.770 0.349 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.034 0.034 99.9 79: (ns/day) (hour/ns) 79: Performance: 42.955 0.559 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.017 99.8 79: (ns/day) (hour/ns) 79: Performance: 87.516 0.274 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (167 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.016 99.8 79: (ns/day) (hour/ns) 79: Performance: 91.378 0.263 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.013 0.013 99.8 79: (ns/day) (hour/ns) 79: Performance: 113.853 0.211 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.012 0.012 99.7 79: (ns/day) (hour/ns) 79: Performance: 122.419 0.196 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.024 0.024 99.8 79: (ns/day) (hour/ns) 79: Performance: 61.343 0.391 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.023 0.023 99.8 79: (ns/day) (hour/ns) 79: Performance: 64.079 0.375 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.019 0.019 99.8 79: (ns/day) (hour/ns) 79: Performance: 78.007 0.308 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (173 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.020 0.020 99.9 79: (ns/day) (hour/ns) 79: Performance: 73.228 0.328 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.023 0.023 99.9 79: (ns/day) (hour/ns) 79: Performance: 64.943 0.370 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 4. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 4. 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.036 0.037 99.9 79: (ns/day) (hour/ns) 79: Performance: 40.200 0.597 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.015 0.015 99.8 79: (ns/day) (hour/ns) 79: Performance: 97.008 0.247 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.030 0.030 99.9 79: (ns/day) (hour/ns) 79: Performance: 48.193 0.498 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.037 0.037 99.9 79: (ns/day) (hour/ns) 79: Performance: 39.761 0.604 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (210 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.020 0.020 99.9 79: (ns/day) (hour/ns) 79: Performance: 71.854 0.334 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.021 99.9 79: (ns/day) (hour/ns) 79: Performance: 69.455 0.346 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.023 0.023 99.9 79: (ns/day) (hour/ns) 79: Performance: 64.995 0.369 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.032 0.032 99.9 79: (ns/day) (hour/ns) 79: Performance: 45.301 0.530 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.026 0.026 99.8 79: (ns/day) (hour/ns) 79: Performance: 56.137 0.428 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.039 0.039 99.9 79: (ns/day) (hour/ns) 79: Performance: 37.671 0.637 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (191 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.017 99.7 79: (ns/day) (hour/ns) 79: Performance: 86.747 0.277 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.016 99.5 79: (ns/day) (hour/ns) 79: Performance: 92.136 0.260 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.023 0.023 99.7 79: (ns/day) (hour/ns) 79: Performance: 63.676 0.377 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.031 0.031 99.8 79: (ns/day) (hour/ns) 79: Performance: 47.060 0.510 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.030 0.030 99.9 79: (ns/day) (hour/ns) 79: Performance: 48.842 0.491 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.031 0.031 99.9 79: (ns/day) (hour/ns) 79: Performance: 46.778 0.513 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (188 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.018 0.018 99.8 79: (ns/day) (hour/ns) 79: Performance: 82.034 0.293 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.020 0.020 99.6 79: (ns/day) (hour/ns) 79: Performance: 74.735 0.321 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.023 0.024 99.8 79: (ns/day) (hour/ns) 79: Performance: 62.433 0.384 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.029 0.030 99.7 79: (ns/day) (hour/ns) 79: Performance: 49.685 0.483 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.029 0.029 99.9 79: (ns/day) (hour/ns) 79: Performance: 49.794 0.482 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.029 0.029 99.9 79: (ns/day) (hour/ns) 79: Performance: 50.690 0.473 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (208 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.020 0.020 99.9 79: (ns/day) (hour/ns) 79: Performance: 72.564 0.331 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.023 0.023 99.9 79: (ns/day) (hour/ns) 79: Performance: 63.624 0.377 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.023 0.023 99.9 79: (ns/day) (hour/ns) 79: Performance: 63.819 0.376 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.030 0.030 99.9 79: (ns/day) (hour/ns) 79: Performance: 48.789 0.492 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.030 0.030 99.9 79: (ns/day) (hour/ns) 79: Performance: 48.810 0.492 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.028 0.028 99.9 79: (ns/day) (hour/ns) 79: Performance: 52.099 0.461 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (212 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.017 99.6 79: (ns/day) (hour/ns) 79: Performance: 84.441 0.284 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.019 0.019 99.8 79: (ns/day) (hour/ns) 79: Performance: 76.802 0.312 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.024 0.024 99.7 79: (ns/day) (hour/ns) 79: Performance: 61.611 0.390 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.024 0.025 99.9 79: (ns/day) (hour/ns) 79: Performance: 59.936 0.400 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.026 0.026 99.9 79: (ns/day) (hour/ns) 79: Performance: 56.466 0.425 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.028 0.028 99.9 79: (ns/day) (hour/ns) 79: Performance: 51.848 0.463 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (209 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.021 99.7 79: (ns/day) (hour/ns) 79: Performance: 70.305 0.341 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.012 0.012 99.7 79: (ns/day) (hour/ns) 79: Performance: 126.296 0.190 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.020 0.020 99.8 79: (ns/day) (hour/ns) 79: Performance: 71.918 0.334 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.031 0.031 99.8 79: (ns/day) (hour/ns) 79: Performance: 47.091 0.510 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.028 0.028 99.8 79: (ns/day) (hour/ns) 79: Performance: 52.460 0.457 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.030 0.030 99.9 79: (ns/day) (hour/ns) 79: Performance: 49.184 0.488 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (209 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: for current Trotter decomposition methods with vv, nsttcouple and 79: nstpcouple must be equal. Both have been reset to 79: min(nsttcouple,nstpcouple) = 2 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.016 0.016 99.8 79: (ns/day) (hour/ns) 79: Performance: 90.510 0.265 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: for current Trotter decomposition methods with vv, nsttcouple and 79: nstpcouple must be equal. Both have been reset to 79: min(nsttcouple,nstpcouple) = 2 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.024 0.024 99.7 79: (ns/day) (hour/ns) 79: Performance: 60.483 0.397 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: for current Trotter decomposition methods with vv, nsttcouple and 79: nstpcouple must be equal. Both have been reset to 79: min(nsttcouple,nstpcouple) = 2 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.017 99.8 79: (ns/day) (hour/ns) 79: Performance: 84.974 0.282 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: for current Trotter decomposition methods with vv, nsttcouple and 79: nstpcouple must be equal. Both have been reset to 79: min(nsttcouple,nstpcouple) = 2 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.028 0.028 99.8 79: (ns/day) (hour/ns) 79: Performance: 51.721 0.464 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: for current Trotter decomposition methods with vv, nsttcouple and 79: nstpcouple must be equal. Both have been reset to 79: min(nsttcouple,nstpcouple) = 2 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.030 0.030 99.8 79: (ns/day) (hour/ns) 79: Performance: 48.271 0.497 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: for current Trotter decomposition methods with vv, nsttcouple and 79: nstpcouple must be equal. Both have been reset to 79: min(nsttcouple,nstpcouple) = 2 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.027 0.027 99.8 79: (ns/day) (hour/ns) 79: Performance: 53.859 0.446 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (206 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.018 0.018 99.8 79: (ns/day) (hour/ns) 79: Performance: 82.545 0.291 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.018 0.018 99.9 79: (ns/day) (hour/ns) 79: Performance: 83.720 0.287 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.021 99.8 79: (ns/day) (hour/ns) 79: Performance: 70.993 0.338 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.027 0.027 99.9 79: (ns/day) (hour/ns) 79: Performance: 54.323 0.442 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.028 0.028 99.9 79: (ns/day) (hour/ns) 79: Performance: 52.284 0.459 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.029 0.029 99.9 79: (ns/day) (hour/ns) 79: Performance: 50.622 0.474 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (208 ms) 79: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (4466 ms total) 79: 79: [----------] Global test environment tear-down 79: [==========] 25 tests from 1 test suite ran. (4506 ms total) 79: [ PASSED ] 25 tests. 79/87 Test #79: MdrunCoordinationCouplingTests1Rank ....... Passed 4.55 sec test 80 Start 80: MdrunCoordinationCouplingTests2Ranks 80: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-coordination-coupling-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunCoordinationCouplingTests2Ranks.xml" 80: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 80: Test timeout computed to be: 1920 80: [==========] Running 25 tests from 1 test suite. 80: [----------] Global test environment set-up. 80: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.7%. 80: The balanceable part of the MD step is 51%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.9%. 80: 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.039 0.020 199.5 80: (ns/day) (hour/ns) 80: Performance: 74.352 0.323 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 5.4%. 80: The balanceable part of the MD step is 52%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 2.8%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.037 0.019 199.5 80: (ns/day) (hour/ns) 80: Performance: 78.680 0.305 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 4. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 4. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 7.5%. 80: The balanceable part of the MD step is 35%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 2.6%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: 80: NOTE: 51 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.030 0.015 199.3 80: (ns/day) (hour/ns) 80: Performance: 97.908 0.245 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 5.8%. 80: The balanceable part of the MD step is 33%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.9%. 80: 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.036 0.018 199.5 80: (ns/day) (hour/ns) 80: Performance: 80.687 0.297 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 6.2%. 80: The balanceable part of the MD step is 28%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.7%. 80: 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.047 0.024 199.4 80: (ns/day) (hour/ns) 80: Performance: 62.091 0.387 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 5.8%. 80: The balanceable part of the MD step is 35%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 2.0%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.043 0.021 199.3 80: (ns/day) (hour/ns) 80: Performance: 68.556 0.350 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (411 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 2.9%. 80: The balanceable part of the MD step is 50%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.4%. 80: 80: 80: NOTE: 50 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.872 0.436 200.0 80: (ns/day) (hour/ns) 80: Performance: 3.370 7.121 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 3.5%. 80: The balanceable part of the MD step is 47%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.7%. 80: 80: 80: NOTE: 50 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.246 0.123 199.9 80: (ns/day) (hour/ns) 80: Performance: 11.947 2.009 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 3.0%. 80: The balanceable part of the MD step is 40%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.2%. 80: 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.030 0.015 199.2 80: (ns/day) (hour/ns) 80: Performance: 99.034 0.242 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 2.0%. 80: The balanceable part of the MD step is 36%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.7%. 80: 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.033 0.017 199.2 80: (ns/day) (hour/ns) 80: Performance: 87.753 0.273 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 3.9%. 80: The balanceable part of the MD step is 41%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.6%. 80: 80: 80: NOTE: 51 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.037 0.019 199.5 80: (ns/day) (hour/ns) 80: Performance: 78.456 0.306 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 5.7%. 80: The balanceable part of the MD step is 33%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.9%. 80: 80: 80: NOTE: 70 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.057 0.045 128.5 80: (ns/day) (hour/ns) 80: Performance: 32.853 0.731 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (944 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 2.4%. 80: The balanceable part of the MD step is 49%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.2%. 80: 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.041 0.021 199.5 80: (ns/day) (hour/ns) 80: Performance: 71.257 0.337 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 3.3%. 80: The balanceable part of the MD step is 48%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.6%. 80: 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.027 0.014 199.4 80: (ns/day) (hour/ns) 80: Performance: 108.348 0.222 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 3.7%. 80: The balanceable part of the MD step is 41%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.5%. 80: 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.027 0.014 199.3 80: (ns/day) (hour/ns) 80: Performance: 108.687 0.221 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 3.6%. 80: The balanceable part of the MD step is 43%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.6%. 80: 80: 80: NOTE: 52 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.049 0.024 199.3 80: (ns/day) (hour/ns) 80: Performance: 60.205 0.399 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 3.0%. 80: The balanceable part of the MD step is 40%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.2%. 80: 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.031 0.016 199.5 80: (ns/day) (hour/ns) 80: Performance: 94.714 0.253 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 2.2%. 80: The balanceable part of the MD step is 43%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.0%. 80: 80: 80: NOTE: 59 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.031 0.016 199.4 80: (ns/day) (hour/ns) 80: Performance: 93.872 0.256 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (239 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 4.7%. 80: The balanceable part of the MD step is 47%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 2.2%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: 80: NOTE: 52 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.038 0.019 199.2 80: (ns/day) (hour/ns) 80: Performance: 77.304 0.310 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 3.2%. 80: The balanceable part of the MD step is 44%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.4%. 80: 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.026 0.013 198.0 80: (ns/day) (hour/ns) 80: Performance: 113.922 0.211 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 4.2%. 80: The balanceable part of the MD step is 6%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.2%. 80: 80: 80: NOTE: 42 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.045 0.022 199.5 80: (ns/day) (hour/ns) 80: Performance: 65.631 0.366 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 4.4%. 80: The balanceable part of the MD step is 41%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.8%. 80: 80: 80: NOTE: 66 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.053 0.027 199.2 80: (ns/day) (hour/ns) 80: Performance: 55.102 0.436 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 5.9%. 80: The balanceable part of the MD step is 37%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 2.2%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: 80: NOTE: 71 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.058 0.033 175.3 80: (ns/day) (hour/ns) 80: Performance: 44.284 0.542 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.9%. 80: The balanceable part of the MD step is 34%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.6%. 80: 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.028 0.014 199.1 80: (ns/day) (hour/ns) 80: Performance: 103.435 0.232 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (489 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.026 0.013 198.9 80: (ns/day) (hour/ns) 80: Performance: 111.675 0.215 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.021 0.011 199.2 80: (ns/day) (hour/ns) 80: Performance: 138.271 0.174 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.017 0.009 199.2 80: (ns/day) (hour/ns) 80: Performance: 169.238 0.142 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.027 0.013 199.1 80: (ns/day) (hour/ns) 80: Performance: 110.075 0.218 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.024 0.012 199.3 80: (ns/day) (hour/ns) 80: Performance: 124.430 0.193 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.025 0.013 198.7 80: (ns/day) (hour/ns) 80: Performance: 115.354 0.208 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (101 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.032 0.016 199.0 80: (ns/day) (hour/ns) 80: Performance: 92.563 0.259 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.019 0.010 198.7 80: (ns/day) (hour/ns) 80: Performance: 152.001 0.158 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.021 0.011 198.5 80: (ns/day) (hour/ns) 80: Performance: 137.378 0.175 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.046 0.023 199.2 80: (ns/day) (hour/ns) 80: Performance: 63.047 0.381 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.045 0.023 199.4 80: (ns/day) (hour/ns) 80: Performance: 65.207 0.368 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.045 0.023 199.5 80: (ns/day) (hour/ns) 80: Performance: 64.853 0.370 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (162 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.027 0.013 199.2 80: (ns/day) (hour/ns) 80: Performance: 110.044 0.218 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.030 0.015 199.1 80: (ns/day) (hour/ns) 80: Performance: 98.443 0.244 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.033 0.017 199.2 80: (ns/day) (hour/ns) 80: Performance: 88.068 0.273 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.050 0.025 199.5 80: (ns/day) (hour/ns) 80: Performance: 58.421 0.411 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.046 0.023 199.5 80: (ns/day) (hour/ns) 80: Performance: 63.107 0.380 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 52 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.038 0.019 199.1 80: (ns/day) (hour/ns) 80: Performance: 76.313 0.314 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (204 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 65 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.053 0.027 195.1 80: (ns/day) (hour/ns) 80: Performance: 53.894 0.445 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.028 0.014 199.0 80: (ns/day) (hour/ns) 80: Performance: 103.643 0.232 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 65 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.051 0.025 199.0 80: (ns/day) (hour/ns) 80: Performance: 57.788 0.415 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.025 0.013 199.2 80: (ns/day) (hour/ns) 80: Performance: 115.354 0.208 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.060 0.030 199.6 80: (ns/day) (hour/ns) 80: Performance: 49.209 0.488 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.031 0.016 199.3 80: (ns/day) (hour/ns) 80: Performance: 93.947 0.255 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (296 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.031 0.015 199.4 80: (ns/day) (hour/ns) 80: Performance: 94.852 0.253 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.021 0.010 198.9 80: (ns/day) (hour/ns) 80: Performance: 140.810 0.170 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.032 0.016 199.0 80: (ns/day) (hour/ns) 80: Performance: 90.439 0.265 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.041 0.021 199.4 80: (ns/day) (hour/ns) 80: Performance: 71.513 0.336 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 51 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.039 0.020 199.4 80: (ns/day) (hour/ns) 80: Performance: 75.112 0.320 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.033 0.017 199.4 80: (ns/day) (hour/ns) 80: Performance: 88.781 0.270 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (326 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.036 0.018 199.4 80: (ns/day) (hour/ns) 80: Performance: 82.417 0.291 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.028 0.014 199.4 80: (ns/day) (hour/ns) 80: Performance: 103.478 0.232 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.030 0.015 199.5 80: (ns/day) (hour/ns) 80: Performance: 98.079 0.245 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.054 0.027 199.4 80: (ns/day) (hour/ns) 80: Performance: 54.440 0.441 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.034 0.017 199.4 80: (ns/day) (hour/ns) 80: Performance: 85.212 0.282 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 70 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.043 0.022 199.2 80: (ns/day) (hour/ns) 80: Performance: 67.536 0.355 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (284 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.028 0.014 199.3 80: (ns/day) (hour/ns) 80: Performance: 105.420 0.228 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.025 0.013 199.3 80: (ns/day) (hour/ns) 80: Performance: 115.723 0.207 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.022 0.011 199.1 80: (ns/day) (hour/ns) 80: Performance: 130.302 0.184 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.035 0.018 199.1 80: (ns/day) (hour/ns) 80: Performance: 83.254 0.288 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.042 0.021 199.2 80: (ns/day) (hour/ns) 80: Performance: 69.562 0.345 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.030 0.015 199.1 80: (ns/day) (hour/ns) 80: Performance: 96.457 0.249 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (303 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.043 0.021 199.5 80: (ns/day) (hour/ns) 80: Performance: 68.695 0.349 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 58 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.054 0.027 199.5 80: (ns/day) (hour/ns) 80: Performance: 54.347 0.442 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.028 0.014 199.2 80: (ns/day) (hour/ns) 80: Performance: 105.096 0.228 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.033 0.017 199.4 80: (ns/day) (hour/ns) 80: Performance: 88.131 0.272 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 50 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.743 0.371 200.0 80: (ns/day) (hour/ns) 80: Performance: 3.954 6.070 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.041 0.021 199.5 80: (ns/day) (hour/ns) 80: Performance: 70.738 0.339 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (741 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.042 0.021 199.5 80: (ns/day) (hour/ns) 80: Performance: 69.826 0.344 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.031 0.016 199.3 80: (ns/day) (hour/ns) 80: Performance: 93.857 0.256 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 4. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 4. 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.041 0.021 199.3 80: (ns/day) (hour/ns) 80: Performance: 70.634 0.340 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 54 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.047 0.023 199.4 80: (ns/day) (hour/ns) 80: Performance: 62.703 0.383 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.038 0.019 199.6 80: (ns/day) (hour/ns) 80: Performance: 78.182 0.307 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.036 0.018 199.5 80: (ns/day) (hour/ns) 80: Performance: 81.772 0.294 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (330 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.049 0.025 199.4 80: (ns/day) (hour/ns) 80: Performance: 59.390 0.404 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 52 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.029 0.015 199.3 80: (ns/day) (hour/ns) 80: Performance: 100.345 0.239 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.029 0.015 199.3 80: (ns/day) (hour/ns) 80: Performance: 100.743 0.238 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.057 0.029 199.1 80: (ns/day) (hour/ns) 80: Performance: 51.067 0.470 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 57 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.045 0.023 199.4 80: (ns/day) (hour/ns) 80: Performance: 64.770 0.371 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.048 0.024 199.2 80: (ns/day) (hour/ns) 80: Performance: 61.495 0.390 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (309 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.045 0.023 199.6 80: (ns/day) (hour/ns) 80: Performance: 65.215 0.368 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.032 0.016 199.3 80: (ns/day) (hour/ns) 80: Performance: 92.534 0.259 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 40 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.046 0.023 198.7 80: (ns/day) (hour/ns) 80: Performance: 62.835 0.382 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.054 0.027 198.7 80: (ns/day) (hour/ns) 80: Performance: 54.409 0.441 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 52 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.046 0.023 199.6 80: (ns/day) (hour/ns) 80: Performance: 64.085 0.375 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.050 0.025 199.0 80: (ns/day) (hour/ns) 80: Performance: 58.558 0.410 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (372 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.043 0.022 199.0 80: (ns/day) (hour/ns) 80: Performance: 67.599 0.355 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.024 0.012 199.3 80: (ns/day) (hour/ns) 80: Performance: 122.253 0.196 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.019 0.010 199.3 80: (ns/day) (hour/ns) 80: Performance: 150.192 0.160 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 50 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.064 0.032 199.8 80: (ns/day) (hour/ns) 80: Performance: 45.557 0.527 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.065 0.033 198.8 80: (ns/day) (hour/ns) 80: Performance: 45.066 0.533 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.038 0.019 197.7 80: (ns/day) (hour/ns) 80: Performance: 76.565 0.313 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (262 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 2.6%. 80: The balanceable part of the MD step is 55%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.4%. 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.047 0.024 198.8 80: (ns/day) (hour/ns) 80: Performance: 62.142 0.386 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 7.5%. 80: The balanceable part of the MD step is 52%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 3.9%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.031 0.016 198.8 80: (ns/day) (hour/ns) 80: Performance: 92.891 0.258 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 4. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 4. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.3%. 80: The balanceable part of the MD step is 45%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.6%. 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.029 0.015 197.2 80: (ns/day) (hour/ns) 80: Performance: 98.827 0.243 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 5.9%. 80: The balanceable part of the MD step is 43%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 2.5%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.058 0.029 199.0 80: (ns/day) (hour/ns) 80: Performance: 50.606 0.474 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 4.3%. 80: The balanceable part of the MD step is 41%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.8%. 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.089 0.044 199.5 80: (ns/day) (hour/ns) 80: Performance: 33.077 0.726 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.8%. 80: The balanceable part of the MD step is 34%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.6%. 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.071 0.036 199.2 80: (ns/day) (hour/ns) 80: Performance: 41.257 0.582 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (420 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 3.7%. 80: The balanceable part of the MD step is 58%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 2.1%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.038 0.019 198.9 80: (ns/day) (hour/ns) 80: Performance: 75.910 0.316 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 3.6%. 80: The balanceable part of the MD step is 56%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 2.0%. 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.034 0.017 198.9 80: (ns/day) (hour/ns) 80: Performance: 85.791 0.280 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 3.3%. 80: The balanceable part of the MD step is 51%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.7%. 80: 80: 80: NOTE: 7 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.038 0.019 198.7 80: (ns/day) (hour/ns) 80: Performance: 75.836 0.316 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 6.3%. 80: The balanceable part of the MD step is 50%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 3.1%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.047 0.023 199.0 80: (ns/day) (hour/ns) 80: Performance: 62.599 0.383 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 3.0%. 80: The balanceable part of the MD step is 49%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.4%. 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.057 0.029 199.0 80: (ns/day) (hour/ns) 80: Performance: 50.993 0.471 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 3.9%. 80: The balanceable part of the MD step is 48%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.9%. 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.038 0.019 198.8 80: (ns/day) (hour/ns) 80: Performance: 76.834 0.312 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (254 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 0.9%. 80: The balanceable part of the MD step is 57%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.5%. 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.048 0.024 199.4 80: (ns/day) (hour/ns) 80: Performance: 61.043 0.393 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 6.6%. 80: The balanceable part of the MD step is 52%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 3.5%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.037 0.019 198.8 80: (ns/day) (hour/ns) 80: Performance: 78.332 0.306 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 2.6%. 80: The balanceable part of the MD step is 50%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.3%. 80: 80: 80: NOTE: 8 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.039 0.020 198.7 80: (ns/day) (hour/ns) 80: Performance: 74.424 0.322 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 5.4%. 80: The balanceable part of the MD step is 49%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 2.6%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.060 0.030 198.9 80: (ns/day) (hour/ns) 80: Performance: 48.456 0.495 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 2.3%. 80: The balanceable part of the MD step is 48%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.1%. 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.050 0.025 199.1 80: (ns/day) (hour/ns) 80: Performance: 57.988 0.414 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 3.9%. 80: The balanceable part of the MD step is 49%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.9%. 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.056 0.028 199.1 80: (ns/day) (hour/ns) 80: Performance: 52.602 0.456 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (323 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.042 0.021 199.1 80: (ns/day) (hour/ns) 80: Performance: 69.571 0.345 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.044 0.022 198.7 80: (ns/day) (hour/ns) 80: Performance: 65.907 0.364 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.054 0.027 198.8 80: (ns/day) (hour/ns) 80: Performance: 54.556 0.440 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.060 0.034 175.5 80: (ns/day) (hour/ns) 80: Performance: 43.063 0.557 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.064 0.032 198.2 80: (ns/day) (hour/ns) 80: Performance: 45.832 0.524 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.054 0.028 197.6 80: (ns/day) (hour/ns) 80: Performance: 53.292 0.450 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (457 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.080 0.040 198.7 80: (ns/day) (hour/ns) 80: Performance: 36.600 0.656 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.034 0.017 198.0 80: (ns/day) (hour/ns) 80: Performance: 86.033 0.279 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.056 0.028 198.8 80: (ns/day) (hour/ns) 80: Performance: 51.904 0.462 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.056 0.028 199.2 80: (ns/day) (hour/ns) 80: Performance: 52.486 0.457 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.065 0.033 198.2 80: (ns/day) (hour/ns) 80: Performance: 44.996 0.533 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.055 0.028 198.2 80: (ns/day) (hour/ns) 80: Performance: 53.367 0.450 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (411 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.048 0.024 198.9 80: (ns/day) (hour/ns) 80: Performance: 60.390 0.397 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.051 0.025 198.8 80: (ns/day) (hour/ns) 80: Performance: 57.728 0.416 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.036 0.018 199.0 80: (ns/day) (hour/ns) 80: Performance: 80.390 0.299 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.065 0.032 199.2 80: (ns/day) (hour/ns) 80: Performance: 45.289 0.530 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.049 0.024 198.9 80: (ns/day) (hour/ns) 80: Performance: 60.119 0.399 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.060 0.030 199.3 80: (ns/day) (hour/ns) 80: Performance: 48.459 0.495 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (400 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.047 0.024 199.2 80: (ns/day) (hour/ns) 80: Performance: 62.323 0.385 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.030 0.015 198.2 80: (ns/day) (hour/ns) 80: Performance: 97.663 0.246 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.025 0.013 198.3 80: (ns/day) (hour/ns) 80: Performance: 115.955 0.207 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.049 0.024 199.2 80: (ns/day) (hour/ns) 80: Performance: 60.018 0.400 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.057 0.029 198.8 80: (ns/day) (hour/ns) 80: Performance: 51.371 0.467 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.046 0.023 198.7 80: (ns/day) (hour/ns) 80: Performance: 63.922 0.375 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (317 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: for current Trotter decomposition methods with vv, nsttcouple and 80: nstpcouple must be equal. Both have been reset to 80: min(nsttcouple,nstpcouple) = 2 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 5 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.086 0.044 198.0 80: (ns/day) (hour/ns) 80: Performance: 33.672 0.713 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: for current Trotter decomposition methods with vv, nsttcouple and 80: nstpcouple must be equal. Both have been reset to 80: min(nsttcouple,nstpcouple) = 2 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.060 0.030 196.8 80: (ns/day) (hour/ns) 80: Performance: 48.223 0.498 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: for current Trotter decomposition methods with vv, nsttcouple and 80: nstpcouple must be equal. Both have been reset to 80: min(nsttcouple,nstpcouple) = 2 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.075 0.038 198.8 80: (ns/day) (hour/ns) 80: Performance: 38.937 0.616 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: for current Trotter decomposition methods with vv, nsttcouple and 80: nstpcouple must be equal. Both have been reset to 80: min(nsttcouple,nstpcouple) = 2 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.048 0.024 198.8 80: (ns/day) (hour/ns) 80: Performance: 61.401 0.391 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: for current Trotter decomposition methods with vv, nsttcouple and 80: nstpcouple must be equal. Both have been reset to 80: min(nsttcouple,nstpcouple) = 2 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.063 0.032 199.0 80: (ns/day) (hour/ns) 80: Performance: 46.508 0.516 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: for current Trotter decomposition methods with vv, nsttcouple and 80: nstpcouple must be equal. Both have been reset to 80: min(nsttcouple,nstpcouple) = 2 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.041 0.021 199.0 80: (ns/day) (hour/ns) 80: Performance: 71.185 0.337 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (469 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.061 0.031 198.9 80: (ns/day) (hour/ns) 80: Performance: 47.924 0.501 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.056 0.028 199.3 80: (ns/day) (hour/ns) 80: Performance: 52.163 0.460 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.038 0.019 198.5 80: (ns/day) (hour/ns) 80: Performance: 77.331 0.310 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.046 0.023 198.7 80: (ns/day) (hour/ns) 80: Performance: 62.850 0.382 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.035 0.018 198.6 80: (ns/day) (hour/ns) 80: Performance: 83.520 0.287 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.039 0.020 198.2 80: (ns/day) (hour/ns) 80: Performance: 74.711 0.321 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (290 ms) 80: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (9133 ms total) 80: 80: [----------] Global test environment tear-down 80: [==========] 25 tests from 1 test suite ran. (9178 ms total) 80: [ PASSED ] 25 tests. 80/87 Test #80: MdrunCoordinationCouplingTests2Ranks ...... Passed 9.20 sec test 81 Start 81: MdrunCoordinationConstraintsTests1Rank 81: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-coordination-constraints-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunCoordinationConstraintsTests1Rank.xml" 81: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 81: Test timeout computed to be: 1920 81: [==========] Running 13 tests from 1 test suite. 81: [----------] Global test environment set-up. 81: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.023 0.023 99.8 81: (ns/day) (hour/ns) 81: Performance: 63.580 0.377 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.017 0.017 99.6 81: (ns/day) (hour/ns) 81: Performance: 88.583 0.271 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 4. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 4. 81: 81: 81: There were 5 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.016 0.016 99.8 81: (ns/day) (hour/ns) 81: Performance: 90.423 0.265 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 5 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.024 0.024 99.7 81: (ns/day) (hour/ns) 81: Performance: 60.605 0.396 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 5 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.114 0.114 99.9 81: (ns/day) (hour/ns) 81: Performance: 12.891 1.862 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 5 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.018 0.018 99.7 81: (ns/day) (hour/ns) 81: Performance: 79.595 0.302 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (2500 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.018 0.018 99.7 81: (ns/day) (hour/ns) 81: Performance: 82.439 0.291 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.015 0.015 99.5 81: (ns/day) (hour/ns) 81: Performance: 96.082 0.250 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.017 0.017 99.8 81: (ns/day) (hour/ns) 81: Performance: 84.983 0.282 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.022 0.022 99.8 81: (ns/day) (hour/ns) 81: Performance: 67.968 0.353 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.017 0.018 99.7 81: (ns/day) (hour/ns) 81: Performance: 83.806 0.286 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.021 0.021 99.8 81: (ns/day) (hour/ns) 81: Performance: 69.765 0.344 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (2306 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.026 0.026 99.9 81: (ns/day) (hour/ns) 81: Performance: 55.646 0.431 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.015 0.015 99.8 81: (ns/day) (hour/ns) 81: Performance: 99.387 0.241 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.013 0.013 99.7 81: (ns/day) (hour/ns) 81: Performance: 114.793 0.209 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.012 0.012 99.5 81: (ns/day) (hour/ns) 81: Performance: 121.458 0.198 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.022 0.022 99.8 81: (ns/day) (hour/ns) 81: Performance: 65.735 0.365 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.326 0.326 100.0 81: (ns/day) (hour/ns) 81: Performance: 4.511 5.321 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (2636 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.017 0.017 99.6 81: (ns/day) (hour/ns) 81: Performance: 86.382 0.278 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.010 0.010 99.6 81: (ns/day) (hour/ns) 81: Performance: 144.632 0.166 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.019 0.019 99.8 81: (ns/day) (hour/ns) 81: Performance: 78.309 0.306 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.017 0.017 99.6 81: (ns/day) (hour/ns) 81: Performance: 87.551 0.274 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.327 0.327 100.0 81: (ns/day) (hour/ns) 81: Performance: 4.491 5.344 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.813 0.813 100.0 81: (ns/day) (hour/ns) 81: Performance: 1.807 13.279 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (3789 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.021 0.021 99.7 81: (ns/day) (hour/ns) 81: Performance: 69.281 0.346 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.013 0.013 99.7 81: (ns/day) (hour/ns) 81: Performance: 116.407 0.206 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.015 0.015 99.8 81: (ns/day) (hour/ns) 81: Performance: 95.589 0.251 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.017 0.017 99.8 81: (ns/day) (hour/ns) 81: Performance: 84.468 0.284 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.015 0.015 99.8 81: (ns/day) (hour/ns) 81: Performance: 95.492 0.251 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.017 0.017 99.8 81: (ns/day) (hour/ns) 81: Performance: 84.868 0.283 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (3019 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.018 0.018 99.7 81: (ns/day) (hour/ns) 81: Performance: 81.943 0.293 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.017 0.017 99.8 81: (ns/day) (hour/ns) 81: Performance: 84.671 0.283 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.009 0.009 99.4 81: (ns/day) (hour/ns) 81: Performance: 164.920 0.146 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.038 0.038 99.9 81: (ns/day) (hour/ns) 81: Performance: 38.990 0.616 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.019 0.019 99.8 81: (ns/day) (hour/ns) 81: Performance: 77.777 0.309 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.016 0.016 99.8 81: (ns/day) (hour/ns) 81: Performance: 91.681 0.262 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (3259 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.016 0.016 99.7 81: (ns/day) (hour/ns) 81: Performance: 92.733 0.259 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.024 0.024 99.8 81: (ns/day) (hour/ns) 81: Performance: 60.378 0.397 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 4. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 4. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.022 0.022 99.8 81: (ns/day) (hour/ns) 81: Performance: 67.507 0.356 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.013 0.013 99.8 81: (ns/day) (hour/ns) 81: Performance: 109.215 0.220 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.017 0.017 99.8 81: (ns/day) (hour/ns) 81: Performance: 86.376 0.278 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.016 0.016 99.8 81: (ns/day) (hour/ns) 81: Performance: 89.150 0.269 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (2712 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.017 0.017 99.8 81: (ns/day) (hour/ns) 81: Performance: 88.518 0.271 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.010 0.010 99.8 81: (ns/day) (hour/ns) 81: Performance: 140.441 0.171 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.014 0.014 99.8 81: (ns/day) (hour/ns) 81: Performance: 104.929 0.229 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.014 0.014 99.8 81: (ns/day) (hour/ns) 81: Performance: 108.193 0.222 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.012 0.012 99.7 81: (ns/day) (hour/ns) 81: Performance: 119.563 0.201 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.012 0.012 99.7 81: (ns/day) (hour/ns) 81: Performance: 122.939 0.195 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (2883 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.016 0.016 99.8 81: (ns/day) (hour/ns) 81: Performance: 90.773 0.264 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.010 0.010 99.7 81: (ns/day) (hour/ns) 81: Performance: 151.254 0.159 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.014 0.014 99.8 81: (ns/day) (hour/ns) 81: Performance: 104.713 0.229 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.023 0.023 99.8 81: (ns/day) (hour/ns) 81: Performance: 64.555 0.372 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.017 0.017 99.8 81: (ns/day) (hour/ns) 81: Performance: 86.100 0.279 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.017 0.017 99.8 81: (ns/day) (hour/ns) 81: Performance: 86.025 0.279 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (2773 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.021 0.021 99.8 81: (ns/day) (hour/ns) 81: Performance: 69.511 0.345 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.026 0.026 99.9 81: (ns/day) (hour/ns) 81: Performance: 56.883 0.422 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 4. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 4. 81: 81: 81: There were 5 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.016 0.016 99.9 81: (ns/day) (hour/ns) 81: Performance: 90.007 0.267 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 5 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.017 0.017 99.8 81: (ns/day) (hour/ns) 81: Performance: 88.290 0.272 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 5 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.016 0.016 99.8 81: (ns/day) (hour/ns) 81: Performance: 92.510 0.259 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 5 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.022 0.022 99.8 81: (ns/day) (hour/ns) 81: Performance: 67.581 0.355 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (2871 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.020 0.020 99.8 81: (ns/day) (hour/ns) 81: Performance: 74.945 0.320 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.012 0.012 99.7 81: (ns/day) (hour/ns) 81: Performance: 123.931 0.194 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.025 0.025 99.9 81: (ns/day) (hour/ns) 81: Performance: 59.769 0.402 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.021 0.021 99.8 81: (ns/day) (hour/ns) 81: Performance: 70.229 0.342 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.020 0.020 99.8 81: (ns/day) (hour/ns) 81: Performance: 72.533 0.331 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.020 0.020 99.8 81: (ns/day) (hour/ns) 81: Performance: 72.280 0.332 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (2440 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.020 0.020 99.9 81: (ns/day) (hour/ns) 81: Performance: 73.193 0.328 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.016 0.016 99.8 81: (ns/day) (hour/ns) 81: Performance: 90.496 0.265 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.017 0.017 99.6 81: (ns/day) (hour/ns) 81: Performance: 86.220 0.278 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.018 0.018 99.7 81: (ns/day) (hour/ns) 81: Performance: 82.249 0.292 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.019 0.019 99.8 81: (ns/day) (hour/ns) 81: Performance: 78.613 0.305 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.019 0.019 99.8 81: (ns/day) (hour/ns) 81: Performance: 77.093 0.311 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (2670 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.029 0.029 99.8 81: (ns/day) (hour/ns) 81: Performance: 50.202 0.478 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.017 0.017 99.9 81: (ns/day) (hour/ns) 81: Performance: 86.347 0.278 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.022 0.022 99.7 81: (ns/day) (hour/ns) 81: Performance: 65.730 0.365 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.020 0.020 99.8 81: (ns/day) (hour/ns) 81: Performance: 72.595 0.331 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.030 0.030 99.8 81: (ns/day) (hour/ns) 81: Performance: 48.904 0.491 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.020 0.020 99.8 81: (ns/day) (hour/ns) 81: Performance: 73.548 0.326 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (2703 ms) 81: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (36575 ms total) 81: 81: [----------] Global test environment tear-down 81: [==========] 13 tests from 1 test suite ran. (36599 ms total) 81: [ PASSED ] 13 tests. 81/87 Test #81: MdrunCoordinationConstraintsTests1Rank .... Passed 36.65 sec test 82 Start 82: MdrunCoordinationConstraintsTests2Ranks 82: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-coordination-constraints-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunCoordinationConstraintsTests2Ranks.xml" 82: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 82: Test timeout computed to be: 1920 82: [==========] Running 13 tests from 1 test suite. 82: [----------] Global test environment set-up. 82: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 4.8%. 82: The balanceable part of the MD step is 4%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.2%. 82: 82: 82: NOTE: 64 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.124 0.084 147.7 82: (ns/day) (hour/ns) 82: Performance: 17.456 1.375 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.1%. 82: The balanceable part of the MD step is 45%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.1%. 82: 82: 82: NOTE: 72 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.049 0.040 120.9 82: (ns/day) (hour/ns) 82: Performance: 36.430 0.659 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 4. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 4. 82: 82: 82: There were 5 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.3%. 82: The balanceable part of the MD step is 38%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.5%. 82: 82: 82: NOTE: 18 % of the run time was spent in domain decomposition, 82: 0 % of the run time was spent in pair search, 82: you might want to increase nstlist (this has no effect on accuracy) 82: 82: NOTE: 24 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 1.088 0.560 194.3 82: (ns/day) (hour/ns) 82: Performance: 2.624 9.148 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 5 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 2.2%. 82: The balanceable part of the MD step is 35%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.8%. 82: 82: 82: NOTE: 52 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.045 0.023 199.6 82: (ns/day) (hour/ns) 82: Performance: 64.449 0.372 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 5 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.1%. 82: The balanceable part of the MD step is 33%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.4%. 82: 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.038 0.019 199.4 82: (ns/day) (hour/ns) 82: Performance: 76.128 0.315 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 5 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.9%. 82: The balanceable part of the MD step is 35%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.3%. 82: 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.035 0.018 199.6 82: (ns/day) (hour/ns) 82: Performance: 83.748 0.287 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (4487 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.2%. 82: The balanceable part of the MD step is 51%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.1%. 82: 82: 82: NOTE: 48 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.043 0.021 199.6 82: (ns/day) (hour/ns) 82: Performance: 68.511 0.350 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB got disabled because it was unsuitable to use. 82: Average load imbalance: 9.6%. 82: The balanceable part of the MD step is 47%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 4.5%. 82: 82: 82: NOTE: 48 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.031 0.016 199.5 82: (ns/day) (hour/ns) 82: Performance: 94.761 0.253 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.4%. 82: The balanceable part of the MD step is 40%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.6%. 82: 82: 82: NOTE: 56 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.039 0.020 199.1 82: (ns/day) (hour/ns) 82: Performance: 75.131 0.319 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 4.0%. 82: The balanceable part of the MD step is 38%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.5%. 82: 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.029 0.015 199.6 82: (ns/day) (hour/ns) 82: Performance: 101.225 0.237 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.3%. 82: The balanceable part of the MD step is 3%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.0%. 82: 82: 82: NOTE: 50 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.934 0.467 200.0 82: (ns/day) (hour/ns) 82: Performance: 3.145 7.631 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 4.9%. 82: The balanceable part of the MD step is 37%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.8%. 82: 82: 82: NOTE: 55 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.037 0.019 199.5 82: (ns/day) (hour/ns) 82: Performance: 78.409 0.306 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (3113 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.3%. 82: The balanceable part of the MD step is 7%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.0%. 82: 82: 82: NOTE: 22 % of the run time was spent in domain decomposition, 82: 0 % of the run time was spent in pair search, 82: you might want to increase nstlist (this has no effect on accuracy) 82: 82: NOTE: 40 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.051 0.026 199.5 82: (ns/day) (hour/ns) 82: Performance: 56.994 0.421 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.2%. 82: The balanceable part of the MD step is 42%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.5%. 82: 82: 82: NOTE: 48 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.036 0.018 199.6 82: (ns/day) (hour/ns) 82: Performance: 81.645 0.294 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.4%. 82: The balanceable part of the MD step is 42%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.2%. 82: 82: 82: NOTE: 48 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.018 0.009 199.0 82: (ns/day) (hour/ns) 82: Performance: 159.191 0.151 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB got disabled because it was unsuitable to use. 82: Average load imbalance: 5.7%. 82: The balanceable part of the MD step is 40%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 2.3%. 82: 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.085 0.042 199.6 82: (ns/day) (hour/ns) 82: Performance: 34.615 0.693 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.4%. 82: The balanceable part of the MD step is 39%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.6%. 82: 82: 82: NOTE: 48 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.028 0.014 199.3 82: (ns/day) (hour/ns) 82: Performance: 104.955 0.229 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.4%. 82: The balanceable part of the MD step is 39%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.5%. 82: 82: 82: NOTE: 54 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.038 0.019 199.4 82: (ns/day) (hour/ns) 82: Performance: 77.719 0.309 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (2360 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.040 0.020 199.5 82: (ns/day) (hour/ns) 82: Performance: 73.364 0.327 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.030 0.015 196.9 82: (ns/day) (hour/ns) 82: Performance: 96.108 0.250 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.033 0.017 199.5 82: (ns/day) (hour/ns) 82: Performance: 88.296 0.272 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.029 0.014 199.4 82: (ns/day) (hour/ns) 82: Performance: 101.362 0.237 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.026 0.013 199.3 82: (ns/day) (hour/ns) 82: Performance: 114.083 0.210 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.029 0.015 199.1 82: (ns/day) (hour/ns) 82: Performance: 100.630 0.238 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (2396 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.054 0.027 199.4 82: (ns/day) (hour/ns) 82: Performance: 53.932 0.445 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.022 0.011 199.2 82: (ns/day) (hour/ns) 82: Performance: 132.057 0.182 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.029 0.014 199.1 82: (ns/day) (hour/ns) 82: Performance: 102.227 0.235 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.036 0.018 199.6 82: (ns/day) (hour/ns) 82: Performance: 80.475 0.298 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.035 0.017 198.9 82: (ns/day) (hour/ns) 82: Performance: 84.097 0.285 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.031 0.016 199.0 82: (ns/day) (hour/ns) 82: Performance: 94.352 0.254 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (2200 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.054 0.027 199.3 82: (ns/day) (hour/ns) 82: Performance: 53.995 0.444 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.031 0.016 198.9 82: (ns/day) (hour/ns) 82: Performance: 94.616 0.254 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.027 0.013 198.8 82: (ns/day) (hour/ns) 82: Performance: 108.842 0.221 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.049 0.024 199.5 82: (ns/day) (hour/ns) 82: Performance: 60.143 0.399 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.024 0.012 199.3 82: (ns/day) (hour/ns) 82: Performance: 121.492 0.198 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.024 0.012 199.2 82: (ns/day) (hour/ns) 82: Performance: 122.211 0.196 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (2175 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.047 0.024 199.6 82: (ns/day) (hour/ns) 82: Performance: 62.055 0.387 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.036 0.018 199.6 82: (ns/day) (hour/ns) 82: Performance: 82.130 0.292 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 4. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 4. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.027 0.014 199.4 82: (ns/day) (hour/ns) 82: Performance: 106.524 0.225 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.039 0.019 199.5 82: (ns/day) (hour/ns) 82: Performance: 75.352 0.319 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.032 0.016 199.3 82: (ns/day) (hour/ns) 82: Performance: 90.758 0.264 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.181 0.091 199.9 82: (ns/day) (hour/ns) 82: Performance: 16.178 1.483 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (2555 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.040 0.020 199.5 82: (ns/day) (hour/ns) 82: Performance: 73.265 0.328 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.028 0.014 199.1 82: (ns/day) (hour/ns) 82: Performance: 104.737 0.229 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.043 0.021 199.4 82: (ns/day) (hour/ns) 82: Performance: 68.905 0.348 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.025 0.013 199.2 82: (ns/day) (hour/ns) 82: Performance: 116.271 0.206 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.026 0.013 199.4 82: (ns/day) (hour/ns) 82: Performance: 111.755 0.215 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.044 0.022 199.6 82: (ns/day) (hour/ns) 82: Performance: 67.352 0.356 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (2370 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.029 0.014 199.3 82: (ns/day) (hour/ns) 82: Performance: 102.211 0.235 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.033 0.016 199.4 82: (ns/day) (hour/ns) 82: Performance: 89.592 0.268 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.031 0.016 199.5 82: (ns/day) (hour/ns) 82: Performance: 93.045 0.258 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.051 0.026 199.4 82: (ns/day) (hour/ns) 82: Performance: 57.461 0.418 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.023 0.012 199.2 82: (ns/day) (hour/ns) 82: Performance: 125.182 0.192 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.025 0.012 199.0 82: (ns/day) (hour/ns) 82: Performance: 118.584 0.202 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (2360 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.6%. 82: The balanceable part of the MD step is 59%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.3%. 82: 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.048 0.024 198.8 82: (ns/day) (hour/ns) 82: Performance: 61.365 0.391 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.0%. 82: The balanceable part of the MD step is 55%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.6%. 82: 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.039 0.020 197.8 82: (ns/day) (hour/ns) 82: Performance: 75.242 0.319 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 4. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 4. 82: 82: 82: There were 5 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB got disabled because it was unsuitable to use. 82: Average load imbalance: 5.0%. 82: The balanceable part of the MD step is 46%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 2.3%. 82: 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.059 0.030 198.9 82: (ns/day) (hour/ns) 82: Performance: 49.576 0.484 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 5 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 2.6%. 82: The balanceable part of the MD step is 41%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.1%. 82: 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.056 0.028 199.1 82: (ns/day) (hour/ns) 82: Performance: 52.385 0.458 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 5 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.8%. 82: The balanceable part of the MD step is 43%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.4%. 82: 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.075 0.038 198.3 82: (ns/day) (hour/ns) 82: Performance: 38.716 0.620 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 5 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 3.7%. 82: The balanceable part of the MD step is 45%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.7%. 82: 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.048 0.024 199.1 82: (ns/day) (hour/ns) 82: Performance: 61.324 0.391 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (2609 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.9%. 82: The balanceable part of the MD step is 51%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.5%. 82: 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.033 0.017 199.0 82: (ns/day) (hour/ns) 82: Performance: 88.403 0.271 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 3.4%. 82: The balanceable part of the MD step is 52%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.8%. 82: 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.030 0.015 198.5 82: (ns/day) (hour/ns) 82: Performance: 98.344 0.244 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB got disabled because it was unsuitable to use. 82: Average load imbalance: 5.8%. 82: The balanceable part of the MD step is 50%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 2.9%. 82: 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.027 0.014 196.6 82: (ns/day) (hour/ns) 82: Performance: 106.154 0.226 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 3.3%. 82: The balanceable part of the MD step is 44%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.4%. 82: 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.032 0.016 198.8 82: (ns/day) (hour/ns) 82: Performance: 91.383 0.263 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 2.9%. 82: The balanceable part of the MD step is 50%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.5%. 82: 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.034 0.017 198.6 82: (ns/day) (hour/ns) 82: Performance: 85.196 0.282 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 2.1%. 82: The balanceable part of the MD step is 53%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.1%. 82: 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.049 0.025 199.2 82: (ns/day) (hour/ns) 82: Performance: 59.544 0.403 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (2528 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.033 0.017 198.9 82: (ns/day) (hour/ns) 82: Performance: 88.218 0.272 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.029 0.014 198.5 82: (ns/day) (hour/ns) 82: Performance: 101.820 0.236 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.039 0.020 195.3 82: (ns/day) (hour/ns) 82: Performance: 72.810 0.330 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.079 0.040 198.9 82: (ns/day) (hour/ns) 82: Performance: 36.940 0.650 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.038 0.019 198.4 82: (ns/day) (hour/ns) 82: Performance: 76.623 0.313 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.055 0.028 198.9 82: (ns/day) (hour/ns) 82: Performance: 53.177 0.451 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (2760 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.047 0.023 199.3 82: (ns/day) (hour/ns) 82: Performance: 62.910 0.381 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.029 0.015 197.8 82: (ns/day) (hour/ns) 82: Performance: 100.544 0.239 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.028 0.014 197.3 82: (ns/day) (hour/ns) 82: Performance: 104.996 0.229 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.059 0.029 199.2 82: (ns/day) (hour/ns) 82: Performance: 49.826 0.482 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.041 0.020 198.9 82: (ns/day) (hour/ns) 82: Performance: 71.912 0.334 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.065 0.033 199.5 82: (ns/day) (hour/ns) 82: Performance: 45.159 0.531 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (2359 ms) 82: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (34283 ms total) 82: 82: [----------] Global test environment tear-down 82: [==========] 13 tests from 1 test suite ran. (34370 ms total) 82: [ PASSED ] 13 tests. 82/87 Test #82: MdrunCoordinationConstraintsTests2Ranks ... Passed 34.42 sec test 83 Start 83: MdrunFEPTests 83: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-fep-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunFEPTests.xml" 83: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 83: Test timeout computed to be: 600 83: [==========] Running 12 tests from 1 test suite. 83: [----------] Global test environment set-up. 83: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_d 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp, line 149]: 83: For proper sampling of the (nearly) decoupled state, stochastic dynamics 83: should be used 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 355.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_d_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 83: Changing nstlist from 10 to 100, rlist from 1 to 1 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: Setting the LD random seed to -1145569412 83: 83: Generated 153 of the 153 non-bonded parameter combinations 83: 83: Generated 153 of the 153 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: 83: Coupling 1 copies of molecule type 'ASN' 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 0.92 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.112 0.056 199.8 83: (ns/day) (hour/ns) 83: Performance: 32.452 0.740 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_d_energy.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 trr version: GMX_trn_file (double precision) 83: 83: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_d (287 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_d 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp, line 148]: 83: For proper sampling of the (nearly) decoupled state, stochastic dynamics 83: should be used 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 355.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_d_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 83: Changing nstlist from 10 to 100, rlist from 1 to 1 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: Setting the LD random seed to -153423938 83: 83: Generated 153 of the 153 non-bonded parameter combinations 83: 83: Generated 153 of the 153 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: 83: Coupling 1 copies of molecule type 'ASN' 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 0.92 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.089 0.044 199.8 83: (ns/day) (hour/ns) 83: Performance: 40.890 0.587 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_d_energy.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 83: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_d (136 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_d 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp, line 147]: 83: For proper sampling of the (nearly) decoupled state, stochastic dynamics 83: should be used 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 83: With PME there is a minor soft core effect present at the cut-off, 83: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 83: energy conservation, but usually other effects dominate. With a common 83: sigma value of 0.34 nm the fraction of the particle-particle potential at 83: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 355.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 4 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_d_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 83: Changing nstlist from 10 to 100, rlist from 1 to 1 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: Setting the LD random seed to -13638673 83: 83: Generated 153 of the 153 non-bonded parameter combinations 83: 83: Generated 153 of the 153 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: 83: Coupling 1 copies of molecule type 'ASN' 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 0.92 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.109 0.054 199.7 83: (ns/day) (hour/ns) 83: Performance: 33.303 0.721 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_d_energy.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 83: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_d (169 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_d 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp, line 147]: 83: For proper sampling of the (nearly) decoupled state, stochastic dynamics 83: should be used 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 83: With PME there is a minor soft core effect present at the cut-off, 83: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 83: energy conservation, but usually other effects dominate. With a common 83: sigma value of 0.34 nm the fraction of the particle-particle potential at 83: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: 83: NOTE 3 [file topol.top, line 155]: 83: System has non-zero total charge: 1.000000 83: Total charge should normally be an integer. See 83: https://manual.gromacs.org/current/user-guide/floating-point.html 83: for discussion on how close it should be to an integer. 83: 83: 83: 83: 83: WARNING 2 [file topol.top, line 155]: 83: You are using Ewald electrostatics in a system with net charge. This can 83: lead to severe artifacts, such as ions moving into regions with low 83: dielectric, due to the uniform background charge. We suggest to 83: neutralize your system with counter ions, possibly in combination with a 83: physiological salt concentration. 83: 83: Setting the LD random seed to 2147463935 83: 83: Generated 171 of the 171 non-bonded parameter combinations 83: 83: Generated 171 of the 171 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: 83: Excluding 1 bonded neighbours molecule type 'NA' 83: 83: turning H bonds into constraints... 83: 83: Coupling 1 copies of molecule type 'ASN' 83: 83: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 83: J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof 83: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 83: Charge 83: J. Chem. Theory Comput. 10 (2014) pp. 381-393 83: -------- -------- --- Thank You --- -------- -------- 83: 83: Number of degrees of freedom in T-Coupling group System is 358.00 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 5 NOTEs 83: 83: There were 2 WARNINGs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_d_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 83: Changing nstlist from 10 to 50, rlist from 1.008 to 1.12 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: There are: 1 Ion residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 83: 83: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 83: 83: Estimate for the relative computational load of the PME mesh part: 0.95 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.091 0.046 199.8 83: (ns/day) (hour/ns) 83: Performance: 39.741 0.604 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_d_energy.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 83: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_d (263 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_d 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp, line 147]: 83: For proper sampling of the (nearly) decoupled state, stochastic dynamics 83: should be used 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 83: With PME there is a minor soft core effect present at the cut-off, 83: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 83: energy conservation, but usually other effects dominate. With a common 83: sigma value of 0.34 nm the fraction of the particle-particle potential at 83: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: 83: NOTE 3 [file topol.top, line 165]: 83: System has non-zero total charge: 1.000000 83: Total charge should normally be an integer. See 83: https://manual.gromacs.org/current/user-guide/floating-point.html 83: for discussion on how close it should be to an integer. 83: 83: 83: 83: 83: WARNING 2 [file topol.top, line 165]: 83: You are using Ewald electrostatics in a system with net charge. This can 83: lead to severe artifacts, such as ions moving into regions with low 83: dielectric, due to the uniform background charge. We suggest to 83: neutralize your system with counter ions, possibly in combination with a 83: physiological salt concentration. 83: 83: Setting the LD random seed to -33817865 83: 83: Generated 190 of the 190 non-bonded parameter combinations 83: 83: Generated 190 of the 190 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: 83: Excluding 1 bonded neighbours molecule type 'NA' 83: 83: turning H bonds into constraints... 83: 83: Excluding 1 bonded neighbours molecule type 'CL' 83: 83: turning H bonds into constraints... 83: 83: Coupling 1 copies of molecule type 'CL' 83: 83: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 83: J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof 83: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 83: Charge 83: J. Chem. Theory Comput. 10 (2014) pp. 381-393 83: -------- -------- --- Thank You --- -------- -------- 83: 83: Number of degrees of freedom in T-Coupling group System is 361.00 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 5 NOTEs 83: 83: There were 2 WARNINGs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_d_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 83: Changing nstlist from 10 to 50, rlist from 1.008 to 1.121 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: There are: 2 Ion residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 83: 83: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 83: 83: Estimate for the relative computational load of the PME mesh part: 0.95 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.123 0.061 199.9 83: (ns/day) (hour/ns) 83: Performance: 29.580 0.811 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_d_energy.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 83: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_d (99 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_d 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp, line 171]: 83: For proper sampling of the (nearly) decoupled state, stochastic dynamics 83: should be used 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 83: Replacing vdwtype=Shift by the equivalent combination of vdwtype=Cut-off 83: and vdw_modifier=Force-switch 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 355.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 4 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_d_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 83: Changing nstlist from 10 to 100, rlist from 1 to 1 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 100 steps, 0.1 ps. 83: Setting the LD random seed to 2063038332 83: 83: Generated 153 of the 153 non-bonded parameter combinations 83: 83: Generated 153 of the 153 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: 83: Coupling 1 copies of molecule type 'ASN' 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 0.92 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.400 0.200 199.9 83: (ns/day) (hour/ns) 83: Performance: 43.662 0.550 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_d_energy.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Reading energy frame 30 time 0.030 Reading energy frame 40 time 0.040 Reading energy frame 50 time 0.050 Reading energy frame 60 time 0.060 Reading energy frame 70 time 0.070 Reading energy frame 80 time 0.080 Reading energy frame 90 time 0.090 Reading energy frame 100 time 0.100 Last energy frame read 100 time 0.100 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_d (312 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_d 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: 83: WARNING 2 [file topol.top, line 72]: 83: No default Bond types for perturbed atoms, using normal values 83: 83: 83: WARNING 3 [file topol.top, line 73]: 83: No default Bond types for perturbed atoms, using normal values 83: 83: 83: WARNING 4 [file topol.top, line 98]: 83: No default Angle types for perturbed atoms, using normal values 83: 83: 83: WARNING 5 [file topol.top, line 99]: 83: No default Angle types for perturbed atoms, using normal values 83: 83: 83: WARNING 6 [file topol.top, line 100]: 83: No default Angle types for perturbed atoms, using normal values 83: 83: 83: WARNING 7 [file topol.top, line 101]: 83: No default Angle types for perturbed atoms, using normal values 83: 83: 83: WARNING 8 [file topol.top, line 111]: 83: No default Ryckaert-Bell. types for perturbed atoms, using normal values 83: 83: 83: WARNING 9 [file topol.top, line 112]: 83: No default Ryckaert-Bell. types for perturbed atoms, using normal values 83: 83: 83: WARNING 10 [file topol.top, line 113]: 83: No default Ryckaert-Bell. types for perturbed atoms, using normal values 83: 83: 83: WARNING 11 [file topol.top, line 114]: 83: No default Ryckaert-Bell. types for perturbed atoms, using normal values 83: 83: Number of degrees of freedom in T-Coupling group System is 355.00 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 2 NOTEs 83: 83: There were 11 WARNINGs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_d_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 83: Changing nstlist from 10 to 100, rlist from 1 to 1 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: Setting the LD random seed to -71663653 83: 83: Generated 136 of the 136 non-bonded parameter combinations 83: 83: Generated 136 of the 136 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 0.92 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.157 0.078 199.7 83: (ns/day) (hour/ns) 83: Performance: 23.124 1.038 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_d_energy.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 83: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_d (217 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_d 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: 83: WARNING 2 [file topol.top, line 72]: 83: No default Bond types for perturbed atoms, using normal values 83: 83: 83: WARNING 3 [file topol.top, line 73]: 83: No default Bond types for perturbed atoms, using normal values 83: 83: 83: WARNING 4 [file topol.top, line 98]: 83: No default Angle types for perturbed atoms, using normal values 83: 83: 83: WARNING 5 [file topol.top, line 99]: 83: No default Angle types for perturbed atoms, using normal values 83: 83: 83: WARNING 6 [file topol.top, line 100]: 83: No default Angle types for perturbed atoms, using normal values 83: 83: 83: WARNING 7 [file topol.top, line 101]: 83: No default Angle types for perturbed atoms, using normal values 83: 83: 83: WARNING 8 [file topol.top, line 111]: 83: No default Ryckaert-Bell. types for perturbed atoms, using normal values 83: 83: 83: WARNING 9 [file topol.top, line 112]: 83: No default Ryckaert-Bell. types for perturbed atoms, using normal values 83: 83: 83: WARNING 10 [file topol.top, line 113]: 83: No default Ryckaert-Bell. types for perturbed atoms, using normal values 83: 83: 83: WARNING 11 [file topol.top, line 114]: 83: No default Ryckaert-Bell. types for perturbed atoms, using normal values 83: 83: Number of degrees of freedom in T-Coupling group System is 355.00 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 83: Removing center of mass motion in the presence of position restraints 83: might cause artifacts. When you are using position restraints to 83: equilibrate a macro-molecule, the artifacts are usually negligible. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 3 NOTEs 83: 83: There were 11 WARNINGs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_d_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 83: Changing nstlist from 10 to 100, rlist from 1 to 1 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: Setting the LD random seed to -886049281 83: 83: Generated 136 of the 136 non-bonded parameter combinations 83: 83: Generated 136 of the 136 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 0.92 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.368 0.184 199.9 83: (ns/day) (hour/ns) 83: Performance: 9.847 2.437 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_d_energy.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 83: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_d (318 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_d 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 355.00 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_d_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 83: Changing nstlist from 10 to 100, rlist from 1 to 1 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: Setting the LD random seed to -671258679 83: 83: Generated 136 of the 136 non-bonded parameter combinations 83: 83: Generated 136 of the 136 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 0.86 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.082 0.041 199.7 83: (ns/day) (hour/ns) 83: Performance: 43.979 0.546 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_d_energy.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 83: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_d (144 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_d 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 355.00 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: There was 1 NOTE 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_d_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 83: Changing nstlist from 10 to 100, rlist from 1 to 1 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.035 0.017 199.3 83: (ns/day) (hour/ns) 83: Performance: 104.643 0.229 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_d_energy.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 83: Setting the LD random seed to 469732607 83: 83: Generated 136 of the 136 non-bonded parameter combinations 83: 83: Generated 136 of the 136 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: Analysing Protein... 83: 83: The largest distance between excluded atoms is 0.331 nm between atom 1 and 9 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 0.86 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_d (120 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_d 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 83: With PME there is a minor soft core effect present at the cut-off, 83: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 83: energy conservation, but usually other effects dominate. With a common 83: sigma value of 0.34 nm the fraction of the particle-particle potential at 83: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 355.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_d_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 83: Changing nstlist from 10 to 100, rlist from 1 to 1 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: Setting the LD random seed to -277031051 83: 83: Generated 136 of the 136 non-bonded parameter combinations 83: 83: Generated 136 of the 136 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 0.92 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.086 0.043 199.6 83: (ns/day) (hour/ns) 83: Performance: 42.280 0.568 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_d_energy.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 83: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_d (199 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_d 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 83: With PME there is a minor soft core effect present at the cut-off, 83: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 83: energy conservation, but usually other effects dominate. With a common 83: sigma value of 0.34 nm the fraction of the particle-particle potential at 83: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 355.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_d_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 83: Changing nstlist from 10 to 100, rlist from 1 to 1 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: Setting the LD random seed to -118505921 83: 83: Generated 136 of the 136 non-bonded parameter combinations 83: 83: Generated 136 of the 136 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.172 nm between atom 8 and 9 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 0.86 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.077 0.039 199.6 83: (ns/day) (hour/ns) 83: Performance: 46.816 0.513 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_d_energy.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 83: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_d (165 ms) 83: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest (2437 ms total) 83: 83: [----------] Global test environment tear-down 83: [==========] 12 tests from 1 test suite ran. (2505 ms total) 83: [ PASSED ] 12 tests. 83/87 Test #83: MdrunFEPTests ............................. Passed 2.54 sec test 84 Start 84: MdrunPullTests 84: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-pull-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunPullTests.xml" 84: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 84: Test timeout computed to be: 600 84: [==========] Running 4 tests from 1 test suite. 84: [----------] Global test environment set-up. 84: [----------] 4 tests from PullTest/PullIntegrationTest 84: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/0 84: Generating 1-4 interactions: fudge = 0.5 84: Pull group 1 'r_1' has 3 atoms 84: Pull group 2 'r_2' has 3 atoms 84: Number of degrees of freedom in T-Coupling group System is 1293.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 303.122 K for 84: determining the Verlet buffer size 84: 84: Pull group natoms pbc atom distance at start reference at t=0 84: 1 3 2 84: 2 3 5 0.575 nm 0.600 nm 84: 84: There was 1 NOTE 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 20 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.088 0.044 199.6 84: (ns/day) (hour/ns) 84: Performance: 41.011 0.585 84: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/0 (499 ms) 84: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/1 84: Generating 1-4 interactions: fudge = 0.5 84: Pull group 1 'r_1' has 3 atoms 84: Pull group 2 'r_2' has 3 atoms 84: Number of degrees of freedom in T-Coupling group System is 1293.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 303.122 K for 84: determining the Verlet buffer size 84: 84: Pull group natoms pbc atom distance at start reference at t=0 84: 1 3 2 84: 2 3 5 0.301 nm 0.400 nm 84: 84: There was 1 NOTE 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 20 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.127 0.064 199.7 84: (ns/day) (hour/ns) 84: Performance: 28.517 0.842 84: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/1 (533 ms) 84: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/2 84: Generating 1-4 interactions: fudge = 0.5 84: Pull group 1 'r_1' has 3 atoms 84: Pull group 2 'r_2' has 3 atoms 84: Pull group 3 'r_3' has 3 atoms 84: Number of degrees of freedom in T-Coupling group System is 1292.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 303.357 K for 84: determining the Verlet buffer size 84: 84: Pull group natoms pbc atom distance at start reference at t=0 84: 1 3 2 84: 2 3 5 0.575 nm 0.500 nm 84: 1 3 2 84: 3 3 8 0.331 nm 0.400 nm 84: 84: There was 1 NOTE 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 20 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.357 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.084 0.042 199.8 84: (ns/day) (hour/ns) 84: Performance: 43.319 0.554 84: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/2 (499 ms) 84: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/3 84: Generating 1-4 interactions: fudge = 0.5 84: Pull group 1 'r_1' has 3 atoms 84: Pull group 2 'r_2' has 3 atoms 84: Number of degrees of freedom in T-Coupling group System is 1293.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 303.122 K for 84: determining the Verlet buffer size 84: 84: Pull group natoms pbc atom distance at start reference at t=0 84: 1 3 2 84: 2 3 5 0.575 nm 0.000 nm 84: 1 3 2 84: 2 3 5 0.050 nm 0.000 nm 84: 84: There was 1 NOTE 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 20 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.093 0.047 199.8 84: (ns/day) (hour/ns) 84: Performance: 39.003 0.615 84: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/3 (402 ms) 84: [----------] 4 tests from PullTest/PullIntegrationTest (1936 ms total) 84: 84: [----------] Global test environment tear-down 84: [==========] 4 tests from 1 test suite ran. (1962 ms total) 84: [ PASSED ] 4 tests. 84/87 Test #84: MdrunPullTests ............................ Passed 1.99 sec test 85 Start 85: MdrunRotationTests 85: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-rotation-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunRotationTests.xml" 85: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 85: Test timeout computed to be: 600 85: [==========] Running 12 tests from 1 test suite. 85: [----------] Global test environment set-up. 85: [----------] 12 tests from RotationWorks/RotationTest 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 85: Enforced rotation: Group 0 (iso) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: trr version: GMX_trn_file (single precision) 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to 2135942059 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.050 0.025 199.7 85: (ns/day) (hour/ns) 85: Performance: 179.837 0.133 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 (37 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 85: Enforced rotation: Group 0 (iso-pf) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to -552484993 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.047 0.023 199.7 85: (ns/day) (hour/ns) 85: Performance: 192.795 0.124 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 (31 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 85: Enforced rotation: Group 0 (pm) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to -10526721 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.046 0.023 199.6 85: (ns/day) (hour/ns) 85: Performance: 195.280 0.123 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 (33 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 85: Enforced rotation: Group 0 (pm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to -546314305 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.043 0.022 199.7 85: (ns/day) (hour/ns) 85: Performance: 206.767 0.116 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 (27 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 85: Enforced rotation: Group 0 (rm) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to -44105939 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.031 0.016 199.6 85: (ns/day) (hour/ns) 85: Performance: 285.388 0.084 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 (34 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 85: Enforced rotation: Group 0 (rm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to -67993866 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.039 0.020 199.7 85: (ns/day) (hour/ns) 85: Performance: 227.438 0.106 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 (33 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 85: Enforced rotation: Group 0 (rm2) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to 1065850667 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.063 0.032 199.8 85: (ns/day) (hour/ns) 85: Performance: 141.592 0.170 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 (39 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 85: Enforced rotation: Group 0 (rm2-pf) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to -689053753 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.032 0.016 199.2 85: (ns/day) (hour/ns) 85: Performance: 280.791 0.085 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 (24 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 85: Enforced rotation: Group 0 (flex) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to -287572491 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.064 0.032 199.5 85: (ns/day) (hour/ns) 85: Performance: 140.990 0.170 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 (38 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 85: Enforced rotation: Group 0 (flex-t) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to 1035418494 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.088 0.044 199.7 85: (ns/day) (hour/ns) 85: Performance: 102.035 0.235 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 (73 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 85: Enforced rotation: Group 0 (flex2) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to -1092674817 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.047 0.024 199.6 85: (ns/day) (hour/ns) 85: Performance: 191.112 0.126 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 (34 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 85: Enforced rotation: Group 0 (flex2-t) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to 2078013023 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.038 0.019 199.6 85: (ns/day) (hour/ns) 85: Performance: 237.658 0.101 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 (29 ms) 85: [----------] 12 tests from RotationWorks/RotationTest (438 ms total) 85: 85: [----------] Global test environment tear-down 85: [==========] 12 tests from 1 test suite ran. (460 ms total) 85: [ PASSED ] 12 tests. 85/87 Test #85: MdrunRotationTests ........................ Passed 0.49 sec test 86 Start 86: MdrunSimulatorComparison 86: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-simulator-comparison-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunSimulatorComparison.xml" 86: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 86: Test timeout computed to be: 600 86: [==========] Running 94 tests from 4 test suites. 86: [----------] Global test environment set-up. 86: [----------] 60 tests from SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/0 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/0 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/1 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.056 0.028 199.9 86: (ns/day) (hour/ns) 86: Performance: 52.371 0.458 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.029 0.015 199.5 86: (ns/day) (hour/ns) 86: Performance: 100.987 0.238 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 trr version: GMX_trn_file (double precision) 86: 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/1 (59 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/2 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.039 0.020 199.8 86: (ns/day) (hour/ns) 86: Performance: 74.629 0.322 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.024 0.012 199.5 86: (ns/day) (hour/ns) 86: Performance: 121.036 0.198 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/2 (44 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/3 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/3 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/4 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/4 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/5 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/5 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/6 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.040 0.020 199.8 86: (ns/day) (hour/ns) 86: Performance: 73.438 0.327 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.029 0.015 199.6 86: (ns/day) (hour/ns) 86: Performance: 101.239 0.237 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/6 (48 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/7 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: 86: There was 1 WARNING 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.032 0.016 199.8 86: (ns/day) (hour/ns) 86: Performance: 92.829 0.259 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.037 0.019 199.7 86: (ns/day) (hour/ns) 86: Performance: 79.041 0.304 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/7 (40 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/8 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.056 0.028 199.9 86: (ns/day) (hour/ns) 86: Performance: 52.640 0.456 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.022 0.011 199.4 86: (ns/day) (hour/ns) 86: Performance: 133.340 0.180 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/8 (48 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/9 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/9 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/10 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/10 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/11 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: 86: There was 1 WARNING 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.061 0.031 199.9 86: (ns/day) (hour/ns) 86: Performance: 47.891 0.501 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.037 0.019 199.7 86: (ns/day) (hour/ns) 86: Performance: 78.815 0.305 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/11 (54 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/12 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: 86: WARNING 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: 86: There were 2 WARNINGs 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.048 0.024 199.8 86: (ns/day) (hour/ns) 86: Performance: 60.537 0.396 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.025 0.012 199.5 86: (ns/day) (hour/ns) 86: Performance: 119.066 0.202 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/12 (51 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/13 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: 86: There was 1 WARNING 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.063 0.032 199.5 86: (ns/day) (hour/ns) 86: Performance: 46.184 0.520 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.035 0.018 199.1 86: (ns/day) (hour/ns) 86: Performance: 83.355 0.288 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/13 (62 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/14 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/14 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/15 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.053 0.027 199.6 86: (ns/day) (hour/ns) 86: Performance: 55.243 0.434 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.036 0.018 199.6 86: (ns/day) (hour/ns) 86: Performance: 81.666 0.294 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/15 (56 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/16 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.456 0.228 200.0 86: (ns/day) (hour/ns) 86: Performance: 6.442 3.726 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.022 0.011 199.4 86: (ns/day) (hour/ns) 86: Performance: 135.705 0.177 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/16 (249 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/17 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/17 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/18 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.054 0.027 199.6 86: (ns/day) (hour/ns) 86: Performance: 54.673 0.439 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.044 0.022 199.7 86: (ns/day) (hour/ns) 86: Performance: 66.245 0.362 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/18 (55 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/19 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.044 0.022 199.7 86: (ns/day) (hour/ns) 86: Performance: 65.992 0.364 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.023 0.012 199.5 86: (ns/day) (hour/ns) 86: Performance: 125.491 0.191 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/19 (51 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/20 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/20 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/21 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 86: Andersen temperature control methods assume nsttcouple = 1; there is no 86: need for larger nsttcouple > 1, since no global parameters are computed. 86: nsttcouple has been reset to 1 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.035 0.018 199.1 86: (ns/day) (hour/ns) 86: Performance: 83.712 0.287 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.021 0.010 199.4 86: (ns/day) (hour/ns) 86: Performance: 142.198 0.169 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/21 (36 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/22 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 86: Andersen temperature control methods assume nsttcouple = 1; there is no 86: need for larger nsttcouple > 1, since no global parameters are computed. 86: nsttcouple has been reset to 1 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.028 0.014 199.6 86: (ns/day) (hour/ns) 86: Performance: 106.447 0.225 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.020 0.010 199.2 86: (ns/day) (hour/ns) 86: Performance: 142.848 0.168 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/22 (30 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/23 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 86: Andersen temperature control methods assume nsttcouple = 1; there is no 86: need for larger nsttcouple > 1, since no global parameters are computed. 86: nsttcouple has been reset to 1 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.041 0.020 199.8 86: (ns/day) (hour/ns) 86: Performance: 72.158 0.333 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.020 0.010 199.4 86: (ns/day) (hour/ns) 86: Performance: 145.530 0.165 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/23 (39 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/24 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/24 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/25 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/25 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/26 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 86: Center of mass removal not necessary for Andersen. All velocities of 86: coupled groups are rerandomized periodically, so flying ice cube errors 86: will not occur. 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 86: Andersen temperature control methods assume nsttcouple = 1; there is no 86: need for larger nsttcouple > 1, since no global parameters are computed. 86: nsttcouple has been reset to 1 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.068 0.034 199.9 86: (ns/day) (hour/ns) 86: Performance: 43.334 0.554 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.020 0.010 199.5 86: (ns/day) (hour/ns) 86: Performance: 142.937 0.168 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/26 (57 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/27 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 86: Center of mass removal not necessary for Andersen. All velocities of 86: coupled groups are rerandomized periodically, so flying ice cube errors 86: will not occur. 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 86: Andersen temperature control methods assume nsttcouple = 1; there is no 86: need for larger nsttcouple > 1, since no global parameters are computed. 86: nsttcouple has been reset to 1 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.060 0.030 199.9 86: (ns/day) (hour/ns) 86: Performance: 48.650 0.493 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.022 0.011 199.5 86: (ns/day) (hour/ns) 86: Performance: 132.494 0.181 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/27 (49 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/28 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 86: Center of mass removal not necessary for Andersen. All velocities of 86: coupled groups are rerandomized periodically, so flying ice cube errors 86: will not occur. 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 86: Andersen temperature control methods assume nsttcouple = 1; there is no 86: need for larger nsttcouple > 1, since no global parameters are computed. 86: nsttcouple has been reset to 1 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.043 0.021 199.8 86: (ns/day) (hour/ns) 86: Performance: 68.903 0.348 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.030 0.015 199.6 86: (ns/day) (hour/ns) 86: Performance: 98.864 0.243 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/28 (50 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/29 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/29 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/30 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/30 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/31 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.053 0.027 199.8 86: (ns/day) (hour/ns) 86: Performance: 55.207 0.435 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.048 0.024 199.7 86: (ns/day) (hour/ns) 86: Performance: 61.456 0.391 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/31 (420 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/32 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: There was 1 WARNING 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.040 0.020 199.8 86: (ns/day) (hour/ns) 86: Performance: 73.988 0.324 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.046 0.023 199.5 86: (ns/day) (hour/ns) 86: Performance: 63.970 0.375 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/32 (392 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/33 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/33 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/34 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/34 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/35 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/35 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/36 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.087 0.044 199.9 86: (ns/day) (hour/ns) 86: Performance: 33.676 0.713 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.062 0.031 199.5 86: (ns/day) (hour/ns) 86: Performance: 46.970 0.511 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/36 (513 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/37 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.049 0.024 199.8 86: (ns/day) (hour/ns) 86: Performance: 60.250 0.398 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.034 0.017 199.2 86: (ns/day) (hour/ns) 86: Performance: 85.822 0.280 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/37 (474 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/38 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.071 0.035 199.8 86: (ns/day) (hour/ns) 86: Performance: 41.421 0.579 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.038 0.019 199.0 86: (ns/day) (hour/ns) 86: Performance: 76.309 0.315 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/38 (497 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/39 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/39 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/40 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/40 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/41 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.066 0.033 199.0 86: (ns/day) (hour/ns) 86: Performance: 44.325 0.541 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.068 0.034 198.9 86: (ns/day) (hour/ns) 86: Performance: 42.913 0.559 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/41 (503 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/42 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: 86: WARNING 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: There were 2 WARNINGs 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.037 0.018 199.6 86: (ns/day) (hour/ns) 86: Performance: 79.773 0.301 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.031 0.016 199.5 86: (ns/day) (hour/ns) 86: Performance: 93.672 0.256 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/42 (411 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/43 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.033 0.016 199.0 86: (ns/day) (hour/ns) 86: Performance: 89.710 0.268 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.026 0.013 198.6 86: (ns/day) (hour/ns) 86: Performance: 112.906 0.213 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/43 (422 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/44 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/44 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/45 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/45 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/46 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.052 0.026 199.7 86: (ns/day) (hour/ns) 86: Performance: 56.699 0.423 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.031 0.016 199.5 86: (ns/day) (hour/ns) 86: Performance: 93.510 0.257 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/46 (454 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/47 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/47 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/48 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.047 0.024 199.7 86: (ns/day) (hour/ns) 86: Performance: 62.035 0.387 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.043 0.022 199.7 86: (ns/day) (hour/ns) 86: Performance: 68.295 0.351 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/48 (476 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/49 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/49 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/50 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/50 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/51 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: 86: Andersen temperature control methods assume nsttcouple = 1; there is no 86: need for larger nsttcouple > 1, since no global parameters are computed. 86: nsttcouple has been reset to 1 86: 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.052 0.026 199.5 86: (ns/day) (hour/ns) 86: Performance: 56.848 0.422 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.055 0.028 198.5 86: (ns/day) (hour/ns) 86: Performance: 52.774 0.455 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/51 (374 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/52 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 86: Andersen temperature control methods assume nsttcouple = 1; there is no 86: need for larger nsttcouple > 1, since no global parameters are computed. 86: nsttcouple has been reset to 1 86: 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: There was 1 WARNING 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.064 0.032 199.5 86: (ns/day) (hour/ns) 86: Performance: 45.963 0.522 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.024 0.012 199.3 86: (ns/day) (hour/ns) 86: Performance: 121.768 0.197 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/52 (378 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/53 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: 86: Andersen temperature control methods assume nsttcouple = 1; there is no 86: need for larger nsttcouple > 1, since no global parameters are computed. 86: nsttcouple has been reset to 1 86: 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.053 0.027 199.5 86: (ns/day) (hour/ns) 86: Performance: 55.382 0.433 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.085 0.043 199.8 86: (ns/day) (hour/ns) 86: Performance: 34.490 0.696 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/53 (495 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/54 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/54 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/55 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/55 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/56 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/56 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/57 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/57 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/58 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/58 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/59 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/59 (0 ms) 86: [----------] 60 tests from SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest (6914 ms total) 86: 86: [----------] 32 tests from SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/0 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.039 0.019 199.6 86: (ns/day) (hour/ns) 86: Performance: 75.885 0.316 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.069 0.035 199.7 86: (ns/day) (hour/ns) 86: Performance: 42.337 0.567 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/0 (68 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/1 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.034 0.017 199.4 86: (ns/day) (hour/ns) 86: Performance: 86.949 0.276 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.320 0.160 199.9 86: (ns/day) (hour/ns) 86: Performance: 9.186 2.613 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/1 (185 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/2 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.032 0.016 199.4 86: (ns/day) (hour/ns) 86: Performance: 90.504 0.265 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.072 0.036 199.8 86: (ns/day) (hour/ns) 86: Performance: 40.683 0.590 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/2 (70 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/3 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/3 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/4 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.040 0.020 199.7 86: (ns/day) (hour/ns) 86: Performance: 74.061 0.324 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.039 0.020 199.4 86: (ns/day) (hour/ns) 86: Performance: 75.231 0.319 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/4 (51 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/5 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.045 0.023 199.4 86: (ns/day) (hour/ns) 86: Performance: 65.020 0.369 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.054 0.027 199.6 86: (ns/day) (hour/ns) 86: Performance: 54.010 0.444 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/5 (61 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/6 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: 86: There was 1 WARNING 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.039 0.020 199.6 86: (ns/day) (hour/ns) 86: Performance: 74.505 0.322 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.087 0.043 199.7 86: (ns/day) (hour/ns) 86: Performance: 33.831 0.709 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/6 (77 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/7 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.037 0.019 199.5 86: (ns/day) (hour/ns) 86: Performance: 78.524 0.306 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.038 0.019 199.7 86: (ns/day) (hour/ns) 86: Performance: 76.996 0.312 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/7 (47 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/8 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: 86: There was 1 WARNING 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.026 0.013 199.4 86: (ns/day) (hour/ns) 86: Performance: 110.591 0.217 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.085 0.043 199.8 86: (ns/day) (hour/ns) 86: Performance: 34.444 0.697 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/8 (66 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/9 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_input.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: 86: There was 1 WARNING 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.038 0.019 199.5 86: (ns/day) (hour/ns) 86: Performance: 76.682 0.313 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.036 0.018 199.7 86: (ns/day) (hour/ns) 86: Performance: 80.842 0.297 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/9 (45 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/10 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: 86: WARNING 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: 86: There were 2 WARNINGs 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.039 0.020 199.5 86: (ns/day) (hour/ns) 86: Performance: 74.235 0.323 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.052 0.026 199.8 86: (ns/day) (hour/ns) 86: Performance: 56.780 0.423 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/10 (58 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/11 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: 86: There was 1 WARNING 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.159 0.080 199.8 86: (ns/day) (hour/ns) 86: Performance: 18.426 1.303 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.167 0.084 199.7 86: (ns/day) (hour/ns) 86: Performance: 17.522 1.370 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/11 (205 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/12 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 86: 1 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.098 0.049 199.8 86: (ns/day) (hour/ns) 86: Performance: 30.081 0.798 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.037 0.019 199.5 86: (ns/day) (hour/ns) 86: Performance: 78.650 0.305 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/12 (86 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/13 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 86: 1 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.033 0.017 199.4 86: (ns/day) (hour/ns) 86: Performance: 88.545 0.271 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.043 0.022 199.7 86: (ns/day) (hour/ns) 86: Performance: 68.169 0.352 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/13 (54 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/14 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: 86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 86: 1 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.053 0.027 199.5 86: (ns/day) (hour/ns) 86: Performance: 55.326 0.434 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.046 0.023 199.5 86: (ns/day) (hour/ns) 86: Performance: 63.114 0.380 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/14 (65 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/15 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 86: 1 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.027 0.013 199.5 86: (ns/day) (hour/ns) 86: Performance: 108.985 0.220 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.111 0.056 199.9 86: (ns/day) (hour/ns) 86: Performance: 26.333 0.911 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/15 (102 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/16 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.050 0.025 199.5 86: (ns/day) (hour/ns) 86: Performance: 59.150 0.406 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.069 0.034 199.7 86: (ns/day) (hour/ns) 86: Performance: 42.754 0.561 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/16 (461 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/17 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.031 0.016 199.1 86: (ns/day) (hour/ns) 86: Performance: 93.993 0.255 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.077 0.038 199.9 86: (ns/day) (hour/ns) 86: Performance: 38.269 0.627 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/17 (470 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/18 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: There was 1 WARNING 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.055 0.027 199.7 86: (ns/day) (hour/ns) 86: Performance: 53.665 0.447 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.066 0.033 199.0 86: (ns/day) (hour/ns) 86: Performance: 43.975 0.546 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/18 (389 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/19 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/19 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/20 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.035 0.017 199.2 86: (ns/day) (hour/ns) 86: Performance: 84.351 0.285 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.044 0.022 199.8 86: (ns/day) (hour/ns) 86: Performance: 66.256 0.362 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/20 (536 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/21 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.034 0.017 199.6 86: (ns/day) (hour/ns) 86: Performance: 86.896 0.276 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.099 0.049 199.9 86: (ns/day) (hour/ns) 86: Performance: 29.680 0.809 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/21 (451 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/22 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.029 0.014 199.2 86: (ns/day) (hour/ns) 86: Performance: 101.329 0.237 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.056 0.028 199.6 86: (ns/day) (hour/ns) 86: Performance: 51.903 0.462 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/22 (412 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/23 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.035 0.018 198.6 86: (ns/day) (hour/ns) 86: Performance: 82.620 0.290 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.049 0.025 199.7 86: (ns/day) (hour/ns) 86: Performance: 59.464 0.404 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/23 (482 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/24 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.028 0.014 198.4 86: (ns/day) (hour/ns) 86: Performance: 105.069 0.228 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.064 0.032 199.5 86: (ns/day) (hour/ns) 86: Performance: 45.649 0.526 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/24 (586 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/25 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.081 0.041 199.5 86: (ns/day) (hour/ns) 86: Performance: 36.112 0.665 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.097 0.049 199.6 86: (ns/day) (hour/ns) 86: Performance: 30.169 0.796 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/25 (638 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/26 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: 86: WARNING 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: There were 2 WARNINGs 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.037 0.018 199.4 86: (ns/day) (hour/ns) 86: Performance: 80.050 0.300 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.063 0.032 199.8 86: (ns/day) (hour/ns) 86: Performance: 46.497 0.516 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/26 (389 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/27 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.028 0.014 198.7 86: (ns/day) (hour/ns) 86: Performance: 103.578 0.232 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.043 0.021 199.5 86: (ns/day) (hour/ns) 86: Performance: 68.549 0.350 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/27 (393 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/28 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 86: 1 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.030 0.015 199.5 86: (ns/day) (hour/ns) 86: Performance: 96.547 0.249 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.048 0.024 199.5 86: (ns/day) (hour/ns) 86: Performance: 60.895 0.394 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/28 (453 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/29 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: 86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 86: 1 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.029 0.014 199.4 86: (ns/day) (hour/ns) 86: Performance: 102.752 0.234 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.048 0.024 199.0 86: (ns/day) (hour/ns) 86: Performance: 60.291 0.398 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/29 (432 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/30 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 86: 1 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: There was 1 WARNING 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.029 0.014 199.4 86: (ns/day) (hour/ns) 86: Performance: 101.447 0.237 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.054 0.027 199.5 86: (ns/day) (hour/ns) 86: Performance: 53.815 0.446 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/30 (522 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/31 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 86: 1 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.028 0.014 198.8 86: (ns/day) (hour/ns) 86: Performance: 103.941 0.231 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.057 0.028 199.7 86: (ns/day) (hour/ns) 86: Performance: 51.571 0.465 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/31 (445 ms) 86: [----------] 32 tests from SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest (8320 ms total) 86: 86: [----------] 1 test from SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest 86: [ RUN ] SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest.WithinTolerances/0 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Pull group 1 'FirstWaterMolecule' has 3 atoms 86: Pull group 2 'SecondWaterMolecule' has 3 atoms 86: Number of degrees of freedom in T-Coupling group System is 9.00 86: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 2573.591 K for 86: determining the Verlet buffer size 86: 86: Pull group natoms pbc atom distance at start reference at t=0 86: 1 3 2 86: 2 3 5 1.112 nm 1.000 nm 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 3 of the 3 non-bonded parameter combinations 86: 86: Generated 3 of the 3 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.045 0.023 199.7 86: (ns/day) (hour/ns) 86: Performance: 65.090 0.369 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.035 0.018 199.5 86: (ns/day) (hour/ns) 86: Performance: 83.303 0.288 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest.WithinTolerances/0 (48 ms) 86: [----------] 1 test from SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest (48 ms total) 86: 86: [----------] 1 test from SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest.WithinTolerances/0 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Pull group 1 'FirstWaterMolecule' has 3 atoms 86: Pull group 2 'SecondWaterMolecule' has 3 atoms 86: Number of degrees of freedom in T-Coupling group System is 9.00 86: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 2573.591 K for 86: determining the Verlet buffer size 86: 86: Pull group natoms pbc atom distance at start reference at t=0 86: 1 3 2 86: 2 3 5 1.112 nm 1.000 nm 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 3 of the 3 non-bonded parameter combinations 86: 86: Generated 3 of the 3 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.039 0.019 199.5 86: (ns/day) (hour/ns) 86: Performance: 75.497 0.318 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.048 0.024 199.4 86: (ns/day) (hour/ns) 86: Performance: 60.598 0.396 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest.WithinTolerances/0 (51 ms) 86: [----------] 1 test from SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest (51 ms total) 86: 86: [----------] Global test environment tear-down 86: [==========] 94 tests from 4 test suites ran. (15457 ms total) 86: [ PASSED ] 94 tests. 86/87 Test #86: MdrunSimulatorComparison .................. Passed 15.49 sec test 87 Start 87: MdrunVirtualSiteTests 87: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-vsites-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunVirtualSiteTests.xml" 87: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 87: Test timeout computed to be: 600 87: [==========] Running 37 tests from 2 test suites. 87: [----------] Global test environment set-up. 87: [----------] 1 test from VirtualSiteVelocityTest 87: [ RUN ] VirtualSiteVelocityTest.ReferenceIsCorrect 87: [ OK ] VirtualSiteVelocityTest.ReferenceIsCorrect (0 ms) 87: [----------] 1 test from VirtualSiteVelocityTest (0 ms total) 87: 87: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 2.9%. 87: The balanceable part of the MD step is 37%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 1.1%. 87: 87: 87: NOTE: 48 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.027 0.014 199.3 87: (ns/day) (hour/ns) 87: Performance: 56.521 0.425 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: trr version: GMX_trn_file (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 (24 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 5.7%. 87: The balanceable part of the MD step is 38%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 2.2%. 87: 87: 87: NOTE: 48 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.025 0.013 198.9 87: (ns/day) (hour/ns) 87: Performance: 61.870 0.388 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 (21 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 5.6%. 87: The balanceable part of the MD step is 40%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 2.3%. 87: 87: 87: NOTE: 48 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.024 0.012 198.8 87: (ns/day) (hour/ns) 87: Performance: 65.325 0.367 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 (19 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 48 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.022 0.011 198.8 87: (ns/day) (hour/ns) 87: Performance: 69.802 0.344 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 (22 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 48 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.024 0.012 199.0 87: (ns/day) (hour/ns) 87: Performance: 64.279 0.373 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 (22 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 48 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.022 0.011 198.7 87: (ns/day) (hour/ns) 87: Performance: 68.873 0.348 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 (21 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 87: 1 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 5 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 47 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.025 0.012 198.7 87: (ns/day) (hour/ns) 87: Performance: 62.234 0.386 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 (25 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 87: 1 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 5 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 48 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.022 0.011 198.8 87: (ns/day) (hour/ns) 87: Performance: 69.655 0.345 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 (24 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 87: 1 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 5 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 48 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.021 0.011 198.8 87: (ns/day) (hour/ns) 87: Performance: 72.488 0.331 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 (23 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 4.1%. 87: The balanceable part of the MD step is 44%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 1.8%. 87: 87: 87: NOTE: 47 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.023 0.011 199.1 87: (ns/day) (hour/ns) 87: Performance: 67.696 0.355 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 (18 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 5.2%. 87: The balanceable part of the MD step is 40%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 2.1%. 87: 87: 87: NOTE: 48 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.021 0.010 198.9 87: (ns/day) (hour/ns) 87: Performance: 74.292 0.323 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 (16 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 48 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.024 0.012 199.1 87: (ns/day) (hour/ns) 87: Performance: 63.566 0.378 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 (22 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 48 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.024 0.012 197.7 87: (ns/day) (hour/ns) 87: Performance: 64.814 0.370 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 (24 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 47 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.026 0.013 198.5 87: (ns/day) (hour/ns) 87: Performance: 58.708 0.409 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 (32 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 48 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.025 0.013 198.0 87: (ns/day) (hour/ns) 87: Performance: 60.944 0.394 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 (27 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 48 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.036 0.018 199.5 87: (ns/day) (hour/ns) 87: Performance: 43.052 0.557 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 (30 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 48 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.024 0.012 198.4 87: (ns/day) (hour/ns) 87: Performance: 63.935 0.375 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 (24 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 47 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.025 0.013 199.1 87: (ns/day) (hour/ns) 87: Performance: 61.175 0.392 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 (24 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Changing nstlist from 8 to 100, rlist from 0.729 to 0.81 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 47 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.027 0.014 198.7 87: (ns/day) (hour/ns) 87: Performance: 57.552 0.417 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 (31 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Changing nstlist from 8 to 100, rlist from 0.729 to 0.81 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 48 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.027 0.014 198.8 87: (ns/day) (hour/ns) 87: Performance: 57.162 0.420 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 (29 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Changing nstlist from 8 to 100, rlist from 0.729 to 0.81 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 48 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.031 0.016 198.7 87: (ns/day) (hour/ns) 87: Performance: 50.082 0.479 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 (31 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 (0 ms) 87: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest (520 ms total) 87: 87: [----------] Global test environment tear-down 87: [==========] 37 tests from 2 test suites ran. (548 ms total) 87: [ PASSED ] 37 tests. 87/87 Test #87: MdrunVirtualSiteTests ..................... Passed 0.57 sec 100% tests passed, 0 tests failed out of 87 Label Time Summary: GTest = 473.35 sec*proc (85 tests) IntegrationTest = 303.61 sec*proc (28 tests) MpiTest = 308.39 sec*proc (21 tests) QuickGpuTest = 65.94 sec*proc (20 tests) SlowGpuTest = 369.34 sec*proc (14 tests) SlowTest = 153.93 sec*proc (13 tests) UnitTest = 15.81 sec*proc (44 tests) Total Test time (real) = 238.36 sec touch build-basic dh_testdir LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2024.4/build/mpi/lib /usr/bin/make -j12 -C build/mpi make[1]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/cmake -P /build/reproducible-path/gromacs-2024.4/build/mpi/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2024.4 -B/build/reproducible-path/gromacs-2024.4/build/mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2024.4/build/mpi/CMakeFiles /build/reproducible-path/gromacs-2024.4/build/mpi//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi 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/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2024.4-Debian_2024.4_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2024.4 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2024.4/build/mpi/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2024.4/build/mpi/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2024.4-1 -P /build/reproducible-path/gromacs-2024.4/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/selection && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/parser.cpp.o -MF CMakeFiles/scanner.dir/parser.cpp.o.d -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/parser.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/selection && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/scanner.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 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src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/atomic.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/lock.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/pthreads.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -MF CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o.d -o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/legacymodules.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 2%] Built target thread_mpi cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractsection.cpp.o -MF CMakeFiles/options.dir/abstractsection.cpp.o.d -o CMakeFiles/options.dir/abstractsection.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/abstractsection.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/basicoptions.cpp.o -MF CMakeFiles/options.dir/basicoptions.cpp.o.d -o CMakeFiles/options.dir/basicoptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/basicoptions.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/nonbonded_bench.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/bwt.c cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/behaviorcollection.cpp.o -MF CMakeFiles/options.dir/behaviorcollection.cpp.o.d -o CMakeFiles/options.dir/behaviorcollection.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/behaviorcollection.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 2%] Built target lmfit_objlib cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o -MF CMakeFiles/linearalgebra.dir/matrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/matrix.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/coder.c [ 2%] Built target energyanalysis cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/sparsematrix.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 2%] Built target gmx_objlib cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvar_neuralnetworkcompute.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoption.cpp.o -MF CMakeFiles/options.dir/filenameoption.cpp.o.d -o CMakeFiles/options.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/filenameoption.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvaratoms.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/dict.c cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/fixpoint.c cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/huffman.c cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/huffmem.c cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/options.cpp.o -MF CMakeFiles/options.dir/options.cpp.o.d -o CMakeFiles/options.dir/options.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/options.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/lz77.c cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/merge_sort.c cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsassigner.cpp.o -MF CMakeFiles/options.dir/optionsassigner.cpp.o.d -o CMakeFiles/options.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionsassigner.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/mtf.c cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsection.cpp.o -MF CMakeFiles/options.dir/optionsection.cpp.o.d -o CMakeFiles/options.dir/optionsection.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionsection.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 2%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarbias.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsvisitor.cpp.o -MF CMakeFiles/options.dir/optionsvisitor.cpp.o.d -o CMakeFiles/options.dir/optionsvisitor.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionsvisitor.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/rle.c cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/tng_compress.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 2%] Built target scanner cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/vals16.c cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/warnmalloc.c cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/widemuldiv.c cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/timeunitmanager.cpp.o -MF CMakeFiles/options.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/timeunitmanager.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 2%] Built target linearalgebra cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarbias_abf.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/xtc2.c cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -MF 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src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/output.cpp.o -MF CMakeFiles/pulling.dir/output.cpp.o.d -o CMakeFiles/pulling.dir/output.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/output.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/treesupport.cpp.o -MF CMakeFiles/options.dir/treesupport.cpp.o.d -o CMakeFiles/options.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/treesupport.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull.cpp.o -MF CMakeFiles/pulling.dir/pull.cpp.o.d -o CMakeFiles/pulling.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/pull.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/xtc3.c cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/lib/tng_io.c cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarbias_histogram_reweight_amd.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarbias_meta.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include 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CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/pullcoordexpressionparser.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarbias_restraint.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_alchlambda.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_angles.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_apath.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/lib/md5.c cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_combination.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_coordnums.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 2%] Built target options cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_distances.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT 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/build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_neuralnetwork.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_protein.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_rotations.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 4%] Built target tng_io_obj cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_volmaps.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvardeps.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvargrid.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 4%] Built target pulling cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/decidegpuusage.cpp /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/modularsimulator 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 8%] Built target colvars_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 11%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2024.4/build/mpi/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2024.4/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -MF CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/exceptions.cpp In file included from /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/binaryinformation.cpp:87: /build/reproducible-path/gromacs-2024.4/build/mpi/src/include/buildinfo.h:73:9: warning: "HWLOC_VERSION" redefined 73 | #define HWLOC_VERSION "2.11.0" | ^~~~~~~~~~~~~ In file included from /usr/include/hwloc.h:56, from /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/binaryinformation.cpp:62: /usr/include/x86_64-linux-gnu/hwloc/autogen/config.h:15:9: note: this is the location of the previous definition 15 | #define HWLOC_VERSION "2.11.2" | ^~~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/fatalerror.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/fileredirector.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/keyvaluetreeserializer.cpp cc1plus: note: unrecognized command-line option '-Wno-cast-function-type-strict' may have been intended to silence earlier diagnostics cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/keyvaluetreetransform.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/logger.cpp.o -MF CMakeFiles/libgromacs.dir/utility/logger.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/logger.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/logger.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/loggerbuilder.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/message_string_collector.cpp.o -MF CMakeFiles/libgromacs.dir/utility/message_string_collector.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/mpiinfo.cpp.o -MF CMakeFiles/libgromacs.dir/utility/mpiinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/mpiinfo.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/mpiinfo.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -MF CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/niceheader.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/path.cpp.o -MF CMakeFiles/libgromacs.dir/utility/path.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/path.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/path.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/physicalnodecommunicator.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -MF CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/pleasecite.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -MF CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/programcontext.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -MF CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -MF CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -MF CMakeFiles/libgromacs.dir/utility/strdb.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/sycl_version_information.cpp.o -MF CMakeFiles/libgromacs.dir/utility/sycl_version_information.cpp.o.d -o 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CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/sysinfo.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -MF CMakeFiles/libgromacs.dir/utility/textreader.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/textreader.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -MF CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/textwriter.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -MF CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/txtdump.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include 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-DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include 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-msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include 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-DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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-DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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-DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include 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-msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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-DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/atomdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/benchmark/bench_setup.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_geometry.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_setup.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlist.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlist_tuning.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlistparams.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlistset.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistwork.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistwork.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistwork.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlistwork.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairsearch.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/prunekerneldispatch.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/simd_prune_kernel.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/simd_prune_kernel.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/simd_prune_kernel.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_prune_kernel.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/cmdlinehelpcontext.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/cmdlinehelpmodule.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/cmdlinehelpwriter.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/cmdlineinit.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -MF CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o.d -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/matrix.cpp.o -MF CMakeFiles/libgromacs.dir/math/matrix.cpp.o.d -o CMakeFiles/libgromacs.dir/math/matrix.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/matrix.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/neldermead.cpp.o -MF CMakeFiles/libgromacs.dir/math/neldermead.cpp.o.d -o CMakeFiles/libgromacs.dir/math/neldermead.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/neldermead.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/nrjac.cpp.o -MF CMakeFiles/libgromacs.dir/math/nrjac.cpp.o.d -o CMakeFiles/libgromacs.dir/math/nrjac.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/nrjac.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/optimization.cpp.o -MF CMakeFiles/libgromacs.dir/math/optimization.cpp.o.d -o CMakeFiles/libgromacs.dir/math/optimization.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/optimization.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/utilities.cpp.o -MF CMakeFiles/libgromacs.dir/math/utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -MF CMakeFiles/libgromacs.dir/math/veccompare.cpp.o.d -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -MF CMakeFiles/libgromacs.dir/math/vecdump.cpp.o.d -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/commrec.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/iforceprovider.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/inputrec.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/interaction_const.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/md_enums.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/multipletimestepping.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/observableshistory.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/observablesreducer.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/state.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/threaded_force_buffer.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/helpformat.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/pbcmethods.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/rmpbc.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/random/seed.cpp.o -MF CMakeFiles/libgromacs.dir/random/seed.cpp.o.d -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/random/seed.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -MF CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o.d -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/random/tabulatednormaldistribution.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -MF CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -MF CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -MF CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -MF CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -MF CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/block.cpp.o -MF CMakeFiles/libgromacs.dir/topology/block.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/block.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -MF CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/exclusionblocks.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -MF CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/idef.cpp.o -MF CMakeFiles/libgromacs.dir/topology/idef.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/idef.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -MF CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/ifunc.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/index.cpp.o -MF CMakeFiles/libgromacs.dir/topology/index.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -MF CMakeFiles/libgromacs.dir/topology/invblock.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o -MF CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -MF CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -MF CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -MF CMakeFiles/libgromacs.dir/topology/symtab.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/topology.cpp.o -MF CMakeFiles/libgromacs.dir/topology/topology.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c 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/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/swapcoords.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -MF CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o.d -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/edsam.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/imd/imd.cpp.o -MF CMakeFiles/libgromacs.dir/imd/imd.cpp.o.d -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/imd/imd.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -MF CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o.d -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/imd/imdsocket.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o -MF CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/communicator_stub.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -MF CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/utilities.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/anadih.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/angle_correction.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/binsearch.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/cluster_methods.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_bundle.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_chi.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_cluster.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_clustsize.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_covar.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_current.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_density.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_densmap.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_densorder.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_dielectric.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_dyecoupl.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_enemat.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_filter.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_gyrate.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_h2order.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_hbond.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_potential.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_principal.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_rama.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_rms.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_traj.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_trjorder.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_vanhove.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_velacc.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wheel.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_xpm2ps.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -c 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/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/thermochemistry.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/add_par.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/calch.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/convparm.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/editconf.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/fflibutil.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/gen_ad.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/genconf.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o -c 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CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/grompp.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/h_db.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/hackblock.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/hizzie.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o.d -o 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/manyautocorrelation.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/polynomials.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o -MF CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o.d -o CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/arraydata.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/dataproxy.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/datastorage.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/modules/average.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o.d -o 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-msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-sans.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-sans.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-sans.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/modules/scattering-debye-sans.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-saxs.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-saxs.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-saxs.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/modules/scattering-debye-saxs.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/dispersioncorrection.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/ebin.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/enerdata_utils.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/energydrifttracker.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/energyoutput.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/expanded_internal.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/force.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c 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/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/md_support.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/mdatoms.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/mdebin_bar.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/mdgraph_gpu_impl.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/mdoutf.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/membed.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/perf_est.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update_constrain_gpu_impl_stubs.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update_vv.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/updategroups.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/updategroupscog.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/vcm.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/vsite.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/wall.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/biassharing.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/biasstate.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/biaswriter.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/coordstate.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/densityfitting/densityfittingparameters.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/qmmm/qmmmoptions.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_comm_gpu_impl.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_coordinate_receiver_gpu_impl.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_force_sender_gpu_impl.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -MF CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/calcgrid.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/fft.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/fft5d.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -MF CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/parallel_3dfft.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/clfftinitializer.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/pmalloc.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/pmalloc.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/pmalloc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/pmalloc.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/cpuinfo.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/detecthardware.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacysimulator.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/md.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/md.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/mdmodules.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/membedholder.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/mimic.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/minimize.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/replicaexchange.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/rerun.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/runner.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/shellfc.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationcontext.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinput.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinputhandle.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/tpi.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/freeenergy.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/handlerestart.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/logging.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o.d -o 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CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/multisim.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/printtime.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/threadaffinity.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/confio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/confio.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/enxio.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/espio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/groio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/md5.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c 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/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/mrcdensitymap.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/mrcdensitymapheader.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/mrcserializer.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/mtxio.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/oenv.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/pdbio.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/readinp.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -MF CMakeFiles/libgromacs.dir/selection/compiler.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -MF CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -MF CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/indexutil.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -MF CMakeFiles/libgromacs.dir/selection/mempool.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/mempool.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -MF CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/nbsearch.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/params.cpp.o -MF CMakeFiles/libgromacs.dir/selection/params.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/params.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/params.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -MF CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/parsetree.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -MF CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/poscalc.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/position.cpp.o -MF CMakeFiles/libgromacs.dir/selection/position.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/position.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/position.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -MF CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/scanner_internal.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selection.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selection.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selection.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/selectioncollection.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/selectionoption.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -MF CMakeFiles/libgromacs.dir/selection/symrec.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/symrec.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file,CMakeFiles/libgromacs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgromacs_mpi.so.9 -o ../../lib/libgromacs_mpi.so.9.0.0 @CMakeFiles/libgromacs.dir/objects1.rsp /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so -lm /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 -lmuparser cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs_mpi.so.9.0.0 ../../lib/libgromacs_mpi.so.9 ../../lib/libgromacs_mpi.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 95%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/gmxapi /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs && /usr/bin/cmake -E 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-isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/resourceassignment.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/exceptions.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/mdmodule.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/session.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/session.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/session.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/session.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -MF CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o.d -o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/gmxcalculatorcpu.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/status.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/status.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/status.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/status.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/system.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/system.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/system.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/system.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/version.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/version.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/version.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/version.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/workflow.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/gmx.dir/link.d CMakeFiles/gmx_objlib.dir/gmx.cpp.o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../bin/gmx_mpi ../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tpr.cpp [ 95%] Built target gmx cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/interactions.cpp.o -MF CMakeFiles/nblib.dir/interactions.cpp.o.d -o CMakeFiles/nblib.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/interactions.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS 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/build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/convertGmxToNblib.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/util/setup.cpp.o -MF CMakeFiles/nblib.dir/util/setup.cpp.o.d -o CMakeFiles/nblib.dir/util/setup.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/util/setup.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file,CMakeFiles/gmxapi.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmxapi_mpi.so.0 -o ../../lib/libgmxapi_mpi.so.0.4.0 CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o CMakeFiles/gmxapi.dir/cpp/context.cpp.o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o CMakeFiles/gmxapi.dir/cpp/md.cpp.o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o CMakeFiles/gmxapi.dir/cpp/session.cpp.o CMakeFiles/gmxapi.dir/cpp/status.cpp.o CMakeFiles/gmxapi.dir/cpp/system.cpp.o CMakeFiles/gmxapi.dir/cpp/version.cpp.o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o ../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgmxapi_mpi.so.0.4.0 ../../lib/libgmxapi_mpi.so.0 ../../lib/libgmxapi_mpi.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 95%] Built target gmxapi /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/depend /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/mpicxx -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/src/cpp -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -MD -MT python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/sessionresources.cpp.o -MF CMakeFiles/gmxapi_extension_resources.dir/sessionresources.cpp.o.d -o CMakeFiles/gmxapi_extension_resources.dir/sessionresources.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/src/cpp/sessionresources.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -isystem /usr/include/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/launch_0_2_1.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/launch_0_2_1.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/launch_0_2_1.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/launch_0_2_1.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -isystem /usr/include/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/module.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/module.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/module.cpp.o -c 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-o CMakeFiles/_gmxapi.dir/src/cpp/export_context.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/export_context.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -isystem /usr/include/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/export_system.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/export_system.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/export_system.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/export_system.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -isystem /usr/include/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 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-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/gmxpy_exceptions.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/gmxpy_exceptions.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/gmxpy_exceptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/gmxpy_exceptions.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/cmake -P CMakeFiles/gmxapi_extension_resources.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi_extension_resources.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libgmxapi_extension_resources.a CMakeFiles/gmxapi_extension_resources.dir/sessionresources.cpp.o /usr/bin/ranlib ../../../../lib/libgmxapi_extension_resources.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -isystem /usr/include/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/pycontext.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/pycontext.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/pycontext.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/pycontext.cpp [ 97%] Built target gmxapi_extension_resources /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/mpicxx -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/src/cpp -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -MD -MT python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/ensemblepotential.cpp.o -MF CMakeFiles/gmxapi_extension_ensemblepotential.dir/ensemblepotential.cpp.o.d -o CMakeFiles/gmxapi_extension_ensemblepotential.dir/ensemblepotential.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/src/cpp/ensemblepotential.cpp /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/gmxpy_exceptions.cpp: In lambda function: /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/gmxpy_exceptions.cpp:131:26: warning: 'void pybind11::exception::operator()(const char*) const [with type = gmxpy::Exception]' is deprecated: Please use py::set_error() instead (https://github.com/pybind/pybind11/pull/4772) [-Wdeprecated-declarations] 131 | baseException(message.c_str()); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/gmxpy_exceptions.h:51, from /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/gmxpy_exceptions.cpp:49: /usr/include/pybind11/pybind11.h:2625:10: note: declared here 2625 | void operator()(const char *message) const { set_error(*this, message); } | ^~~~~~~~ /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/gmxpy_exceptions.cpp:137:29: warning: 'void pybind11::exception::operator()(const char*) const [with type = gmxpy::detail::export_exceptions(pybind11::module&)::UnknownExceptionPlaceHolder]' is deprecated: Please use py::set_error() instead (https://github.com/pybind/pybind11/pull/4772) [-Wdeprecated-declarations] 137 | unknownException(message.c_str()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /usr/include/pybind11/pybind11.h:2625:10: note: declared here 2625 | void operator()(const char *message) const { set_error(*this, message); } | ^~~~~~~~ cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/cmake -P CMakeFiles/gmxapi_extension_ensemblepotential.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi_extension_ensemblepotential.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libgmxapi_extension_ensemblepotential.a CMakeFiles/gmxapi_extension_ensemblepotential.dir/ensemblepotential.cpp.o /usr/bin/ranlib ../../../../lib/libgmxapi_extension_ensemblepotential.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 97%] Built target gmxapi_extension_ensemblepotential cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -isystem /usr/include/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/pysystem.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/pysystem.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/pysystem.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/pysystem.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -isystem /usr/include/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/wrapped_exceptions_0_3_1.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/wrapped_exceptions_0_3_1.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/wrapped_exceptions_0_3_1.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/wrapped_exceptions_0_3_1.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -isystem /usr/include/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/mpi_bindings.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/mpi_bindings.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/mpi_bindings.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/mpi_bindings.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -isystem /usr/include/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/pycontext_create.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/pycontext_create.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/pycontext_create.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/pycontext_create.cpp /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/mpicxx -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/src/cpp -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -MD -MT python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/nullpotential.cpp.o -MF CMakeFiles/gmxapi_extension_test.dir/nullpotential.cpp.o.d -o CMakeFiles/gmxapi_extension_test.dir/nullpotential.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/src/cpp/nullpotential.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -isystem /usr/include/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/mpi_gromacs_support.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/mpi_gromacs_support.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/mpi_gromacs_support.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/mpi_gromacs_support.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/cmake -P CMakeFiles/gmxapi_extension_test.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi_extension_test.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libgmxapi_extension_test.a CMakeFiles/gmxapi_extension_test.dir/nullpotential.cpp.o /usr/bin/ranlib ../../../../lib/libgmxapi_extension_test.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 97%] Built target gmxapi_extension_test /usr/bin/make -f python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/build.make python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/src/pythonmodule /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/pythonmodule /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/build.make python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/pythonmodule && /usr/bin/mpicxx -DGMX_DOUBLE=0 -Dgmxapi_extension_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/src/cpp -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /usr/include/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -MD -MT python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/export_plugin.cpp.o -MF CMakeFiles/gmxapi_extension.dir/export_plugin.cpp.o.d -o CMakeFiles/gmxapi_extension.dir/export_plugin.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/src/pythonmodule/export_plugin.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi && /usr/bin/cmake -E cmake_link_script CMakeFiles/_gmxapi.dir/link.txt --verbose=1 lto-wrapper: warning: using serial compilation of 4 LTRANS jobs lto-wrapper: note: see the '-flto' option documentation for more information cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/pythonmodule && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi_extension.dir/link.txt --verbose=1 lto-wrapper: warning: using serial compilation of 3 LTRANS jobs lto-wrapper: note: see the '-flto' option documentation for more information /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -Wl,--dependency-file,CMakeFiles/gmxapi_extension.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../lib/myplugin.cpython-312-x86_64-linux-gnu.so CMakeFiles/gmxapi_extension.dir/export_plugin.cpp.o ../../../../lib/libgmxapi_extension_ensemblepotential.a ../../../../lib/libgmxapi_extension_test.a ../../../../lib/libgmxapi_extension_resources.a ../../../../lib/libgmxapi_mpi.so.0.4.0 -Wl,-rpath-link,/build/reproducible-path/gromacs-2024.4/build/mpi/lib cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/pythonmodule && /usr/bin/strip /build/reproducible-path/gromacs-2024.4/build/mpi/lib/myplugin.cpython-312-x86_64-linux-gnu.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 97%] Built target gmxapi_extension /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -Wl,--dependency-file,CMakeFiles/_gmxapi.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o gmxapi_staging/gmxapi/_gmxapi.cpython-312-x86_64-linux-gnu.so CMakeFiles/_gmxapi.dir/src/cpp/launch_0_2_1.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/module.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/export_context.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/export_system.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/export_tprfile.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/gmxpy_exceptions.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/pycontext.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/pysystem.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/wrapped_exceptions_0_3_1.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/mpi_bindings.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/pycontext_create.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/mpi_gromacs_support.cpp.o ../../lib/libgmxapi_mpi.so.0.4.0 -Wl,-rpath-link,/build/reproducible-path/gromacs-2024.4/build/mpi/lib cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi && /usr/bin/strip /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi/gmxapi_staging/gmxapi/_gmxapi.cpython-312-x86_64-linux-gnu.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 97%] Built target _gmxapi cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file,CMakeFiles/nblib.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libnblib_gmx.so.0 -o ../../lib/libnblib_gmx.so.0.1.0 CMakeFiles/nblib.dir/box.cpp.o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o CMakeFiles/nblib.dir/integrator.cpp.o CMakeFiles/nblib.dir/interactions.cpp.o CMakeFiles/nblib.dir/molecules.cpp.o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o CMakeFiles/nblib.dir/particlesequencer.cpp.o CMakeFiles/nblib.dir/particletype.cpp.o CMakeFiles/nblib.dir/simulationstate.cpp.o CMakeFiles/nblib.dir/topologyhelpers.cpp.o CMakeFiles/nblib.dir/topology.cpp.o CMakeFiles/nblib.dir/tpr.cpp.o CMakeFiles/nblib.dir/virials.cpp.o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o CMakeFiles/nblib.dir/util/setup.cpp.o -lm ../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib && /usr/bin/cmake -E cmake_symlink_library ../../lib/libnblib_gmx.so.0.1.0 ../../lib/libnblib_gmx.so.0 ../../lib/libnblib_gmx.so make[3]: Leaving directory 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'/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/samples && /usr/bin/mpicxx -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -MF CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o.d -o CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/samples/methane-water-integration.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/methane-water-integration.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/argon-forces-integration.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/methane-water-integration.dir/link.d "CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o" -o ../../../bin/methane-water-integration ../../../lib/libnblib_gmx.so.0.1.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2024.4/build/mpi/lib make[3]: Leaving directory 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'/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/scanner.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs 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src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/lock.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT 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CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/bwt.c cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/coder.c cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -MF CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o.d -o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/legacymodules.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' [ 2%] Built target thread_mpi cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/dict.c cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractsection.cpp.o -MF CMakeFiles/options.dir/abstractsection.cpp.o.d -o CMakeFiles/options.dir/abstractsection.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/abstractsection.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/basicoptions.cpp.o -MF CMakeFiles/options.dir/basicoptions.cpp.o.d -o CMakeFiles/options.dir/basicoptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/basicoptions.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/behaviorcollection.cpp.o -MF CMakeFiles/options.dir/behaviorcollection.cpp.o.d -o CMakeFiles/options.dir/behaviorcollection.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/behaviorcollection.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/fixpoint.c cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/huffman.c cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/huffmem.c cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvar_neuralnetworkcompute.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/nonbonded_bench.cpp [ 2%] Built target lmfit_objlib cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvaratoms.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarbias.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/lz77.c [ 2%] Built target energyanalysis cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoption.cpp.o -MF CMakeFiles/options.dir/filenameoption.cpp.o.d -o CMakeFiles/options.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/filenameoption.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarbias_abf.cpp [ 2%] Built target gmx_objlib cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarbias_alb.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/merge_sort.c cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/mtf.c cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/rle.c cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/tng_compress.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' [ 2%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/vals16.c cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarbias_histogram.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' [ 2%] Built target scanner cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o -MF CMakeFiles/linearalgebra.dir/matrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/matrix.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/options.cpp.o -MF CMakeFiles/options.dir/options.cpp.o.d -o CMakeFiles/options.dir/options.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/options.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/warnmalloc.c cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/widemuldiv.c cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/xtc2.c cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsassigner.cpp.o -MF CMakeFiles/options.dir/optionsassigner.cpp.o.d -o CMakeFiles/options.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionsassigner.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' [ 4%] Built target linearalgebra cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsection.cpp.o -MF CMakeFiles/options.dir/optionsection.cpp.o.d -o CMakeFiles/options.dir/optionsection.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionsection.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsvisitor.cpp.o -MF CMakeFiles/options.dir/optionsvisitor.cpp.o.d -o CMakeFiles/options.dir/optionsvisitor.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionsvisitor.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/xtc3.c cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/lib/tng_io.c /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/pulling /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/lib/md5.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/output.cpp.o -MF CMakeFiles/pulling.dir/output.cpp.o.d -o CMakeFiles/pulling.dir/output.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/output.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarbias_histogram_reweight_amd.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarbias_meta.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/timeunitmanager.cpp.o -MF CMakeFiles/options.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_alchlambda.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_angles.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_apath.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull_rotation.cpp.o -MF CMakeFiles/pulling.dir/pull_rotation.cpp.o.d -o CMakeFiles/pulling.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/pull_rotation.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -MF CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o.d -o CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/pullcoordexpressionparser.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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-msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullutil.cpp.o -MF CMakeFiles/pulling.dir/pullutil.cpp.o.d -o CMakeFiles/pulling.dir/pullutil.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/pullutil.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/treesupport.cpp.o -MF CMakeFiles/options.dir/treesupport.cpp.o.d -o CMakeFiles/options.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/treesupport.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -MF CMakeFiles/pulling.dir/transformationcoordinate.cpp.o.d -o CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/transformationcoordinate.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG 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/build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_distances.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_gpath.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_neuralnetwork.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_protein.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_rotations.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' [ 6%] Built target tng_io_obj cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_volmaps.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvardeps.cpp [ 8%] Built target options cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvargrid.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarmodule.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarparams.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarparse.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarproxy.cpp [ 10%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/taskassignment /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/decidegpuusage.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarproxy_io.cpp /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -MF CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o.d -o CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/decidesimulationworkload.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f 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/build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarproxy_system.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarproxy_tcl.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarproxy_volmaps.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/firstorderpressurecoupling.cpp make[3]: Leaving directory 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -MF CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o.d -o CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/simulatoralgorithm.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/topologyholder.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -MF CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/trajectoryelement.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' [ 14%] Built target colvars_objlib cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' [ 16%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2024.4/build/mpi-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2024.4/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/alignedallocator.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/any.cpp.o -MF CMakeFiles/libgromacs.dir/utility/any.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/any.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -MF CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/basenetwork.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include 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/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/directoryenumerator.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/errorcodes.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/errorformat.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -MF CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/exceptions.cpp In file included from /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/binaryinformation.cpp:87: /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include/buildinfo.h:73:9: warning: "HWLOC_VERSION" redefined 73 | #define HWLOC_VERSION "2.11.0" | ^~~~~~~~~~~~~ In file included from /usr/include/hwloc.h:56, from /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/binaryinformation.cpp:62: /usr/include/x86_64-linux-gnu/hwloc/autogen/config.h:15:9: note: this is the location of the previous definition 15 | #define HWLOC_VERSION "2.11.2" | ^~~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/fatalerror.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/fileredirector.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -MF CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/int64_to_int.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/keyvaluetree.cpp cc1plus: note: unrecognized command-line option '-Wno-cast-function-type-strict' may have been intended to silence earlier diagnostics cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/keyvaluetreemdpwriter.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include 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-O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/keyvaluetreetransform.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/logger.cpp.o -MF CMakeFiles/libgromacs.dir/utility/logger.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/logger.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/logger.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/loggerbuilder.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include 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/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/path.cpp.o -MF CMakeFiles/libgromacs.dir/utility/path.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/path.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/path.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/physicalnodecommunicator.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -MF CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/pleasecite.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -MF CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/programcontext.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -MF CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/smalloc.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -MF CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/strconvert.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -MF CMakeFiles/libgromacs.dir/utility/strdb.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/strdb.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -MF CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/stringstream.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/stringutil.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/sycl_version_information.cpp.o -MF CMakeFiles/libgromacs.dir/utility/sycl_version_information.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/sycl_version_information.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/sycl_version_information.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -MF CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/sysinfo.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -MF CMakeFiles/libgromacs.dir/utility/textreader.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/textreader.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -MF CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/textwriter.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -MF CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/txtdump.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/atomdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/benchmark/bench_setup.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/benchmark/bench_system.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/exclusionchecker.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/exclusionchecker.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/exclusionchecker.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/exclusionchecker.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/freeenergydispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/freeenergydispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/freeenergydispatch.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/freeenergydispatch.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/gridset.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernel_common.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kerneldispatch.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -MF 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include 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-O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_geometry.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_setup.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlist.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlistset.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/prunekerneldispatch.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/simd_prune_kernel.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/simd_prune_kernel.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/simd_prune_kernel.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_prune_kernel.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include 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/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/cmdlinehelpmodule.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/domdec_setup.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dump.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/dump.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/ga2la.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/localatomset.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/localatomsetdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/localatomsetmanager.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localtopology.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localtopology.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localtopology.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/localtopology.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localtopologychecker.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localtopologychecker.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localtopologychecker.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/makebondedlinks.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/makebondedlinks.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/makebondedlinks.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/makebondedlinks.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/mdsetup.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/nsgrid.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/partition.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/partition.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/redistribute.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/reversetopology.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/utility.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -MF CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o.d -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -MF CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o.d -o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -MF CMakeFiles/libgromacs.dir/math/densityfit.cpp.o.d -o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/densityfit.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -MF CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o.d -o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/densityfittingforce.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -MF CMakeFiles/libgromacs.dir/math/do_fit.cpp.o.d -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/do_fit.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -MF CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o.d -o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/exponentialmovingaverage.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/functions.cpp.o -MF CMakeFiles/libgromacs.dir/math/functions.cpp.o.d -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/functions.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -MF CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o.d -o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/gausstransform.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -MF CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o.d -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/invertmatrix.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/matrix.cpp.o -MF CMakeFiles/libgromacs.dir/math/matrix.cpp.o.d -o CMakeFiles/libgromacs.dir/math/matrix.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/matrix.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/neldermead.cpp.o -MF CMakeFiles/libgromacs.dir/math/neldermead.cpp.o.d -o CMakeFiles/libgromacs.dir/math/neldermead.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/neldermead.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/nrjac.cpp.o -MF CMakeFiles/libgromacs.dir/math/nrjac.cpp.o.d -o CMakeFiles/libgromacs.dir/math/nrjac.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/nrjac.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/optimization.cpp.o -MF CMakeFiles/libgromacs.dir/math/optimization.cpp.o.d -o CMakeFiles/libgromacs.dir/math/optimization.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/utilities.cpp.o -MF CMakeFiles/libgromacs.dir/math/utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -MF CMakeFiles/libgromacs.dir/math/veccompare.cpp.o.d -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/veccompare.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -MF CMakeFiles/libgromacs.dir/math/vecdump.cpp.o.d -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/commrec.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/df_history.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/energyhistory.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/forcebuffers.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/group.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/iforceprovider.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/inputrec.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/interaction_const.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/md_enums.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/multipletimestepping.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/observableshistory.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/observablesreducer.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/state.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/threaded_force_buffer.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/helpformat.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/helpmanager.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/helptopic.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/helpwritercontext.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/rstparser.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/com.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/mshift.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/pbc.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/pbc_simd.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/pbcenums.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/rmpbc.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/random/seed.cpp.o -MF CMakeFiles/libgromacs.dir/random/seed.cpp.o.d -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/random/seed.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -MF CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o.d -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/random/tabulatednormaldistribution.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -MF CMakeFiles/libgromacs.dir/restraint/manager.cpp.o.d -o 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -MF CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/restraintmdmodule.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -MF CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -MF CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/timing/cyclecounter.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -MF CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/timing/wallcycle.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -MF CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/timing/walltime_accounting.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/atomprop.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atoms.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/atoms.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/atomsbuilder.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/block.cpp.o -MF CMakeFiles/libgromacs.dir/topology/block.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/block.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -MF CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/exclusionblocks.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -MF CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/idef.cpp.o -MF CMakeFiles/libgromacs.dir/topology/idef.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/idef.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -MF CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/ifunc.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/index.cpp.o -MF CMakeFiles/libgromacs.dir/topology/index.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/index.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -MF CMakeFiles/libgromacs.dir/topology/invblock.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/invblock.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o -MF CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -MF CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -MF CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -MF CMakeFiles/libgromacs.dir/topology/symtab.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/topology.cpp.o -MF CMakeFiles/libgromacs.dir/topology/topology.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -MF CMakeFiles/libgromacs.dir/topology/topsort.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -MF CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -MF CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/trajectoryframe.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -MF CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o.d -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/swap/swapcoords.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -MF CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o.d -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/edsam.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/imd/imd.cpp.o -MF CMakeFiles/libgromacs.dir/imd/imd.cpp.o.d -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/imd/imd.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -MF CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o.d -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/imd/imdsocket.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o -MF CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/communicator_stub.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -MF CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/utilities.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/anadih.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/dlist.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/fitahx.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_anaeig.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_analyze.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_angle.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_awh.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_bar.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_confrms.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_covar.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_current.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_dos.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_dyecoupl.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_enemat.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_energy.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_filter.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_gyrate.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_h2order.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_nmeig.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_nmens.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_nmr.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_nmtraj.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_order.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_polystat.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_rmsdist.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_rmsf.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_rotacf.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_sorient.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_spatial.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_spol.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_tcaf.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_trjorder.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_vanhove.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_xpm2ps.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/powerspect.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/pp2shift.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/princ.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/sfactor.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/thermochemistry.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/add_par.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/calch.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/editconf.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -MF 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o.d 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/hizzie.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/insert_molecules.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H 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/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/massrepartitioning.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/massrepartitioning.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/massrepartitioning.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/massrepartitioning.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/nm2type.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2top.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pgutil.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/readir.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/readpull.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/readrot.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/resall.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/solvate.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/specbond.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/ter_db.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tomorse.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/topdirs.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/xlate.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o -MF 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/arraydata.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/dataframe.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/datamodule.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o.d -o 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/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/outputadapters/setstarttime.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx 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CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/outputadapters/settimestep.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-saxs.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-saxs.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-saxs.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/modules/scattering-debye-saxs.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -MF CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -MF CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nrnb.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o.d -o 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CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/calcmu.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/calcvir.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/compute_io.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/constr.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constraint_gpu_helpers.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constraint_gpu_helpers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constraint_gpu_helpers.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/constraintrange.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/coupling.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/energydrifttracker.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/energyoutput.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/expanded.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/expanded_internal.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/force.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/force.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/forcerec.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/freeenergyparameters.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl_stubs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl_stubs.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/groupcoord.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/lincs.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/md_support.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/mdatoms.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/mdebin_bar.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/membed.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/perf_est.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/rbin.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/resethandler.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/rf_util.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/settle.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/shake.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/sighandler.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/sim_util.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/simulationsignal.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/splitter.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/stat.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tgroup.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update_vv.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/updategroups.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/updategroupscog.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/vcm.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/vsite.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/wall.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/wholemoleculetransform.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/electricfield.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/awh.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/bias.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/biasgrid.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/biasparams.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o -MF 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include 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-Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/read_params.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/densityfitting/densityfitting.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/densityfitting/densityfittingamplitudelookup.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/densityfitting/densityfittingforceprovider.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include 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-Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmtopologypreprocessor.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmtopologypreprocessor.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmtopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/qmmm/qmmmtopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/qmmm/qmmmoptions.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/qmmm/qmmm.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_internal.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/manage_threading.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_solve.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_spline_work.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_spread.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_comm_gpu_impl.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/clfftinitializer.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/gpueventsynchronizer_helpers.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/gpueventsynchronizer_helpers.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/gpueventsynchronizer_helpers.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer_helpers.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/nvshmem_utils.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/nvshmem_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/nvshmem_utils.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/nvshmem_utils.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/device_context.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/device_stream.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/pmalloc.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/pmalloc.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/pmalloc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/pmalloc.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/cpuinfo.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/detecthardware.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/device_management_common.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/hardwaretopology.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacysimulator.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/membedholder.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/mimic.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinputhandle.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/tpi.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/freeenergy.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/handlerestart.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/logging.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/mdmodulesnotifiers.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/multisim.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/printtime.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/threadaffinity.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include 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-O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/selectionoption.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/selectionoptionbehavior.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -MF 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/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -MF CMakeFiles/libgromacs.dir/selection/symrec.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/symrec.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file,CMakeFiles/libgromacs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgromacs_mpi_d.so.9 -o ../../lib/libgromacs_mpi_d.so.9.0.0 @CMakeFiles/libgromacs.dir/objects1.rsp /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so -lm /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 -lmuparser cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs_mpi_d.so.9.0.0 ../../lib/libgromacs_mpi_d.so.9 ../../lib/libgromacs_mpi_d.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' [ 95%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/gmxapi /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/programs /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/resourceassignment.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/context.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/context.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/context.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/context.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/box.cpp.o -MF CMakeFiles/nblib.dir/box.cpp.o.d -o CMakeFiles/nblib.dir/box.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/box.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/exceptions.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -MF CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o.d -o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/gmxcalculatorcpu.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/gmxapi.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/integrator.cpp.o -MF CMakeFiles/nblib.dir/integrator.cpp.o.d -o CMakeFiles/nblib.dir/integrator.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/integrator.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/md.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/md.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/md.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/md.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/interactions.cpp.o -MF CMakeFiles/nblib.dir/interactions.cpp.o.d -o CMakeFiles/nblib.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/interactions.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/mdmodule.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/molecules.cpp.o -MF CMakeFiles/nblib.dir/molecules.cpp.o.d -o CMakeFiles/nblib.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/molecules.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/mdsignals.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/session.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/session.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/session.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/session.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/gmx.dir/link.d CMakeFiles/gmx_objlib.dir/gmx.cpp.o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../bin/gmx_mpi_d ../../lib/libgromacs_mpi_d.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/status.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/status.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/status.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/status.cpp [ 95%] Built target gmx cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -MF CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o.d -o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/nbnxmsetuphelpers.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/particlesequencer.cpp.o -MF CMakeFiles/nblib.dir/particlesequencer.cpp.o.d -o CMakeFiles/nblib.dir/particlesequencer.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/particlesequencer.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 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-I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/version.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/version.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/version.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/version.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS 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/build/reproducible-path/gromacs-2024.4/api/nblib/topologyhelpers.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include 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CMakeFiles/nblib.dir/topology.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/topology.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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api/nblib/CMakeFiles/nblib.dir/tpr.cpp.o -MF CMakeFiles/nblib.dir/tpr.cpp.o.d -o CMakeFiles/nblib.dir/tpr.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tpr.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/transformations.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/conversions.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/convertGmxToNblib.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/util/setup.cpp.o -MF CMakeFiles/nblib.dir/util/setup.cpp.o.d -o CMakeFiles/nblib.dir/util/setup.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/util/setup.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file,CMakeFiles/gmxapi.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmxapi_mpi_d.so.0 -o ../../lib/libgmxapi_mpi_d.so.0.4.0 CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o CMakeFiles/gmxapi.dir/cpp/context.cpp.o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o CMakeFiles/gmxapi.dir/cpp/md.cpp.o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o CMakeFiles/gmxapi.dir/cpp/session.cpp.o CMakeFiles/gmxapi.dir/cpp/status.cpp.o CMakeFiles/gmxapi.dir/cpp/system.cpp.o CMakeFiles/gmxapi.dir/cpp/version.cpp.o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o ../../lib/libgromacs_mpi_d.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgmxapi_mpi_d.so.0.4.0 ../../lib/libgmxapi_mpi_d.so.0 ../../lib/libgmxapi_mpi_d.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' [ 97%] Built target gmxapi cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file,CMakeFiles/nblib.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libnblib_gmx.so.0 -o ../../lib/libnblib_gmx.so.0.1.0 CMakeFiles/nblib.dir/box.cpp.o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o CMakeFiles/nblib.dir/integrator.cpp.o CMakeFiles/nblib.dir/interactions.cpp.o CMakeFiles/nblib.dir/molecules.cpp.o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o CMakeFiles/nblib.dir/particlesequencer.cpp.o CMakeFiles/nblib.dir/particletype.cpp.o CMakeFiles/nblib.dir/simulationstate.cpp.o CMakeFiles/nblib.dir/topologyhelpers.cpp.o CMakeFiles/nblib.dir/topology.cpp.o CMakeFiles/nblib.dir/tpr.cpp.o CMakeFiles/nblib.dir/virials.cpp.o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o CMakeFiles/nblib.dir/util/setup.cpp.o -lm ../../lib/libgromacs_mpi_d.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib && /usr/bin/cmake -E cmake_symlink_library ../../lib/libnblib_gmx.so.0.1.0 ../../lib/libnblib_gmx.so.0 ../../lib/libnblib_gmx.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' [100%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib/samples && /usr/bin/mpicxx -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -MF CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o.d -o CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/samples/methane-water-integration.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib/samples && /usr/bin/mpicxx -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -MF CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o.d -o CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/samples/argon-forces-integration.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/argon-forces-integration.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/argon-forces-integration.dir/link.d "CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o" -o ../../../bin/argon-forces-integration ../../../lib/libnblib_gmx.so.0.1.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2024.4/build/mpi-dp/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' [100%] Built target argon-forces-integration cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/methane-water-integration.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/methane-water-integration.dir/link.d "CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o" -o ../../../bin/methane-water-integration ../../../lib/libnblib_gmx.so.0.1.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2024.4/build/mpi-dp/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' [100%] Built target methane-water-integration make[2]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2024.4/build/mpi-dp/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2024.4/build/mpi/lib /usr/bin/make -j12 -C build/mpi tests make[1]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/cmake -P /build/reproducible-path/gromacs-2024.4/build/mpi/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2024.4 -B/build/reproducible-path/gromacs-2024.4/build/mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 tests make[2]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/cmake -P /build/reproducible-path/gromacs-2024.4/build/mpi/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2024.4 -B/build/reproducible-path/gromacs-2024.4/build/mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2024.4/build/mpi/CMakeFiles 77 /usr/bin/make -f CMakeFiles/Makefile2 CMakeFiles/tests.dir/all make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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'/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi 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target mdrun_objlib [ 1%] Built target lmfit_objlib [ 2%] Built target tng_io_obj [ 2%] Built target linearalgebra /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/pulling /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" [ 2%] Built target release-version-info [ 2%] Built target options make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make 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src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/taskassignment /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[4]: Nothing to be done for 'src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 5%] Built target taskassignment make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 6%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 55%] Built target libgromacs /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/gmxapi /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[4]: Nothing to be done for 'src/programs/CMakeFiles/gmx.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[4]: Nothing to be done for 'api/gmxapi/CMakeFiles/gmxapi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 55%] Built target gmx /usr/bin/make -f python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_spc2_water_box.dir/build.make python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_spc2_water_box.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/tests /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_spc2_water_box.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build [ 55%] Built target gmxapi /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_spc2_water_box.dir/build.make python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_spc2_water_box.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/tests && /build/reproducible-path/gromacs-2024.4/build/mpi/bin/gmx_mpi -quiet grompp -f /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/tests/grompp.mdp -c /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2.gro -p /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2.top [ 57%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[4]: Nothing to be done for 'python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 58%] Built target gmxapi_extension_resources make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[4]: Nothing to be done for 'api/nblib/samples/CMakeFiles/methane-water-integration.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[4]: Nothing to be done for 'api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 58%] Built target argon-forces-integration [ 58%] Built target methane-water-integration make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[4]: Nothing to be done for 'python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 58%] Built target gmxapi_extension_ensemblepotential Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group rest is 9.00 The integrator does not provide a ensemble temperature, there is no system ensemble temperature NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/tests/grompp.mdp]: NVE simulation: will use the initial temperature of 2573.591 K for determining the Verlet buffer size NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/tests/grompp.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 NOTEs Setting the LD random seed to -131091 Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Analysing residue names: There are: 2 Water residues Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 58%] Built target gmxapi_extension_spc2_water_box cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/external/googletest/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file,CMakeFiles/gtest.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgtest.so.1.13.0 -o ../../../../lib/libgtest.so.1.13.0 "CMakeFiles/gtest.dir/src/gtest-all.cc.o" cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/external/googletest/googletest && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgtest.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 58%] Built target gtest /usr/bin/make -f src/external/googletest/googletest/CMakeFiles/gtest_main.dir/build.make src/external/googletest/googletest/CMakeFiles/gtest_main.dir/depend /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/external/googletest/googletest /build/reproducible-path/gromacs-2024.4/build/mpi/src/external/googletest/googletest/CMakeFiles/gtest_main.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/external/googletest/googlemock /build/reproducible-path/gromacs-2024.4/build/mpi/src/external/googletest/googlemock/CMakeFiles/gmock.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/external/googletest/googletest/CMakeFiles/gtest_main.dir/build.make src/external/googletest/googletest/CMakeFiles/gtest_main.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/external/googletest/googletest && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -Dgtest_main_EXPORTS -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -Wall -Wshadow -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -MD -MT src/external/googletest/googletest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o -MF CMakeFiles/gtest_main.dir/src/gtest_main.cc.o.d -o CMakeFiles/gtest_main.dir/src/gtest_main.cc.o -c /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/src/gtest_main.cc /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/external/googletest/googlemock && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_CREATE_SHARED_LIBRARY=1 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Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 58%] Built target gtest_main /usr/bin/make -f python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_bounding-test.dir/build.make python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_bounding-test.dir/depend /usr/bin/make -f python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_histogram-test.dir/build.make python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_histogram-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/tests /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_bounding-test.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/tests /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_histogram-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_histogram-test.dir/build.make python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_histogram-test.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/tests -I/build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/src/cpp -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fvisibility=hidden -MD -MT python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_histogram-test.dir/test_histogram.cpp.o -MF CMakeFiles/gmxapi_extension_histogram-test.dir/test_histogram.cpp.o.d -o CMakeFiles/gmxapi_extension_histogram-test.dir/test_histogram.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/tests/test_histogram.cpp /usr/bin/make -f python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_bounding-test.dir/build.make python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_bounding-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/tests -I/build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/src/cpp -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fvisibility=hidden -MD -MT python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_bounding-test.dir/test_bounding_restraint.cpp.o -MF CMakeFiles/gmxapi_extension_bounding-test.dir/test_bounding_restraint.cpp.o.d -o CMakeFiles/gmxapi_extension_bounding-test.dir/test_bounding_restraint.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/tests/test_bounding_restraint.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi_extension_histogram-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/gmxapi_extension_histogram-test.dir/link.d "CMakeFiles/gmxapi_extension_histogram-test.dir/test_histogram.cpp.o" -o ../../../bin/gmxapi_extension_histogram-test ../../../lib/libgmxapi_extension_ensemblepotential.a ../../../lib/libgtest_main.so.1.13.0 ../../../lib/libgmxapi_extension_resources.a ../../../lib/libgmxapi_mpi.so.0.4.0 ../../../lib/libgtest.so.1.13.0 -Wl,-rpath-link,/build/reproducible-path/gromacs-2024.4/build/mpi/lib make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi_extension_bounding-test.dir/link.txt --verbose=1 [ 58%] Built target gmxapi_extension_histogram-test /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/gmxapi_extension_bounding-test.dir/link.d "CMakeFiles/gmxapi_extension_bounding-test.dir/test_bounding_restraint.cpp.o" -o ../../../bin/gmxapi_extension_bounding-test ../../../lib/libgmxapi_extension_ensemblepotential.a ../../../lib/libgtest_main.so.1.13.0 ../../../lib/libgmxapi_extension_resources.a ../../../lib/libgmxapi_mpi.so.0.4.0 ../../../lib/libgtest.so.1.13.0 -Wl,-rpath-link,/build/reproducible-path/gromacs-2024.4/build/mpi/lib make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 58%] Built target gmxapi_extension_bounding-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/external/googletest/googlemock && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file,CMakeFiles/gmock.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmock.so.1.13.0 -o ../../../../lib/libgmock.so.1.13.0 "CMakeFiles/gmock.dir/src/gmock-all.cc.o" ../../../../lib/libgtest.so.1.13.0 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/external/googletest/googlemock && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgmock.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 58%] Built target gmock /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 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-I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/cmdlinetest.cpp.o -MF CMakeFiles/testutils.dir/cmdlinetest.cpp.o.d -o CMakeFiles/testutils.dir/cmdlinetest.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/cmdlinetest.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/testutils && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/testutils -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/tinyxml2 -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT 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'/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/awh/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem 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-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/qmmm/tests/qmmminputgenerator.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build.make src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/calcvir.cpp.o -MF CMakeFiles/mdlib-test.dir/calcvir.cpp.o.d -o CMakeFiles/mdlib-test.dir/calcvir.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/calcvir.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/testutils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -MF CMakeFiles/testutils-test.dir/refdata_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/tests/refdata_tests.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/utility-mpi-test.dir/link.d "CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o" "CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 59%] Built target utility-mpi-test /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -MF CMakeFiles/applied_forces-test.dir/electricfield.cpp.o.d -o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/tests/electricfield.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/densityfitting/tests/densityfittingamplitudelookup.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/tests/colvarsoptions.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/testutils-mpi-test.dir/link.d "CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o" "CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o" -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libtestutils.a ../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 59%] Built target testutils-mpi-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 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/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem 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CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem 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CMakeFiles/utility-test.dir/booltype.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/booltype.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/densityfitting/tests/densityfittingoptions.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/applied_forces-test.dir/link.d "CMakeFiles/applied_forces-test.dir/electricfield.cpp.o" 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-I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/testutils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -MF CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/tests/testasserts_tests.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests && /usr/bin/cmake -P CMakeFiles/nblib_test_infrastructure.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib_test_infrastructure.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../lib/libnblib_test_infrastructure.a CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o /usr/bin/ranlib ../../../lib/libnblib_test_infrastructure.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 59%] Built target nblib_test_infrastructure cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxlib/nonbonded/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxlib/nonbonded/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxlib/nonbonded/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -DGMX_CP2K=0 -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 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-DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem 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CMakeFiles/nonbonded-fep-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/nonbonded-fep-test.dir/link.d "CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o" "CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/nonbonded-fep-test ../../../../../lib/libtestutils.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_mpi.so.9.0.0 -lm ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 59%] Built target nonbonded-fep-test cd 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/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/biasgrid.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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../../../lib/libtestutils.a ../../../lib/libtestutils.a ../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 59%] Built target testutils-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o 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../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 61%] Built target density_fitting_applied_forces-test /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/bonded.cpp.o -MF CMakeFiles/listed_forces-test.dir/bonded.cpp.o.d -o CMakeFiles/listed_forces-test.dir/bonded.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/tests/bonded.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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-I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/awh/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -MF CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o.d -o CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/qmmm_applied_forces-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/qmmm_applied_forces-test.dir/link.d "CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/qmmm_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask64.cpp.o -MF CMakeFiles/utility-test.dir/bitmask64.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/bitmask64.cpp [ 61%] Built target qmmm_applied_forces-test /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/nbnxm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/exclusions.cpp.o -MF CMakeFiles/nbnxm-test.dir/exclusions.cpp.o.d -o CMakeFiles/nbnxm-test.dir/exclusions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/exclusions.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/pairs.cpp.o -MF CMakeFiles/listed_forces-test.dir/pairs.cpp.o.d -o CMakeFiles/listed_forces-test.dir/pairs.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/tests/pairs.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/expanded.cpp.o -MF CMakeFiles/mdlib-test.dir/expanded.cpp.o.d -o CMakeFiles/mdlib-test.dir/expanded.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/expanded.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask128.cpp.o -MF CMakeFiles/utility-test.dir/bitmask128.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/bitmask128.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/cstringutil.cpp.o -MF CMakeFiles/utility-test.dir/cstringutil.cpp.o.d -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/cstringutil.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/colvars_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -P CMakeFiles/mdrun_test_infrastructure.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun_test_infrastructure.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/colvars_applied_forces-test.dir/link.d "CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/colvars_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm ../../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/ar qc ../../../../lib/libmdrun_test_infrastructure.a CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o /usr/bin/ranlib ../../../../lib/libmdrun_test_infrastructure.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 61%] Built target colvars_applied_forces-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o -MF CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o.d -o CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/tests/position_restraints.cpp [ 62%] Built target mdrun_test_infrastructure cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/nbnxm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o -MF CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o.d -o CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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-DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem 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-I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/leapfrogtestdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/domdec/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF 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/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nbnxm-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/domdec/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake "--color=" /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/listed_forces-test.dir/link.d "CMakeFiles/listed_forces-test.dir/bonded.cpp.o" "CMakeFiles/listed_forces-test.dir/pairs.cpp.o" "CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o" "CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/listed_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build [ 64%] Built target listed_forces-test make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/ewald/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fft/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fft/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fft/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fft/tests/CMakeFiles/fft-test.dir/fft.cpp.o -MF CMakeFiles/fft-test.dir/fft.cpp.o.d -o CMakeFiles/fft-test.dir/fft.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests/fft.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/nbnxm-test.dir/link.d "CMakeFiles/nbnxm-test.dir/exclusions.cpp.o" "CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o" "CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o" "CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nbnxm-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 66%] Built target nbnxm-test /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem 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/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/tests/clfftinitializer.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -MF CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o.d -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/keyvaluetreeserializer.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now 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'/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/hardware/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem 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-DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/tests/device_availability.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/ewald/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -MF CMakeFiles/ewald-test.dir/pmegathertest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmegathertest.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fft/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fft/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fft/tests/CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -MF CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o.d -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/keyvaluetreetransform.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settle.cpp.o -MF CMakeFiles/mdlib-test.dir/settle.cpp.o.d -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/settle.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/tests/device_stream_manager.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/domdec-test.dir/link.d "CMakeFiles/domdec-test.dir/hashedmap.cpp.o" "CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o" "CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/domdec-mpi-test.dir/link.d "CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o" "CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 66%] Built target domdec-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/hardware/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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'/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -MF CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/tests/devicetransfers.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/fft-test.dir/link.d "CMakeFiles/fft-test.dir/fft.cpp.o" "CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 66%] Built target fft-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/settletestrunners.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src 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src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/boxmatrix.cpp.o -MF CMakeFiles/math-test.dir/boxmatrix.cpp.o.d -o CMakeFiles/math-test.dir/boxmatrix.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/boxmatrix.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src 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/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdspan/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include 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-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -MF CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o.d -o CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/tests/accessor_policy.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -MF CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmesolvetest.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -MF CMakeFiles/math-test.dir/coordinatetransformation.cpp.o.d -o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/coordinatetransformation.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libmdrunutility-test-shared.a "CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o" "CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libmdrunutility-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 66%] Built target mdrunutility-test-shared /usr/bin/make -f src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build.make src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdtypes/tests 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/enerdata.cpp.o -MF CMakeFiles/mdtypes-test.dir/enerdata.cpp.o.d -o CMakeFiles/mdtypes-test.dir/enerdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/enerdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/shake.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/hardware/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o 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src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/tests/helpformat.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdspan/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o -MF CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o.d -o CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/observablesreducer.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/message_string_collector.cpp.o -MF CMakeFiles/utility-test.dir/message_string_collector.cpp.o.d -o CMakeFiles/utility-test.dir/message_string_collector.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/message_string_collector.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/hardware-test.dir/link.d "CMakeFiles/hardware-test.dir/cpuinfo.cpp.o" "CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/device_management.cpp.o" "CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 66%] Built target hardware-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/ewald/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 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'/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/options/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/ewald/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -MF CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o.d -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/tests/abstractoptionstorage.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" 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/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT 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'/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/pbcutil/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 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-I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoption.cpp.o -MF CMakeFiles/options-test.dir/filenameoption.cpp.o.d -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/tests/filenameoption.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/ewald/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pme.cpp.o -MF CMakeFiles/ewald-test.dir/pme.cpp.o.d -o CMakeFiles/ewald-test.dir/pme.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pme.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/onlinehelp-test.dir/link.d "CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o" "CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 66%] Built target onlinehelp-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 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-I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/constrtestrunners_gpu.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 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/usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 67%] Built target gpu_utils-test /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/random/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/random/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/random/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -MF CMakeFiles/random-test.dir/exponentialdistribution.cpp.o.d -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/random/tests/exponentialdistribution.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/random/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/gammadistribution.cpp.o -MF CMakeFiles/random-test.dir/gammadistribution.cpp.o.d -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/random/tests/gammadistribution.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdspan-test.dir/link.d "CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o" "CMakeFiles/mdspan-test.dir/extents.cpp.o" "CMakeFiles/mdspan-test.dir/extensions.cpp.o" "CMakeFiles/mdspan-test.dir/layouts.cpp.o" "CMakeFiles/mdspan-test.dir/mdspan.cpp.o" "CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 67%] Built target mdspan-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/random/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/normaldistribution.cpp.o -MF CMakeFiles/random-test.dir/normaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/random/tests/normaldistribution.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/strconvert.cpp.o -MF CMakeFiles/utility-test.dir/strconvert.cpp.o.d -o CMakeFiles/utility-test.dir/strconvert.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/strconvert.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/ewald/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include 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-DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/tests/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/ewald-test.dir/link.d "CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o" "CMakeFiles/ewald-test.dir/pmegathertest.cpp.o" "CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o" "CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o" "CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o" "CMakeFiles/ewald-test.dir/pme.cpp.o" "CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 67%] Built target ewald-test /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/restraint/tests 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-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/manager.cpp.o -MF CMakeFiles/restraintpotential-test.dir/manager.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/tests/manager.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o -MF CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o.d -o CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/stringtoenumvalueconverter.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/restraint/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/restraint/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem 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/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/pbcutil/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem 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CMakeFiles/pbcutil-test.dir/mshift.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/tests/mshift.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/options/tests/option.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/settletestrunners_gpu.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/functions.cpp.o -MF CMakeFiles/math-test.dir/functions.cpp.o.d -o CMakeFiles/math-test.dir/functions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/functions.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/pbcutil/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbc.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbc.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/tests/pbc.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/optionsassigner.cpp.o -MF CMakeFiles/options-test.dir/optionsassigner.cpp.o.d -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/tests/optionsassigner.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem 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/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/wholemoleculetransform.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/restraintpotential-test.dir/link.d "CMakeFiles/restraintpotential-test.dir/manager.cpp.o" "CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 67%] Built target restraintpotential-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem 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-o CMakeFiles/math-test.dir/gausstransform.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/gausstransform.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdtypes/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include 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-I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/densityfittingforce.cpp.o -MF CMakeFiles/math-test.dir/densityfittingforce.cpp.o.d -o CMakeFiles/math-test.dir/densityfittingforce.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/densityfittingforce.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdtypes/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o -MF CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o.d -o CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/multipletimestepping.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdlib-test.dir/link.d "CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o" "CMakeFiles/mdlib-test.dir/calcvir.cpp.o" "CMakeFiles/mdlib-test.dir/constr.cpp.o" 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"CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o" "CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o" "CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 68%] Built target mdlib-test /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/tables/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tables/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tables/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tables/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tables/tests/CMakeFiles/table-test.dir/splinetable.cpp.o -MF CMakeFiles/table-test.dir/splinetable.cpp.o.d -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/tables/tests/splinetable.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/pbcutil-test.dir/link.d "CMakeFiles/pbcutil-test.dir/com.cpp.o" "CMakeFiles/pbcutil-test.dir/mshift.cpp.o" "CMakeFiles/pbcutil-test.dir/pbc.cpp.o" "CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o" "CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 68%] Built target pbcutil-test /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/taskassignment/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 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CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include 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-I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -MF CMakeFiles/random-test.dir/uniformintdistribution.cpp.o.d -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/random/tests/uniformintdistribution.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tables/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tables/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tables/tests/CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/timing/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/timing/tests 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-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/timing/tests/CMakeFiles/timing-test.dir/timing.cpp.o -MF CMakeFiles/timing-test.dir/timing.cpp.o.d -o CMakeFiles/timing-test.dir/timing.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/timing/tests/timing.cpp /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests /build/reproducible-path/gromacs-2024.4/build/mpi 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/atoms.cpp.o -MF CMakeFiles/topology-test.dir/atoms.cpp.o.d -o CMakeFiles/topology-test.dir/atoms.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/atoms.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/pulling/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/pulling/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY 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-I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/matrix.cpp.o -MF CMakeFiles/math-test.dir/matrix.cpp.o.d -o CMakeFiles/math-test.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/matrix.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/random/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY 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-O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -MF CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o.d -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/random/tests/uniformrealdistribution.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/multidimarray.cpp.o -MF CMakeFiles/math-test.dir/multidimarray.cpp.o.d -o CMakeFiles/math-test.dir/multidimarray.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/multidimarray.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/timing/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/timing/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/timing/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/timing/tests/CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/textreader.cpp.o -MF CMakeFiles/utility-test.dir/textreader.cpp.o.d -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/textreader.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/timing/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/timing-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdtypes/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/timing-test.dir/link.d "CMakeFiles/timing-test.dir/timing.cpp.o" "CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/timing-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 68%] Built target timing-test /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/compat/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/mp11.cpp.o -MF CMakeFiles/compat-test.dir/mp11.cpp.o.d -o CMakeFiles/compat-test.dir/mp11.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/tests/mp11.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/taskassignment-test.dir/link.d "CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o" "CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o ../CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o ../CMakeFiles/taskassignment.dir/findallgputasks.cpp.o ../CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o ../CMakeFiles/taskassignment.dir/resourcedivision.cpp.o ../CMakeFiles/taskassignment.dir/taskassignment.cpp.o ../CMakeFiles/taskassignment.dir/usergpuids.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 70%] Built target taskassignment-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/textwriter.cpp.o -MF CMakeFiles/utility-test.dir/textwriter.cpp.o.d -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/textwriter.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -MF CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o.d -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/bootstrap_loadstore.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/pulling/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/pulling/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdtypes/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdtypes-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/random/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/compat/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/pointers.cpp.o -MF CMakeFiles/compat-test.dir/pointers.cpp.o.d -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/tests/pointers.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdtypes-test.dir/link.d "CMakeFiles/mdtypes-test.dir/enerdata.cpp.o" "CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o" "CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o" "CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o" "CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o" "CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdtypes-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 71%] Built target mdtypes-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar.cpp.o -MF CMakeFiles/simd-test.dir/scalar.cpp.o.d -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/scalar.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/options-test.dir/link.d "CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o" "CMakeFiles/options-test.dir/filenameoption.cpp.o" "CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o" "CMakeFiles/options-test.dir/option.cpp.o" "CMakeFiles/options-test.dir/optionsassigner.cpp.o" "CMakeFiles/options-test.dir/repeatingsection.cpp.o" "CMakeFiles/options-test.dir/timeunitmanager.cpp.o" "CMakeFiles/options-test.dir/treesupport.cpp.o" "CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 72%] Built target options-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_util.cpp.o -MF CMakeFiles/simd-test.dir/scalar_util.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/scalar_util.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_math.cpp.o -MF CMakeFiles/simd-test.dir/scalar_math.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/scalar_math.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd.cpp.o -MF CMakeFiles/simd-test.dir/simd.cpp.o.d -o CMakeFiles/simd-test.dir/simd.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/simd.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/typetraits.cpp.o -MF CMakeFiles/utility-test.dir/typetraits.cpp.o.d -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/typetraits.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/neldermead.cpp.o -MF CMakeFiles/math-test.dir/neldermead.cpp.o.d -o CMakeFiles/math-test.dir/neldermead.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/neldermead.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/pull-test.dir/link.d "CMakeFiles/pull-test.dir/pull.cpp.o" "CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/pulling.dir/output.cpp.o ../CMakeFiles/pulling.dir/pull.cpp.o ../CMakeFiles/pulling.dir/pull_rotation.cpp.o ../CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o ../CMakeFiles/pulling.dir/pullutil.cpp.o ../CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lmuparser -lm ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 74%] Built target pull-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/random-test.dir/link.d "CMakeFiles/random-test.dir/exponentialdistribution.cpp.o" "CMakeFiles/random-test.dir/gammadistribution.cpp.o" "CMakeFiles/random-test.dir/normaldistribution.cpp.o" "CMakeFiles/random-test.dir/seed.cpp.o" "CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o" "CMakeFiles/random-test.dir/threefry.cpp.o" "CMakeFiles/random-test.dir/uniformintdistribution.cpp.o" "CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o" "CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 75%] Built target random-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/optimization.cpp.o -MF CMakeFiles/math-test.dir/optimization.cpp.o.d -o CMakeFiles/math-test.dir/optimization.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/optimization.cpp cd 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/build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/topology/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -MF CMakeFiles/topology-test.dir/exclusionblocks.cpp.o.d -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/exclusionblocks.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/topology/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/idef.cpp.o -MF CMakeFiles/topology-test.dir/idef.cpp.o.d -o CMakeFiles/topology-test.dir/idef.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/idef.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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/usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 75%] Built target table-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/vectypes.cpp.o -MF CMakeFiles/math-test.dir/vectypes.cpp.o.d -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/vectypes.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection 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../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 76%] Built target compat-test /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxana/tests 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src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/topology/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/index.cpp.o -MF CMakeFiles/topology-test.dir/index.cpp.o.d -o CMakeFiles/topology-test.dir/index.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/index.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src 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-I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/tests/gmx_chi.cpp /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests 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-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/topology/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/mtop.cpp.o -MF CMakeFiles/topology-test.dir/mtop.cpp.o.d -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/mtop.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/topology/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/symtab.cpp.o -MF CMakeFiles/topology-test.dir/symtab.cpp.o.d -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/symtab.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/utility-test.dir/link.d "CMakeFiles/utility-test.dir/alignedallocator.cpp.o" "CMakeFiles/utility-test.dir/arrayref.cpp.o" "CMakeFiles/utility-test.dir/booltype.cpp.o" "CMakeFiles/utility-test.dir/bitmask32.cpp.o" "CMakeFiles/utility-test.dir/bitmask64.cpp.o" "CMakeFiles/utility-test.dir/bitmask128.cpp.o" "CMakeFiles/utility-test.dir/cstringutil.cpp.o" "CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o" 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../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 77%] Built target utility-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/topology/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src 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-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/topsort.cpp.o -MF CMakeFiles/topology-test.dir/topsort.cpp.o.d -o CMakeFiles/topology-test.dir/topsort.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/topsort.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxana/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/tests/gmx_mindist.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxana/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/tests/gmx_traj.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxana/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/genion.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 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src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/correlationfunctions/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/autocorr.cpp.o -MF CMakeFiles/correlations-test.dir/autocorr.cpp.o.d -o CMakeFiles/correlations-test.dir/autocorr.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/tests/autocorr.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem 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/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/correlationfunctions/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -MF CMakeFiles/correlations-test.dir/correlationdataset.cpp.o.d -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/tests/correlationdataset.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_math.cpp.o -MF CMakeFiles/simd-test.dir/simd_math.cpp.o.d -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/simd_math.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/gmxana-test.dir/link.d "CMakeFiles/gmxana-test.dir/entropy.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o" "CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 79%] Built target gmxana-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/correlationfunctions/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/expfit.cpp.o -MF CMakeFiles/correlations-test.dir/expfit.cpp.o.d -o CMakeFiles/correlations-test.dir/expfit.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/tests/expfit.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/topology/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_memory.cpp.o -MF CMakeFiles/simd-test.dir/simd_memory.cpp.o.d -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/simd_memory.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/gen_maxwell_velocities.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/pdb2gmx1-test.dir/link.d "CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx1-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 79%] Built target pdb2gmx1-test /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/tests/datatest.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/correlationfunctions/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -MF 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -MF CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o.d -o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/tests/outputadaptercontainer.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/topology-test.dir/link.d "CMakeFiles/topology-test.dir/atoms.cpp.o" "CMakeFiles/topology-test.dir/exclusionblocks.cpp.o" "CMakeFiles/topology-test.dir/idef.cpp.o" "CMakeFiles/topology-test.dir/index.cpp.o" "CMakeFiles/topology-test.dir/mtop.cpp.o" "CMakeFiles/topology-test.dir/symtab.cpp.o" "CMakeFiles/topology-test.dir/topsort.cpp.o" "CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 79%] Built target topology-test /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend make[4]: 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-DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/tests/mock_datamodule.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/simd_vector_operations.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/energyanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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-DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx3-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/pdb2gmx3-test.dir/link.d "CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx3-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 79%] Built target pdb2gmx3-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/correlations-test.dir/link.d "CMakeFiles/correlations-test.dir/autocorr.cpp.o" "CMakeFiles/correlations-test.dir/correlationdataset.cpp.o" "CMakeFiles/correlations-test.dir/expfit.cpp.o" "CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o" "CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 79%] Built target correlations-test /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/tools/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/dump.cpp.o -MF CMakeFiles/tool-test.dir/dump.cpp.o.d -o CMakeFiles/tool-test.dir/dump.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/tools/tests/dump.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem 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CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/grompp_directives.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/helpwriting.cpp.o -MF CMakeFiles/tool-test.dir/helpwriting.cpp.o.d -o CMakeFiles/tool-test.dir/helpwriting.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/tools/tests/helpwriting.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/make_ndx.cpp.o -MF CMakeFiles/tool-test.dir/make_ndx.cpp.o.d -o CMakeFiles/tool-test.dir/make_ndx.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/tools/tests/make_ndx.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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-DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem 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-DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/massrepartitioning.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/energyanalysis-test.dir/link.d "CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o" "CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o" "CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend [ 80%] Built target energyanalysis-test /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests 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-DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/indexutil.cpp.o -MF CMakeFiles/selection-test.dir/indexutil.cpp.o.d -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/indexutil.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/simd4_floatingpoint.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/filemd5.cpp.o -MF CMakeFiles/fileio-test.dir/filemd5.cpp.o.d -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/filemd5.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/filetypes.cpp.o -MF CMakeFiles/fileio-test.dir/filetypes.cpp.o.d -o CMakeFiles/fileio-test.dir/filetypes.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/filetypes.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -MF CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/compressed_x_output.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/solvate.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/convert-tpr.cpp.o -MF CMakeFiles/tool-test.dir/convert-tpr.cpp.o.d -o CMakeFiles/tool-test.dir/convert-tpr.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/tools/tests/convert-tpr.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_math.cpp.o -MF CMakeFiles/simd-test.dir/simd4_math.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/simd4_math.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/math-test.dir/link.d "CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o" "CMakeFiles/math-test.dir/boxmatrix.cpp.o" "CMakeFiles/math-test.dir/coordinatetransformation.cpp.o" "CMakeFiles/math-test.dir/densityfit.cpp.o" "CMakeFiles/math-test.dir/dofit.cpp.o" "CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o" "CMakeFiles/math-test.dir/functions.cpp.o" "CMakeFiles/math-test.dir/gausstransform.cpp.o" "CMakeFiles/math-test.dir/densityfittingforce.cpp.o" "CMakeFiles/math-test.dir/invertmatrix.cpp.o" "CMakeFiles/math-test.dir/matrix.cpp.o" "CMakeFiles/math-test.dir/multidimarray.cpp.o" "CMakeFiles/math-test.dir/neldermead.cpp.o" "CMakeFiles/math-test.dir/optimization.cpp.o" "CMakeFiles/math-test.dir/paddedvector.cpp.o" "CMakeFiles/math-test.dir/vectypes.cpp.o" "CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 81%] Built target math-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/simd4_vector_operations.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/cmake -P CMakeFiles/analysisdata-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test-shared.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/ar qc ../../../../lib/libanalysisdata-test-shared.a "CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o" "CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o" "CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libanalysisdata-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 83%] Built target analysisdata-test-shared cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/selection/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectionoption.cpp.o -MF CMakeFiles/selection-test.dir/selectionoption.cpp.o.d -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/selectionoption.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/topdirs.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -MF CMakeFiles/fileio-test.dir/mrcserializer.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/mrcserializer.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -MF CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/helpwriting.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/simd-test.dir/link.d "CMakeFiles/simd-test.dir/base.cpp.o" "CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o" "CMakeFiles/simd-test.dir/scalar.cpp.o" "CMakeFiles/simd-test.dir/scalar_util.cpp.o" "CMakeFiles/simd-test.dir/scalar_math.cpp.o" "CMakeFiles/simd-test.dir/simd.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o" "CMakeFiles/simd-test.dir/simd_integer.cpp.o" "CMakeFiles/simd-test.dir/simd_math.cpp.o" "CMakeFiles/simd-test.dir/simd_memory.cpp.o" "CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/simd4.cpp.o" "CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd4_math.cpp.o" "CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 84%] Built target simd-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/densityfittingmodule.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/interactiveMD.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -MF CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/outputfiles.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/mrcdensitymap.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/gmxpreprocess-test.dir/link.d "CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 84%] Built target gmxpreprocess-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -MF CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/trajectory_writing.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/tool-test.dir/link.d "CMakeFiles/tool-test.dir/dump.cpp.o" "CMakeFiles/tool-test.dir/helpwriting.cpp.o" "CMakeFiles/tool-test.dir/make_ndx.cpp.o" "CMakeFiles/tool-test.dir/report_methods.cpp.o" "CMakeFiles/tool-test.dir/trjconv.cpp.o" "CMakeFiles/tool-test.dir/convert-tpr.cpp.o" "CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 84%] Built target tool-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/selection/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/toputils.cpp.o -MF CMakeFiles/selection-test.dir/toputils.cpp.o.d -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/toputils.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/selection/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -MF CMakeFiles/coordinateio-test.dir/testmodule.cpp.o.d -o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/tests/testmodule.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/coordinateio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -MF CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/checkpoint.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/readinp.cpp.o -MF CMakeFiles/fileio-test.dir/readinp.cpp.o.d -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/readinp.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY 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-O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o -MF CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o.d -o CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/multiple_time_stepping.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY 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-O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -MF CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/exactcontinuation.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-output-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/timecontrol.cpp.o -MF CMakeFiles/fileio-test.dir/timecontrol.cpp.o.d -o CMakeFiles/fileio-test.dir/timecontrol.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/timecontrol.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/depend cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/grompp.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/dispersion_correction.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-output-test.dir/link.d "CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o" "CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o" "CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o" "CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o" "CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-output-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 85%] Built target mdrun-output-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -MF CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/initialconstraints.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/termination.cpp.o -MF CMakeFiles/mdrun-io-test.dir/termination.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/termination.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/termination.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-modules-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/coordinateio-test.dir/link.d "CMakeFiles/coordinateio-test.dir/builder.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o" "CMakeFiles/coordinateio-test.dir/register.cpp.o" "CMakeFiles/coordinateio-test.dir/requirements.cpp.o" "CMakeFiles/coordinateio-test.dir/setatoms.cpp.o" "CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o" "CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o" "CMakeFiles/coordinateio-test.dir/settimestep.cpp.o" "CMakeFiles/coordinateio-test.dir/testmodule.cpp.o" "CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 85%] Built target coordinateio-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem 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make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 85%] Built target mdrun-modules-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -MF CMakeFiles/mdrun-test.dir/swapcoords.cpp.o.d -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/swapcoords.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -MF 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o -MF 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'/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/nonbonded_bench.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/tngio.cpp.o -MF CMakeFiles/fileio-test.dir/tngio.cpp.o.d -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/tngio.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/selection-test.dir/link.d "CMakeFiles/selection-test.dir/indexutil.cpp.o" "CMakeFiles/selection-test.dir/nbsearch.cpp.o" "CMakeFiles/selection-test.dir/poscalc.cpp.o" "CMakeFiles/selection-test.dir/selectioncollection.cpp.o" "CMakeFiles/selection-test.dir/selectionoption.cpp.o" "CMakeFiles/selection-test.dir/toputils.cpp.o" "CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 87%] Built target selection-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem 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-Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -MF CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o.d -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.txt --verbose=1 /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/multisim.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.d "CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-single-rank-algorithms-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 87%] Built target mdrun-single-rank-algorithms-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/mimic.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem 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-Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/multisimtest.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-tpi-test.dir/link.d "CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o" "CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 87%] Built target mdrun-tpi-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src 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-fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/replicaexchange.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/minimize-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-io-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/minimize-test.dir/link.d "CMakeFiles/minimize-test.dir/minimize.cpp.o" "CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/minimize-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 87%] Built target minimize-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-io-test.dir/link.d "CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o" "CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o" "CMakeFiles/mdrun-io-test.dir/grompp.cpp.o" "CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o" "CMakeFiles/mdrun-io-test.dir/termination.cpp.o" "CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-io-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 87%] Built target mdrun-io-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem 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src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simple_mdrun.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/multisimtest.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o -MF CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o.d -o CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/boxdeformation.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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-g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/fileio-test.dir/link.d "CMakeFiles/fileio-test.dir/checkpoint.cpp.o" "CMakeFiles/fileio-test.dir/confio.cpp.o" "CMakeFiles/fileio-test.dir/filemd5.cpp.o" "CMakeFiles/fileio-test.dir/filetypes.cpp.o" "CMakeFiles/fileio-test.dir/mrcserializer.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o" "CMakeFiles/fileio-test.dir/readinp.cpp.o" "CMakeFiles/fileio-test.dir/timecontrol.cpp.o" "CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o" "CMakeFiles/fileio-test.dir/tngio.cpp.o" "CMakeFiles/fileio-test.dir/xvgio.cpp.o" "CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 88%] Built target fileio-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 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-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/periodicactions.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" 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Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/periodicactions.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-multisim-test.dir/link.d "CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 88%] Built target mdrun-multisim-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/DependInfo.cmake "--color=" /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-mpi-test.dir/link.d "CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/periodicactions.cpp [ 89%] Built target mdrun-mpi-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/freeenergy.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -MF CMakeFiles/mdrun-pull-test.dir/pull.cpp.o.d -o CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/pull.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/replicaexchange_equivalence.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/periodicactions_coupling.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-non-integrator-test.dir/link.d "CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 89%] Built target mdrun-non-integrator-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-multisim-replex-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 89%] Built target mdrun-multisim-replex-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-pme-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-mpi-pme-test.dir/link.d "CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o" "CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-pme-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 89%] Built target mdrun-mpi-pme-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/periodicactions_basic.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-test.dir/link.d "CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o" "CMakeFiles/mdrun-test.dir/swapcoords.cpp.o" "CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o" "CMakeFiles/mdrun-test.dir/freezegroups.cpp.o" "CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o" "CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o" "CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 90%] Built target mdrun-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 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/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem 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-fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-coordination-coupling-test.dir/link.d "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-coupling-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 90%] Built target mdrun-coordination-coupling-test /usr/bin/make -f api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -MF CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o.d -o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests/stopsignaler.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-fep-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-fep-test.dir/link.d "CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o" "CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-fep-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 92%] Built target mdrun-fep-test /usr/bin/make -f api/gmxapi/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build.make api/gmxapi/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 92%] Built target mdrun-coordination-basic-test /usr/bin/make -f api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/workflow/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong 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/build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build.make api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/workflow/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/workflow.cpp.o -MF CMakeFiles/workflow-details-mpi-test.dir/workflow.cpp.o.d -o CMakeFiles/workflow-details-mpi-test.dir/workflow.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/workflow/tests/workflow.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-constraints-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o -MF CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o.d -o CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests/restraint.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-coordination-constraints-test.dir/link.d "CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o" "CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-constraints-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 92%] Built target mdrun-coordination-constraints-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem 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CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/box.cpp.o -MF CMakeFiles/nblib-setup-test.dir/box.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/box.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/box.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script 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-I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 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../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-rotation-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 92%] Built target mdrun-rotation-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/runner.cpp.o -MF CMakeFiles/gmxapi-mpi-test.dir/runner.cpp.o.d -o CMakeFiles/gmxapi-mpi-test.dir/runner.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests/runner.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o -MF CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o.d -o CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests/status.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-simulator-comparison-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-pull-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-simulator-comparison-test.dir/link.d "CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o" "CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-simulator-comparison-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 92%] Built target mdrun-simulator-comparison-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/version.cpp.o -MF CMakeFiles/gmxapi-test.dir/version.cpp.o.d -o CMakeFiles/gmxapi-test.dir/version.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests/version.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-vsites-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-pull-test.dir/link.d "CMakeFiles/mdrun-pull-test.dir/pull.cpp.o" "CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-pull-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 92%] Built target mdrun-pull-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o -MF CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o.d -o CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/tpr.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 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'/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/CMakeFiles/nblib-integration-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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api/nblib/tests/CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/gmxcalculator.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-equivalence-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/workflow-details-test.dir/link.d "CMakeFiles/workflow-details-test.dir/workflow.cpp.o" "CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi_mpi.so.0.4.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 92%] Built target mdrun-multisim-replex-equivalence-test /usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make 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&& /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/util/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/util/tests /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/util/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/setup.cpp.o -MF CMakeFiles/nblib-util-test.dir/setup.cpp.o.d -o CMakeFiles/nblib-util-test.dir/setup.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/util/tests/setup.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/workflow-details-mpi-test.dir/link.d "CMakeFiles/workflow-details-mpi-test.dir/workflow.cpp.o" "CMakeFiles/workflow-details-mpi-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-mpi-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi_mpi.so.0.4.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 93%] Built target workflow-details-mpi-test /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/commandline/tests 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/tests/gmxcalculator.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/gmxapi-test.dir/link.d "CMakeFiles/gmxapi-test.dir/restraint.cpp.o" "CMakeFiles/gmxapi-test.dir/runner.cpp.o" "CMakeFiles/gmxapi-test.dir/status.cpp.o" "CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o" "CMakeFiles/gmxapi-test.dir/system.cpp.o" "CMakeFiles/gmxapi-test.dir/version.cpp.o" "CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi_mpi.so.0.4.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 93%] Built target gmxapi-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/commandline/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/util/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/traits.cpp.o -MF CMakeFiles/nblib-util-test.dir/traits.cpp.o.d -o CMakeFiles/nblib-util-test.dir/traits.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/util/tests/traits.cpp /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2024.4/build/mpi 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -MF CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/tests/analysisdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -MF CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/tests/threadaffinity.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integrator-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -MF CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/nbkernelsystem.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o -MF CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o.d -o CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests/stopsignaler.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/nblib-integrator-test.dir/link.d "CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o" "CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integrator-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 93%] Built target nblib-integrator-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o -MF CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o.d -o CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests/system.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem 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CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -MF CMakeFiles/nblib-setup-test.dir/particletype.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/particletype.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/util/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -c 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/build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o -MF CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o.d -o CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests/version.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/util/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-util-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-tpr-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxapi-mpi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxapi-mpi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/nblib-util-test.dir/link.d "CMakeFiles/nblib-util-test.dir/setup.cpp.o" "CMakeFiles/nblib-util-test.dir/traits.cpp.o" "CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-util-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 93%] Built target nblib-util-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -MF CMakeFiles/analysisdata-test.dir/arraydata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/tests/arraydata.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/nblib-tpr-test.dir/link.d "CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o" "CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-tpr-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 93%] Built target nblib-tpr-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrunutility-mpi-test.dir/link.d "CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o" "CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 93%] Built target mdrunutility-mpi-test /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem 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-I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -MF CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/pbcholder.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -MF CMakeFiles/nblib-setup-test.dir/molecules.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/molecules.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/angle.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o -MF CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/nbnxmsetup.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrunutility-test.dir/link.d "CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o" "CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o" "CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 93%] Built target mdrunutility-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -MF CMakeFiles/nblib-integration-test.dir/simstate.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/simstate.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/topology.cpp.o -MF CMakeFiles/nblib-setup-test.dir/topology.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/topology.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/topology.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/commandline/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/gmxapi-mpi-test.dir/link.d "CMakeFiles/gmxapi-mpi-test.dir/context.cpp.o" "CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o" "CMakeFiles/gmxapi-mpi-test.dir/runner.cpp.o" "CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o" "CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o" "CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o" "CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o" "CMakeFiles/gmxapi-mpi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi_mpi.so.0.4.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 94%] Built target gmxapi-mpi-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/commandline/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/tests/cmdlineparser.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 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-I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/histogram.cpp.o -MF CMakeFiles/analysisdata-test.dir/histogram.cpp.o.d -o CMakeFiles/analysisdata-test.dir/histogram.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/tests/histogram.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/nblib-integration-test.dir/link.d "CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o" 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/convert_trj.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem 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-I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/commandline-test.dir/link.d "CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o" "CMakeFiles/commandline-test.dir/filenm.cpp.o" "CMakeFiles/commandline-test.dir/pargs.cpp.o" "CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 96%] Built target commandline-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/analysisdata-test.dir/link.d "CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o" "CMakeFiles/analysisdata-test.dir/arraydata.cpp.o" "CMakeFiles/analysisdata-test.dir/average.cpp.o" "CMakeFiles/analysisdata-test.dir/histogram.cpp.o" "CMakeFiles/analysisdata-test.dir/lifetime.cpp.o" "CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 96%] Built target analysisdata-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/gyrate.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/hbond.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 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-I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/pairdist.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/rdf.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/sasa.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/select.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/scattering.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-setup-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/nblib-setup-test.dir/link.d "CMakeFiles/nblib-setup-test.dir/box.cpp.o" "CMakeFiles/nblib-setup-test.dir/interactions.cpp.o" "CMakeFiles/nblib-setup-test.dir/particletype.cpp.o" "CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o" "CMakeFiles/nblib-setup-test.dir/molecules.cpp.o" "CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o" "CMakeFiles/nblib-setup-test.dir/topology.cpp.o" "CMakeFiles/nblib-setup-test.dir/virials.cpp.o" "CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-setup-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 97%] Built target nblib-setup-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/topologyinformation.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trajectory.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/unionfind.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/CMakeFiles/nblib-tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib-tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 97%] Built target nblib-tests cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-listed-forces-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/trajectoryanalysis-test.dir/link.d "CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [100%] Built target trajectoryanalysis-test /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/nblib-listed-forces-test.dir/link.d "CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [100%] Built target nblib-listed-forces-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/CMakeFiles/tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [100%] Built target tests make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2024.4/build/mpi/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[1]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' (cd build/mpi ; LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2024.4/build/mpi/lib \ OMPI_MCA_rmaps_base_oversubscribe=1 \ PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe \ ctest -V) UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2024.4/build/mpi/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2024.4/build/mpi/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2024.4/build/mpi/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2024.4/build/mpi/DartConfiguration.tcl Test project /build/reproducible-path/gromacs-2024.4/build/mpi Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: GmxapiExternalInterfaceTests 1: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/gmxapi-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/GmxapiExternalInterfaceTests.xml" 1: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests 1: Test timeout computed to be: 600 1: [==========] Running 9 tests from 1 test suite. 1: [----------] Global test environment set-up. 1: [----------] 9 tests from GmxApiTest 1: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI process 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -436216130 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.036 0.018 199.5 1: (ns/day) (hour/ns) 1: Performance: 27.988 0.858 1: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (580 ms) 1: [ RUN ] GmxApiTest.RunnerBasicMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI process 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -1403389745 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.437 0.219 199.9 1: (ns/day) (hour/ns) 1: Performance: 2.314 10.373 1: [ OK ] GmxApiTest.RunnerBasicMD (692 ms) 1: [ RUN ] GmxApiTest.RunnerReinitialize 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI process 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: 1: Received the remote INT/TERM signal, stopping within 200 steps 1: 1: Setting the LD random seed to -18514201 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.046 0.023 199.5 1: (ns/day) (hour/ns) 1: Performance: 154.850 0.155 1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI process 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.045 0.022 199.7 1: (ns/day) (hour/ns) 1: Performance: 157.530 0.152 1: [ OK ] GmxApiTest.RunnerReinitialize (500 ms) 1: [ RUN ] GmxApiTest.RunnerChainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI process 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to 1744295903 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.187 0.094 199.8 1: (ns/day) (hour/ns) 1: Performance: 5.401 4.444 1: trr version: GMX_trn_file (single precision) 1: 1: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 1: Setting nsteps to 4 1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI process 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 1: Input file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 2 1: Runtime for the run 0.00390625 ps 1: Run end step 2 1: Run end time 0.00390625 ps 1: 1: 1: Output file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 4 1: Runtime for the run 0.0078125 ps 1: Run end step 4 1: Run end time 0.0078125 ps 1: 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.072 0.036 199.8 1: (ns/day) (hour/ns) 1: Performance: 14.114 1.700 1: 1: [ OK ] GmxApiTest.RunnerChainedMD (463 ms) 1: [ RUN ] GmxApiTest.Status 1: [ OK ] GmxApiTest.Status (0 ms) 1: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 1: Changing nstlist from 10 to 1, rlist from 1.057 to 1 1: 1: Using 1 MPI process 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: Setting the LD random seed to -33957137 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.049 0.024 199.5 1: (ns/day) (hour/ns) 1: Performance: 34.592 0.694 1: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 1: Overriding nsteps with value passed on the command line: 4 steps, 0.00781 ps 1: Changing nstlist from 10 to 1, rlist from 1.057 to 1 1: 1: 1: Using 1 MPI process 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.035 0.018 199.4 1: (ns/day) (hour/ns) 1: Performance: 19.039 1.261 1: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (423 ms) 1: [ RUN ] GmxApiTest.SystemConstruction 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Setting the LD random seed to 1825470462 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: [ OK ] GmxApiTest.SystemConstruction (279 ms) 1: [ RUN ] GmxApiTest.SaneVersionComparisons 1: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms) 1: [ RUN ] GmxApiTest.VersionNamed0_1_Features 1: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) 1: [----------] 9 tests from GmxApiTest (2941 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 9 tests from 1 test suite ran. (2984 ms total) 1: [ PASSED ] 9 tests. 1/91 Test #1: GmxapiExternalInterfaceTests ................. Passed 3.45 sec test 2 Start 2: GmxapiMpiTests 2: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/gmxapi-mpi-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/GmxapiMpiTests.xml" 2: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests 2: Test timeout computed to be: 600 2: [==========] Running 13 tests from 1 test suite. 2: [----------] Global test environment set-up. 2: [----------] 13 tests from GmxApiTest 2: [ RUN ] GmxApiTest.AllContext 2: [ OK ] GmxApiTest.AllContext (112 ms) 2: [ RUN ] GmxApiTest.NullContext 2: [ OK ] GmxApiTest.NullContext (0 ms) 2: [ RUN ] GmxApiTest.MpiWorldContext 2: [ OK ] GmxApiTest.MpiWorldContext (128 ms) 2: [ RUN ] GmxApiTest.MpiSplitContext 2: Setting the LD random seed to -302711041 2: [ OK ] GmxApiTest.MpiSplitContext (100 ms) 2: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD 2: Setting the LD random seed to -9799841 2: 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: Generating 1-4 interactions: fudge = 0.5 2: 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: This run will generate roughly 0 Mb of data 2: 2: There were 2 NOTEs 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 2: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 2: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 2: 2: Using 2 MPI processes 2: Using 2 OpenMP threads per MPI process 2: 2: 2: NOTE: The number of threads is not equal to the number of (logical) cpus 2: and the -pin option is set to auto: will not pin threads to cpus. 2: This can lead to significant performance degradation. 2: Consider using -pin on (and -pinoffset in case you run multiple jobs). 2: starting mdrun 'Water and methane' 2: 2 steps, 0.0 ps. 2: 2: Writing final coordinates. 2: 2: NOTE: 21 % of the run time was spent in domain decomposition, 2: 0 % of the run time was spent in pair search, 2: you might want to increase nstlist (this has no effect on accuracy) 2: 2: NOTE: 17 % of the run time was spent communicating energies, 2: you might want to increase some nst* mdp options 2: 2: Core t (s) Wall t (s) (%) 2: Time: 0.803 0.208 386.4 2: (ns/day) (hour/ns) 2: Performance: 2.437 9.849 2: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (1224 ms) 2: [ RUN ] GmxApiTest.RunnerBasicMD 2: Setting the LD random seed to -169148483 2: Setting the LD random seed to -180753543 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: 2: This run will generate roughly 0 Mb of data 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 2: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 2: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 2: 2: Using 2 MPI processes 2: Using 2 OpenMP threads per MPI process 2: 2: 2: NOTE: The number of threads is not equal to the number of (logical) cpus 2: and the -pin option is set to auto: will not pin threads to cpus. 2: This can lead to significant performance degradation. 2: Consider using -pin on (and -pinoffset in case you run multiple jobs). 2: starting mdrun 'Water and methane' 2: 2 steps, 0.0 ps. 2: 2: Writing final coordinates. 2: 2: NOTE: 18 % of the run time was spent in domain decomposition, 2: 0 % of the run time was spent in pair search, 2: you might want to increase nstlist (this has no effect on accuracy) 2: 2: NOTE: 30 % of the run time was spent communicating energies, 2: you might want to increase some nst* mdp options 2: 2: Core t (s) Wall t (s) (%) 2: Time: 0.888 0.222 399.9 2: (ns/day) (hour/ns) 2: Performance: 2.280 10.528 2: [ OK ] GmxApiTest.RunnerBasicMD (1191 ms) 2: [ RUN ] GmxApiTest.RunnerReinitialize 2: Setting the LD random seed to 1004173013 2: Setting the LD random seed to -135333894 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 2: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 2: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 2: 2: Using 2 MPI processes 2: Using 2 OpenMP threads per MPI process 2: 2: 2: NOTE: The number of threads is not equal to the number of (logical) cpus 2: and the -pin option is set to auto: will not pin threads to cpus. 2: This can lead to significant performance degradation. 2: Consider using -pin on (and -pinoffset in case you run multiple jobs). 2: starting mdrun 'Water and methane' 2: 20 steps, 0.0 ps. 2: 2: 2: Received the remote INT/TERM signal, stopping within 200 steps 2: 2: 2: 2: Received the remote INT/TERM signal, stopping within 200 steps 2: 2: 2: Writing final coordinates. 2: 2: NOTE: 11 % of the run time was spent in domain decomposition, 2: 5 % of the run time was spent in pair search, 2: you might want to increase nstlist (this has no effect on accuracy) 2: 2: NOTE: 8 % of the run time was spent communicating energies, 2: you might want to increase some nst* mdp options 2: 2: Core t (s) Wall t (s) (%) 2: Time: 2.064 0.516 399.9 2: (ns/day) (hour/ns) 2: Performance: 6.865 3.496 2: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 2: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 2: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 2: 2: Using 2 MPI processes 2: Using 2 OpenMP threads per MPI process 2: 2: 2: NOTE: The number of threads is not equal to the number of (logical) cpus 2: and the -pin option is set to auto: will not pin threads to cpus. 2: This can lead to significant performance degradation. 2: Consider using -pin on (and -pinoffset in case you run multiple jobs). 2: starting mdrun 'Water and methane' 2: 20 steps, 0.0 ps. 2: 2: Writing final coordinates. 2: 2: NOTE: 14 % of the run time was spent in domain decomposition, 2: 5 % of the run time was spent in pair search, 2: you might want to increase nstlist (this has no effect on accuracy) 2: 2: Core t (s) Wall t (s) (%) 2: Time: 2.522 0.631 400.0 2: (ns/day) (hour/ns) 2: Performance: 5.620 4.271 2: [ OK ] GmxApiTest.RunnerReinitialize (2127 ms) 2: [ RUN ] GmxApiTest.RunnerChainedMD 2: Setting the LD random seed to -78906674 2: Setting the LD random seed to -1749690369 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generating 1-4 interactions: fudge = 0.5 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 2: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 2: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 2: 2: Using 2 MPI processes 2: Using 2 OpenMP threads per MPI process 2: 2: 2: NOTE: The number of threads is not equal to the number of (logical) cpus 2: and the -pin option is set to auto: will not pin threads to cpus. 2: This can lead to significant performance degradation. 2: Consider using -pin on (and -pinoffset in case you run multiple jobs). 2: starting mdrun 'Water and methane' 2: 2 steps, 0.0 ps. 2: 2: Writing final coordinates. 2: 2: NOTE: 28 % of the run time was spent in domain decomposition, 2: 0 % of the run time was spent in pair search, 2: you might want to increase nstlist (this has no effect on accuracy) 2: 2: NOTE: 33 % of the run time was spent communicating energies, 2: you might want to increase some nst* mdp options 2: 2: Core t (s) Wall t (s) (%) 2: Time: 0.141 0.035 399.2 2: (ns/day) (hour/ns) 2: Performance: 14.369 1.670 2: trr version: GMX_trn_file (single precision) 2: 2: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 2: Input file: 2: trr version: GMX_trn_file (single precision) 2: 2: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 2: Input file: 2: Run start step 0 2: Run start time 0 ps 2: Step to be made during run 2 2: Runtime for the run 0.00390625 ps 2: Run end step 2 2: Run end time 0.00390625 ps 2: 2: Setting nsteps to 4 2: 2: Output file: 2: Run start step 0 2: Run start time 0 ps 2: Step to be made during run 4 2: Runtime for the run 0.0078125 ps 2: Run end step 4 2: Run end time 0.0078125 ps 2: 2: Run start step 0 2: Run start time 0 ps 2: Step to be made during run 2 2: Setting nsteps to 4 2: Runtime for the run 0.00390625 ps 2: Run end step 2 2: Run end time 0.00390625 ps 2: 2: 2: Output file: 2: Run start step 0 2: Run start time 0 ps 2: Step to be made during run 4 2: Runtime for the run 0.0078125 ps 2: Run end step 4 2: Run end time 0.0078125 ps 2: 2: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 2: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 2: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 2: 2: Using 2 MPI processes 2: Using 2 OpenMP threads per MPI process 2: 2: 2: NOTE: The number of threads is not equal to the number of (logical) cpus 2: and the -pin option is set to auto: will not pin threads to cpus. 2: This can lead to significant performance degradation. 2: Consider using -pin on (and -pinoffset in case you run multiple jobs). 2: starting mdrun 'Water and methane' 2: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 2: 2: Writing final coordinates. 2: 2: NOTE: 11 % of the run time was spent in pair search, 2: you might want to increase nstlist (this has no effect on accuracy) 2: 2: NOTE: 20 % of the run time was spent communicating energies, 2: you might want to increase some nst* mdp options 2: 2: Core t (s) Wall t (s) (%) 2: Time: 0.352 0.088 399.6 2: (ns/day) (hour/ns) 2: Performance: 5.750 4.174 2: 2: 2: [ OK ] GmxApiTest.RunnerChainedMD (1144 ms) 2: [ RUN ] GmxApiTest.Status 2: [ OK ] GmxApiTest.Status (0 ms) 2: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient 2: Setting the LD random seed to -440729627 2: Setting the LD random seed to -1360007753 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: 2: There were 2 NOTEs 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 2: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 2: Changing nstlist from 10 to 1, rlist from 1.057 to 1 2: 2: Using 2 MPI processes 2: Using 2 OpenMP threads per MPI process 2: 2: 2: NOTE: The number of threads is not equal to the number of (logical) cpus 2: and the -pin option is set to auto: will not pin threads to cpus. 2: This can lead to significant performance degradation. 2: Consider using -pin on (and -pinoffset in case you run multiple jobs). 2: starting mdrun 'Water and methane' 2: 4 steps, 0.0 ps. 2: 2: Writing final coordinates. 2: 2: 2: Dynamic load balancing report: 2: DLB was off during the run due to low measured imbalance. 2: Average load imbalance: 18.8%. 2: The balanceable part of the MD step is 0%, load imbalance is computed from this. 2: Part of the total run time spent waiting due to load imbalance: 0.0%. 2: 2: 2: NOTE: 50 % of the run time was spent in domain decomposition, 2: 0 % of the run time was spent in pair search, 2: you might want to increase nstlist (this has no effect on accuracy) 2: 2: NOTE: 23 % of the run time was spent communicating energies, 2: you might want to increase some nst* mdp options 2: 2: Core t (s) Wall t (s) (%) 2: Time: 0.372 0.093 399.7 2: (ns/day) (hour/ns) 2: Performance: 9.059 2.649 2: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 2: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 2: Overriding nsteps with value passed on the command line: 4 steps, 0.00781 ps 2: Changing nstlist from 10 to 1, rlist from 1.057 to 1 2: 2: 2: Using 2 MPI processes 2: Using 2 OpenMP threads per MPI process 2: 2: 2: NOTE: The number of threads is not equal to the number of (logical) cpus 2: and the -pin option is set to auto: will not pin threads to cpus. 2: This can lead to significant performance degradation. 2: Consider using -pin on (and -pinoffset in case you run multiple jobs). 2: starting mdrun 'Water and methane' 2: 4 steps, 0.0 ps. 2: 2: 2: Dynamic load balancing report: 2: DLB was off during the run due to low measured imbalance. 2: Average load imbalance: 14.0%. 2: The balanceable part of the MD step is 11%, load imbalance is computed from this. 2: Part of the total run time spent waiting due to load imbalance: 1.5%. 2: 2: 2: NOTE: 49 % of the run time was spent communicating energies, 2: you might want to increase some nst* mdp options 2: 2: Core t (s) Wall t (s) (%) 2: Time: 0.086 0.022 391.2 2: (ns/day) (hour/ns) 2: Performance: 15.327 1.566 2: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (961 ms) 2: [ RUN ] GmxApiTest.SystemConstruction 2: Setting the LD random seed to -151048200 2: Setting the LD random seed to -554729997 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: This run will generate roughly 0 Mb of data 2: 2: There were 2 NOTEs 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: This run will generate roughly 0 Mb of data 2: 2: There were 2 NOTEs 2: [ OK ] GmxApiTest.SystemConstruction (671 ms) 2: [ RUN ] GmxApiTest.SaneVersionComparisons 2: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms) 2: [ RUN ] GmxApiTest.VersionNamed0_1_Features 2: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) 2: [----------] 13 tests from GmxApiTest (7726 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 13 tests from 1 test suite ran. (7822 ms total) 2: [ PASSED ] 13 tests. 2/91 Test #2: GmxapiMpiTests ............................... Passed 8.35 sec test 3 Start 3: GmxapiInternalInterfaceTests 3: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/workflow-details-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/GmxapiInternalInterfaceTests.xml" 3: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/workflow/tests 3: Test timeout computed to be: 600 3: [==========] Running 2 tests from 1 test suite. 3: [----------] Global test environment set-up. 3: [----------] 2 tests from GmxApiTest 3: [ RUN ] GmxApiTest.BuildApiWorkflowImpl 3: Generating 1-4 interactions: fudge = 0.5 3: 3: NOTE 1 [file spc_and_methane.top, line 33]: 3: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 3: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 3: the time step of 2.0e-03 ps. 3: Maybe you forgot to change the constraints mdp option. 3: 3: Number of degrees of freedom in T-Coupling group System is 18.00 3: 3: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 3: You are using a plain Coulomb cut-off, which might produce artifacts. 3: You might want to consider using PME electrostatics. 3: 3: 3: 3: There were 2 NOTEs 3: Setting the LD random seed to -1317086261 3: 3: Generated 331705 of the 331705 non-bonded parameter combinations 3: 3: Generated 331705 of the 331705 1-4 parameter combinations 3: 3: Excluding 2 bonded neighbours molecule type 'SOL' 3: 3: Excluding 3 bonded neighbours molecule type 'methane' 3: 3: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 3: 3: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 3: 3: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 3: 3: Note that mdrun will redetermine rlist based on the actual pair-list setup 3: 3: This run will generate roughly 0 Mb of data 3: [ OK ] GmxApiTest.BuildApiWorkflowImpl (391 ms) 3: [ RUN ] GmxApiTest.CreateApiWorkflow 3: Generating 1-4 interactions: fudge = 0.5 3: 3: NOTE 1 [file spc_and_methane.top, line 33]: 3: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 3: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 3: the time step of 2.0e-03 ps. 3: Maybe you forgot to change the constraints mdp option. 3: 3: Number of degrees of freedom in T-Coupling group System is 18.00 3: 3: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 3: You are using a plain Coulomb cut-off, which might produce artifacts. 3: You might want to consider using PME electrostatics. 3: 3: 3: 3: There were 2 NOTEs 3: Setting the LD random seed to 264174335 3: 3: Generated 331705 of the 331705 non-bonded parameter combinations 3: 3: Generated 331705 of the 331705 1-4 parameter combinations 3: 3: Excluding 2 bonded neighbours molecule type 'SOL' 3: 3: Excluding 3 bonded neighbours molecule type 'methane' 3: 3: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 3: 3: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 3: 3: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 3: 3: Note that mdrun will redetermine rlist based on the actual pair-list setup 3: 3: This run will generate roughly 0 Mb of data 3: [ OK ] GmxApiTest.CreateApiWorkflow (307 ms) 3: [----------] 2 tests from GmxApiTest (700 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 2 tests from 1 test suite ran. (734 ms total) 3: [ PASSED ] 2 tests. 3/91 Test #3: GmxapiInternalInterfaceTests ................. Passed 1.09 sec test 4 Start 4: GmxapiInternalsMpiTests 4: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/workflow-details-mpi-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/GmxapiInternalsMpiTests.xml" 4: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/workflow/tests 4: Test timeout computed to be: 600 4: [==========] Running 2 tests from 1 test suite. 4: [----------] Global test environment set-up. 4: [----------] 2 tests from GmxApiTest 4: [ RUN ] GmxApiTest.BuildApiWorkflowImpl 4: Setting the LD random seed to 1058524543 4: Setting the LD random seed to -540025370 4: 4: Generated 331705 of the 331705 non-bonded parameter combinations 4: Generating 1-4 interactions: fudge = 0.5 4: 4: Generated 331705 of the 331705 non-bonded parameter combinations 4: Generating 1-4 interactions: fudge = 0.5 4: 4: Generated 331705 of the 331705 1-4 parameter combinations 4: 4: Excluding 2 bonded neighbours molecule type 'SOL' 4: 4: Excluding 3 bonded neighbours molecule type 'methane' 4: 4: 4: NOTE 1 [file spc_and_methane.top, line 33]: 4: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 4: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 4: the time step of 2.0e-03 ps. 4: Maybe you forgot to change the constraints mdp option. 4: 4: Number of degrees of freedom in T-Coupling group System is 18.00 4: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 4: 4: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 4: 4: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 4: 4: Note that mdrun will redetermine rlist based on the actual pair-list setup 4: 4: This run will generate roughly 0 Mb of data 4: 4: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 4: You are using a plain Coulomb cut-off, which might produce artifacts. 4: You might want to consider using PME electrostatics. 4: 4: 4: 4: There were 2 NOTEs 4: 4: Generated 331705 of the 331705 1-4 parameter combinations 4: 4: Excluding 2 bonded neighbours molecule type 'SOL' 4: 4: Excluding 3 bonded neighbours molecule type 'methane' 4: 4: NOTE 1 [file spc_and_methane.top, line 33]: 4: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 4: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 4: the time step of 2.0e-03 ps. 4: Maybe you forgot to change the constraints mdp option. 4: 4: Number of degrees of freedom in T-Coupling group System is 18.00 4: 4: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 4: 4: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 4: 4: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 4: 4: Note that mdrun will redetermine rlist based on the actual pair-list setup 4: 4: This run will generate roughly 0 Mb of data 4: 4: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 4: You are using a plain Coulomb cut-off, which might produce artifacts. 4: You might want to consider using PME electrostatics. 4: 4: 4: 4: There were 2 NOTEs 4: [ OK ] GmxApiTest.BuildApiWorkflowImpl (578 ms) 4: [ RUN ] GmxApiTest.CreateApiWorkflow 4: Setting the LD random seed to -713035788 4: Setting the LD random seed to -42348545 4: 4: Generated 331705 of the 331705 non-bonded parameter combinations 4: Generating 1-4 interactions: fudge = 0.5 4: 4: Generated 331705 of the 331705 non-bonded parameter combinations 4: Generating 1-4 interactions: fudge = 0.5 4: 4: Generated 331705 of the 331705 1-4 parameter combinations 4: 4: Excluding 2 bonded neighbours molecule type 'SOL' 4: 4: Excluding 3 bonded neighbours molecule type 'methane' 4: 4: NOTE 1 [file spc_and_methane.top, line 33]: 4: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 4: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 4: the time step of 2.0e-03 ps. 4: Maybe you forgot to change the constraints mdp option. 4: 4: Number of degrees of freedom in T-Coupling group System is 18.00 4: 4: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 4: 4: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 4: 4: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 4: 4: Note that mdrun will redetermine rlist based on the actual pair-list setup 4: 4: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 4: You are using a plain Coulomb cut-off, which might produce artifacts. 4: You might want to consider using PME electrostatics. 4: 4: 4: 4: This run will generate roughly 0 Mb of data 4: 4: There were 2 NOTEs 4: 4: Generated 331705 of the 331705 1-4 parameter combinations 4: 4: Excluding 2 bonded neighbours molecule type 'SOL' 4: 4: Excluding 3 bonded neighbours molecule type 'methane' 4: 4: NOTE 1 [file spc_and_methane.top, line 33]: 4: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 4: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 4: the time step of 2.0e-03 ps. 4: Maybe you forgot to change the constraints mdp option. 4: 4: Number of degrees of freedom in T-Coupling group System is 18.00 4: 4: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 4: You are using a plain Coulomb cut-off, which might produce artifacts. 4: You might want to consider using PME electrostatics. 4: 4: 4: 4: There were 2 NOTEs 4: 4: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 4: 4: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 4: 4: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 4: 4: Note that mdrun will redetermine rlist based on the actual pair-list setup 4: 4: This run will generate roughly 0 Mb of data 4: [ OK ] GmxApiTest.CreateApiWorkflow (420 ms) 4: [----------] 2 tests from GmxApiTest (999 ms total) 4: 4: [----------] Global test environment tear-down 4: [==========] 2 tests from 1 test suite ran. (1067 ms total) 4: [ PASSED ] 2 tests. 4/91 Test #4: GmxapiInternalsMpiTests ...................... Passed 1.61 sec test 5 Start 5: NbLibListedForcesTests 5: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/nblib-listed-forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/NbLibListedForcesTests.xml" 5: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/listed_forces/tests 5: Test timeout computed to be: 600 5: [==========] Running 44 tests from 22 test suites. 5: [----------] Global test environment set-up. 5: [----------] 8 tests from NBlibTest 5: [ RUN ] NBlibTest.BondTypesOperatorEqualWorks 5: [ OK ] NBlibTest.BondTypesOperatorEqualWorks (0 ms) 5: [ RUN ] NBlibTest.BondTypesLessThanWorks 5: [ OK ] NBlibTest.BondTypesLessThanWorks (0 ms) 5: [ RUN ] NBlibTest.CanSplitListedWork 5: [ OK ] NBlibTest.CanSplitListedWork (0 ms) 5: [ RUN ] NBlibTest.ListedForceBuffer 5: [ OK ] NBlibTest.ListedForceBuffer (0 ms) 5: [ RUN ] NBlibTest.ListedForceCalculatorCanConstruct 5: [ OK ] NBlibTest.ListedForceCalculatorCanConstruct (0 ms) 5: [ RUN ] NBlibTest.GmxToNblibConversionAllTypes 5: [ OK ] NBlibTest.GmxToNblibConversionAllTypes (0 ms) 5: [ RUN ] NBlibTest.EndToEndListedComparison 5: [ OK ] NBlibTest.EndToEndListedComparison (0 ms) 5: [ RUN ] NBlibTest.shiftForcesAreCorrect 5: [ OK ] NBlibTest.shiftForcesAreCorrect (19 ms) 5: [----------] 8 tests from NBlibTest (21 ms total) 5: 5: [----------] 1 test from Kernels 5: [ RUN ] Kernels.HarmonicScalarKernelCanCompute 5: [ OK ] Kernels.HarmonicScalarKernelCanCompute (0 ms) 5: [----------] 1 test from Kernels (0 ms total) 5: 5: [----------] 1 test from FourCenter 5: [ RUN ] FourCenter.ListedForcesProperDihedralTest 5: [ OK ] FourCenter.ListedForcesProperDihedralTest (0 ms) 5: [----------] 1 test from FourCenter (0 ms total) 5: 5: [----------] 7 tests from ThreeCenter 5: [ RUN ] ThreeCenter.ListedForcesG96AngleTest 5: [ OK ] ThreeCenter.ListedForcesG96AngleTest (0 ms) 5: [ RUN ] ThreeCenter.ListedForcesHarmonicAngleTest 5: [ OK ] ThreeCenter.ListedForcesHarmonicAngleTest (0 ms) 5: [ RUN ] ThreeCenter.ListedForcesLinearAngleTest 5: [ OK ] ThreeCenter.ListedForcesLinearAngleTest (0 ms) 5: [ RUN ] ThreeCenter.ListedForcesCrossBondBondTest 5: [ OK ] ThreeCenter.ListedForcesCrossBondBondTest (0 ms) 5: [ RUN ] ThreeCenter.ListedForcesCrossBondAngleTest 5: [ OK ] ThreeCenter.ListedForcesCrossBondAngleTest (0 ms) 5: [ RUN ] ThreeCenter.ListedForcesQuarticAngleTest 5: [ OK ] ThreeCenter.ListedForcesQuarticAngleTest (0 ms) 5: [ RUN ] ThreeCenter.ListedForcesRestrictedAngleTest 5: [ OK ] ThreeCenter.ListedForcesRestrictedAngleTest (0 ms) 5: [----------] 7 tests from ThreeCenter (1 ms total) 5: 5: [----------] 5 tests from TwoCenter 5: [ RUN ] TwoCenter.ListedForcesHarmonicBondTest 5: [ OK ] TwoCenter.ListedForcesHarmonicBondTest (0 ms) 5: [ RUN ] TwoCenter.ListedForcesG96BondTest 5: [ OK ] TwoCenter.ListedForcesG96BondTest (0 ms) 5: [ RUN ] TwoCenter.ListedForcesCubicBondTest 5: [ OK ] TwoCenter.ListedForcesCubicBondTest (0 ms) 5: [ RUN ] TwoCenter.ListedForcesMorseBondTest 5: [ OK ] TwoCenter.ListedForcesMorseBondTest (0 ms) 5: [ RUN ] TwoCenter.ListedForcesFeneBondTest 5: [ OK ] TwoCenter.ListedForcesFeneBondTest (0 ms) 5: [----------] 5 tests from TwoCenter (0 ms total) 5: 5: [----------] 5 tests from ListedExampleData 5: [ RUN ] ListedExampleData.ComputeHarmonicBondForces 5: [ OK ] ListedExampleData.ComputeHarmonicBondForces (0 ms) 5: [ RUN ] ListedExampleData.ComputeHarmonicBondEnergies 5: [ OK ] ListedExampleData.ComputeHarmonicBondEnergies (0 ms) 5: [ RUN ] ListedExampleData.ComputeHarmonicAngleForces 5: [ OK ] ListedExampleData.ComputeHarmonicAngleForces (0 ms) 5: [ RUN ] ListedExampleData.CanReduceForces 5: [ OK ] ListedExampleData.CanReduceForces (0 ms) 5: [ RUN ] ListedExampleData.CanReduceEnergies 5: [ OK ] ListedExampleData.CanReduceEnergies (0 ms) 5: [----------] 5 tests from ListedExampleData (0 ms total) 5: 5: [----------] 1 test from LinearChainDataFixture 5: [ RUN ] LinearChainDataFixture.Multithreading 5: [ OK ] LinearChainDataFixture.Multithreading (23 ms) 5: [----------] 1 test from LinearChainDataFixture (23 ms total) 5: 5: [----------] 2 tests from ListedShims 5: [ RUN ] ListedShims.ParameterConversion 5: [ OK ] ListedShims.ParameterConversion (0 ms) 5: [ RUN ] ListedShims.GmxToNblibConversion 5: [ OK ] ListedShims.GmxToNblibConversion (0 ms) 5: [----------] 2 tests from ListedShims (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0, where TypeParam = nblib::TwoParameterInteraction 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1, where TypeParam = nblib::G96BondType 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2, where TypeParam = nblib::CubicBondType 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3, where TypeParam = nblib::MorseBondType 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4, where TypeParam = nblib::TwoParameterInteraction 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5, where TypeParam = nblib::AngleInteractionType 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6, where TypeParam = nblib::CosineParamAngle 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7, where TypeParam = nblib::CosineParamAngle 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7 (3 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8, where TypeParam = nblib::TwoParameterInteraction 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9, where TypeParam = nblib::QuarticAngle 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10, where TypeParam = nblib::CrossBondBond 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11, where TypeParam = nblib::CrossBondAngle 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12, where TypeParam = nblib::ProperDihedral 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12 (0 ms total) 5: 5: [----------] 1 test from ListedTransformations 5: [ RUN ] ListedTransformations.SortInteractionIndices 5: [ OK ] ListedTransformations.SortInteractionIndices (0 ms) 5: [----------] 1 test from ListedTransformations (0 ms total) 5: 5: [----------] Global test environment tear-down 5: [==========] 44 tests from 22 test suites ran. (58 ms total) 5: [ PASSED ] 44 tests. 5/91 Test #5: NbLibListedForcesTests ....................... Passed 0.40 sec test 6 Start 6: NbLibSamplesTestArgon 6: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/argon-forces-integration 6: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/samples 6: Test timeout computed to be: 1500 6: initial forces on particle 0: x 0.000000 y 0.000000 z 0.000000 6: final forces on particle 0: x -0.412993 y -1.098256 z -0.113191 6: initial position of particle 0: x 0.794000 y 1.439000 z 0.610000 6: final position of particle 0: x 0.789162 y 1.271508 z 0.819867 6/91 Test #6: NbLibSamplesTestArgon ........................ Passed 0.30 sec test 7 Start 7: NbLibSamplesTestMethaneWater 7: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/methane-water-integration 7: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/samples 7: Test timeout computed to be: 1500 7: initial position of particle 0: x 0.005000 y 0.600000 z 0.244000 7: final position of particle 9: x 77.358398 y 5.324913 z -80.600098 7/91 Test #7: NbLibSamplesTestMethaneWater ................. Passed 0.31 sec test 8 Start 8: NbLibUtilTests 8: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/nblib-util-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/NbLibUtilTests.xml" 8: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/util/tests 8: Test timeout computed to be: 30 8: [==========] Running 16 tests from 2 test suites. 8: [----------] Global test environment set-up. 8: [----------] 6 tests from NBlibTest 8: [ RUN ] NBlibTest.isRealValued 8: [ OK ] NBlibTest.isRealValued (0 ms) 8: [ RUN ] NBlibTest.checkNumericValuesHasNan 8: [ OK ] NBlibTest.checkNumericValuesHasNan (0 ms) 8: [ RUN ] NBlibTest.checkNumericValuesHasInf 8: [ OK ] NBlibTest.checkNumericValuesHasInf (0 ms) 8: [ RUN ] NBlibTest.GeneratedVelocitiesAreCorrect 8: Velocities were taken from a Maxwell distribution at 300 K 8: [ OK ] NBlibTest.GeneratedVelocitiesAreCorrect (0 ms) 8: [ RUN ] NBlibTest.generateVelocitySize 8: Velocities were taken from a Maxwell distribution at 300 K 8: [ OK ] NBlibTest.generateVelocitySize (0 ms) 8: [ RUN ] NBlibTest.generateVelocityCheckNumbers 8: Velocities were taken from a Maxwell distribution at 300 K 8: [ OK ] NBlibTest.generateVelocityCheckNumbers (0 ms) 8: [----------] 6 tests from NBlibTest (0 ms total) 8: 8: [----------] 10 tests from NblibTraitsUtils 8: [ RUN ] NblibTraitsUtils.FuseTwo 8: [ OK ] NblibTraitsUtils.FuseTwo (0 ms) 8: [ RUN ] NblibTraitsUtils.Fuse 8: [ OK ] NblibTraitsUtils.Fuse (0 ms) 8: [ RUN ] NblibTraitsUtils.Repeat 8: [ OK ] NblibTraitsUtils.Repeat (0 ms) 8: [ RUN ] NblibTraitsUtils.FindIndexTuple1 8: [ OK ] NblibTraitsUtils.FindIndexTuple1 (0 ms) 8: [ RUN ] NblibTraitsUtils.FindIndexTuple2 8: [ OK ] NblibTraitsUtils.FindIndexTuple2 (0 ms) 8: [ RUN ] NblibTraitsUtils.FindIndexTypeList1 8: [ OK ] NblibTraitsUtils.FindIndexTypeList1 (0 ms) 8: [ RUN ] NblibTraitsUtils.FindIndexTypeList2 8: [ OK ] NblibTraitsUtils.FindIndexTypeList2 (0 ms) 8: [ RUN ] NblibTraitsUtils.Contains 8: [ OK ] NblibTraitsUtils.Contains (0 ms) 8: [ RUN ] NblibTraitsUtils.FindIndexTupleRepeated 8: [ OK ] NblibTraitsUtils.FindIndexTupleRepeated (0 ms) 8: [ RUN ] NblibTraitsUtils.FindIndexTypeListRepeated 8: [ OK ] NblibTraitsUtils.FindIndexTypeListRepeated (0 ms) 8: [----------] 10 tests from NblibTraitsUtils (0 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 16 tests from 2 test suites ran. (0 ms total) 8: [ PASSED ] 16 tests. 8/91 Test #8: NbLibUtilTests ............................... Passed 0.37 sec test 9 Start 9: NbLibSetupTests 9: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/nblib-setup-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/NbLibSetupTests.xml" 9: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests 9: Test timeout computed to be: 600 9: [==========] Running 57 tests from 3 test suites. 9: [----------] Global test environment set-up. 9: [----------] 41 tests from NBlibTest 9: [ RUN ] NBlibTest.CubicBoxCannotHaveNaN 9: [ OK ] NBlibTest.CubicBoxCannotHaveNaN (0 ms) 9: [ RUN ] NBlibTest.CubicBoxCannotHaveInf 9: [ OK ] NBlibTest.CubicBoxCannotHaveInf (0 ms) 9: [ RUN ] NBlibTest.RectangularBoxCannotHaveNaN 9: [ OK ] NBlibTest.RectangularBoxCannotHaveNaN (0 ms) 9: [ RUN ] NBlibTest.RectangularBoxCannotHaveInf 9: [ OK ] NBlibTest.RectangularBoxCannotHaveInf (0 ms) 9: [ RUN ] NBlibTest.CubicBoxWorks 9: [ OK ] NBlibTest.CubicBoxWorks (0 ms) 9: [ RUN ] NBlibTest.BoxEqual 9: [ OK ] NBlibTest.BoxEqual (0 ms) 9: [ RUN ] NBlibTest.NonBondedForceParamsCorrect 9: [ OK ] NBlibTest.NonBondedForceParamsCorrect (0 ms) 9: [ RUN ] NBlibTest.CanMergeInteractions 9: [ OK ] NBlibTest.CanMergeInteractions (0 ms) 9: [ RUN ] NBlibTest.ParticleTypeNameCanBeConstructed 9: [ OK ] NBlibTest.ParticleTypeNameCanBeConstructed (0 ms) 9: [ RUN ] NBlibTest.ParticleTypeMassCanBeConstructed 9: [ OK ] NBlibTest.ParticleTypeMassCanBeConstructed (0 ms) 9: [ RUN ] NBlibTest.PbcHolderWorks 9: [ OK ] NBlibTest.PbcHolderWorks (0 ms) 9: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName 9: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName (0 ms) 9: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName 9: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName (0 ms) 9: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName 9: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName (0 ms) 9: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName 9: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName (0 ms) 9: [ RUN ] NBlibTest.CanGetNumParticlesInMolecule 9: [ OK ] NBlibTest.CanGetNumParticlesInMolecule (0 ms) 9: [ RUN ] NBlibTest.CanConstructExclusionListFromNames 9: [ OK ] NBlibTest.CanConstructExclusionListFromNames (0 ms) 9: [ RUN ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed 9: [ OK ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed (0 ms) 9: [ RUN ] NBlibTest.AtWorks 9: [ OK ] NBlibTest.AtWorks (0 ms) 9: [ RUN ] NBlibTest.AtThrows 9: [ OK ] NBlibTest.AtThrows (0 ms) 9: [ RUN ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass 9: [ OK ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass (0 ms) 9: [ RUN ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass 9: [ OK ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass (0 ms) 9: [ RUN ] NBlibTest.MoleculeNoThrowsSameParticleTypeName 9: [ OK ] NBlibTest.MoleculeNoThrowsSameParticleTypeName (0 ms) 9: [ RUN ] NBlibTest.CanAddInteractions 9: [ OK ] NBlibTest.CanAddInteractions (0 ms) 9: [ RUN ] NBlibTest.CanAddUreyBradley 9: [ OK ] NBlibTest.CanAddUreyBradley (0 ms) 9: [ RUN ] NBlibTest.TopologyHasNumParticles 9: [ OK ] NBlibTest.TopologyHasNumParticles (0 ms) 9: [ RUN ] NBlibTest.TopologyHasCharges 9: [ OK ] NBlibTest.TopologyHasCharges (0 ms) 9: [ RUN ] NBlibTest.TopologyHasMasses 9: [ OK ] NBlibTest.TopologyHasMasses (0 ms) 9: [ RUN ] NBlibTest.TopologyHasParticleTypes 9: [ OK ] NBlibTest.TopologyHasParticleTypes (0 ms) 9: [ RUN ] NBlibTest.TopologyHasParticleTypeIds 9: [ OK ] NBlibTest.TopologyHasParticleTypeIds (0 ms) 9: [ RUN ] NBlibTest.TopologyThrowsIdenticalParticleType 9: [ OK ] NBlibTest.TopologyThrowsIdenticalParticleType (0 ms) 9: [ RUN ] NBlibTest.TopologyHasExclusions 9: [ OK ] NBlibTest.TopologyHasExclusions (0 ms) 9: [ RUN ] NBlibTest.TopologyHasSequencing 9: [ OK ] NBlibTest.TopologyHasSequencing (0 ms) 9: [ RUN ] NBlibTest.TopologyCanAggregateBonds 9: [ OK ] NBlibTest.TopologyCanAggregateBonds (0 ms) 9: [ RUN ] NBlibTest.TopologyCanSequencePairIDs 9: [ OK ] NBlibTest.TopologyCanSequencePairIDs (0 ms) 9: [ RUN ] NBlibTest.TopologySequenceIdThrows 9: No particle O-Atom in residue SOL in molecule SOL found 9: [ OK ] NBlibTest.TopologySequenceIdThrows (0 ms) 9: [ RUN ] NBlibTest.TopologyCanEliminateDuplicateBonds 9: [ OK ] NBlibTest.TopologyCanEliminateDuplicateBonds (0 ms) 9: [ RUN ] NBlibTest.TopologyListedInteractions 9: [ OK ] NBlibTest.TopologyListedInteractions (0 ms) 9: [ RUN ] NBlibTest.TopologyListedInteractionsMultipleTypes 9: [ OK ] NBlibTest.TopologyListedInteractionsMultipleTypes (0 ms) 9: [ RUN ] NBlibTest.TopologyInvalidParticleInInteractionThrows 9: No particle Iron in residue SOL in molecule SOL found 9: [ OK ] NBlibTest.TopologyInvalidParticleInInteractionThrows (0 ms) 9: [ RUN ] NBlibTest.toGmxExclusionBlockWorks 9: [ OK ] NBlibTest.toGmxExclusionBlockWorks (0 ms) 9: [----------] 41 tests from NBlibTest (1 ms total) 9: 9: [----------] 15 tests from NbnxmSetupTest 9: [ RUN ] NbnxmSetupTest.findNumEnergyGroups 9: [ OK ] NbnxmSetupTest.findNumEnergyGroups (0 ms) 9: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto 9: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto (0 ms) 9: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumNo 9: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumNo (0 ms) 9: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM 9: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM (0 ms) 9: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM 9: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM (0 ms) 9: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsAuto 9: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsAuto (0 ms) 9: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsCount 9: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsCount (0 ms) 9: [ RUN ] NbnxmSetupTest.canCreateKernelSetupPlain 9: [ OK ] NbnxmSetupTest.canCreateKernelSetupPlain (0 ms) 9: [ RUN ] NbnxmSetupTest.canCreateParticleInfoAllVdv 9: [ OK ] NbnxmSetupTest.canCreateParticleInfoAllVdv (0 ms) 9: [ RUN ] NbnxmSetupTest.ewaldCoeffWorks 9: [ OK ] NbnxmSetupTest.ewaldCoeffWorks (0 ms) 9: [ RUN ] NbnxmSetupTest.updateForcerecWorks 9: [ OK ] NbnxmSetupTest.updateForcerecWorks (0 ms) 9: [ RUN ] NbnxmSetupTest.canCheckKernelSetup 9: [ OK ] NbnxmSetupTest.canCheckKernelSetup (0 ms) 9: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM 9: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM (0 ms) 9: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM 9: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM (0 ms) 9: [ RUN ] NbnxmSetupTest.CanCreateNbnxmCPU 9: [ OK ] NbnxmSetupTest.CanCreateNbnxmCPU (0 ms) 9: [----------] 15 tests from NbnxmSetupTest (0 ms total) 9: 9: [----------] 1 test from VirialsTest 9: [ RUN ] VirialsTest.computeVirialTensorWorks 9: [ OK ] VirialsTest.computeVirialTensorWorks (0 ms) 9: [----------] 1 test from VirialsTest (0 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 57 tests from 3 test suites ran. (1 ms total) 9: [ PASSED ] 57 tests. 9/91 Test #9: NbLibSetupTests .............................. Passed 0.40 sec test 10 Start 10: NbLibTprTests 10: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/nblib-tpr-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/NbLibTprTests.xml" 10: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests 10: Test timeout computed to be: 30 10: [==========] Running 4 tests from 1 test suite. 10: [----------] Global test environment set-up. 10: [----------] 4 tests from TprReaderTest 10: [ RUN ] TprReaderTest.SimDBTprIsCreated 10: 10: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 10: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 10: that with the Verlet scheme, nstlist has no effect on the accuracy of 10: your simulation. 10: 10: 10: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 10: Setting nstcalcenergy (100) equal to nstenergy (4) 10: 10: Number of degrees of freedom in T-Coupling group System is 33.00 10: 10: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 10: NVE simulation: will use the initial temperature of 68.810 K for 10: determining the Verlet buffer size 10: 10: 10: There were 3 NOTEs 10: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 10: Generated 1 of the 1 non-bonded parameter combinations 10: 10: Excluding 1 bonded neighbours molecule type 'Argon' 10: 10: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 10: 10: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 10: 10: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 10: 10: Note that mdrun will redetermine rlist based on the actual pair-list setup 10: 10: This run will generate roughly 0 Mb of data 10: [ OK ] TprReaderTest.SimDBTprIsCreated (43 ms) 10: [ RUN ] TprReaderTest.Spc2Reads 10: 10: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 10: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 10: that with the Verlet scheme, nstlist has no effect on the accuracy of 10: your simulation. 10: 10: 10: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 10: Setting nstcalcenergy (100) equal to nstenergy (4) 10: 10: Generating 1-4 interactions: fudge = 0.5 10: Number of degrees of freedom in T-Coupling group System is 9.00 10: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 10: 10: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 10: NVE simulation: will use the initial temperature of 2573.591 K for 10: determining the Verlet buffer size 10: 10: 10: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 10: You are using a plain Coulomb cut-off, which might produce artifacts. 10: You might want to consider using PME electrostatics. 10: 10: 10: 10: There were 4 NOTEs 10: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 10: Generated 3 of the 3 non-bonded parameter combinations 10: 10: Generated 3 of the 3 1-4 parameter combinations 10: 10: Excluding 2 bonded neighbours molecule type 'SOL' 10: 10: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 10: 10: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 10: 10: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 10: 10: Note that mdrun will redetermine rlist based on the actual pair-list setup 10: 10: This run will generate roughly 0 Mb of data 10: [ OK ] TprReaderTest.Spc2Reads (18 ms) 10: [ RUN ] TprReaderTest.ArgonImportedDataIsCorrect 10: 10: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 10: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 10: that with the Verlet scheme, nstlist has no effect on the accuracy of 10: your simulation. 10: 10: 10: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 10: Setting nstcalcenergy (100) equal to nstenergy (4) 10: 10: Number of degrees of freedom in T-Coupling group System is 33.00 10: 10: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 10: NVE simulation: will use the initial temperature of 68.810 K for 10: determining the Verlet buffer size 10: 10: 10: There were 3 NOTEs 10: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 10: Generated 1 of the 1 non-bonded parameter combinations 10: 10: Excluding 1 bonded neighbours molecule type 'Argon' 10: 10: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 10: 10: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 10: 10: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 10: 10: Note that mdrun will redetermine rlist based on the actual pair-list setup 10: 10: This run will generate roughly 0 Mb of data 10: [ OK ] TprReaderTest.ArgonImportedDataIsCorrect (19 ms) 10: [ RUN ] TprReaderTest.FCfromTprDataWorks 10: 10: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 10: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 10: that with the Verlet scheme, nstlist has no effect on the accuracy of 10: your simulation. 10: 10: 10: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 10: Setting nstcalcenergy (100) equal to nstenergy (4) 10: 10: Number of degrees of freedom in T-Coupling group System is 33.00 10: 10: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 10: NVE simulation: will use the initial temperature of 68.810 K for 10: determining the Verlet buffer size 10: 10: 10: There were 3 NOTEs 10: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 10: Generated 1 of the 1 non-bonded parameter combinations 10: 10: Excluding 1 bonded neighbours molecule type 'Argon' 10: 10: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 10: 10: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 10: 10: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 10: 10: Note that mdrun will redetermine rlist based on the actual pair-list setup 10: 10: This run will generate roughly 0 Mb of data 10: [ OK ] TprReaderTest.FCfromTprDataWorks (15 ms) 10: [----------] 4 tests from TprReaderTest (100 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 4 tests from 1 test suite ran. (133 ms total) 10: [ PASSED ] 4 tests. 10/91 Test #10: NbLibTprTests ................................ Passed 0.45 sec test 11 Start 11: NbLibIntegrationTests 11: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/nblib-integration-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/NbLibIntegrationTests.xml" 11: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests 11: Test timeout computed to be: 600 11: [==========] Running 20 tests from 1 test suite. 11: [----------] Global test environment set-up. 11: [----------] 20 tests from NBlibTest 11: [ RUN ] NBlibTest.GmxForceCalculatorCanCompute 11: [ OK ] NBlibTest.GmxForceCalculatorCanCompute (0 ms) 11: [ RUN ] NBlibTest.ArgonVirialsAreCorrect 11: [ OK ] NBlibTest.ArgonVirialsAreCorrect (0 ms) 11: [ RUN ] NBlibTest.ArgonEnergiesAreCorrect 11: [ OK ] NBlibTest.ArgonEnergiesAreCorrect (0 ms) 11: [ RUN ] NBlibTest.SpcMethanolEnergiesAreCorrect 11: [ OK ] NBlibTest.SpcMethanolEnergiesAreCorrect (0 ms) 11: [ RUN ] NBlibTest.SpcMethanolForcesAreCorrect 11: [ OK ] NBlibTest.SpcMethanolForcesAreCorrect (0 ms) 11: [ RUN ] NBlibTest.ExpectedNumberOfForces 11: [ OK ] NBlibTest.ExpectedNumberOfForces (0 ms) 11: [ RUN ] NBlibTest.CanIntegrateSystem 11: [ OK ] NBlibTest.CanIntegrateSystem (0 ms) 11: [ RUN ] NBlibTest.UpdateChangesForces 11: [ OK ] NBlibTest.UpdateChangesForces (0 ms) 11: [ RUN ] NBlibTest.ArgonOplsaForcesAreCorrect 11: [ OK ] NBlibTest.ArgonOplsaForcesAreCorrect (0 ms) 11: [ RUN ] NBlibTest.ArgonGromos43A1ForcesAreCorrect 11: [ OK ] NBlibTest.ArgonGromos43A1ForcesAreCorrect (0 ms) 11: [ RUN ] NBlibTest.CanConstructSimulationState 11: [ OK ] NBlibTest.CanConstructSimulationState (0 ms) 11: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateNAN 11: [ OK ] NBlibTest.SimulationStateThrowsCoordinateNAN (0 ms) 11: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateINF 11: [ OK ] NBlibTest.SimulationStateThrowsCoordinateINF (0 ms) 11: [ RUN ] NBlibTest.SimulationStateThrowsVelocityNAN 11: [ OK ] NBlibTest.SimulationStateThrowsVelocityNAN (0 ms) 11: [ RUN ] NBlibTest.SimulationStateThrowsVelocityINF 11: [ OK ] NBlibTest.SimulationStateThrowsVelocityINF (0 ms) 11: [ RUN ] NBlibTest.SimulationStateCanMove 11: [ OK ] NBlibTest.SimulationStateCanMove (0 ms) 11: [ RUN ] NBlibTest.SimulationStateCanAssign 11: [ OK ] NBlibTest.SimulationStateCanAssign (0 ms) 11: [ RUN ] NBlibTest.SimulationStateHasBox 11: [ OK ] NBlibTest.SimulationStateHasBox (0 ms) 11: [ RUN ] NBlibTest.SimulationStateHasCorrectCoordinates 11: [ OK ] NBlibTest.SimulationStateHasCorrectCoordinates (0 ms) 11: [ RUN ] NBlibTest.SimulationStateHasCorrectVelocities 11: [ OK ] NBlibTest.SimulationStateHasCorrectVelocities (0 ms) 11: [----------] 20 tests from NBlibTest (10 ms total) 11: 11: [----------] Global test environment tear-down 11: [==========] 20 tests from 1 test suite ran. (10 ms total) 11: [ PASSED ] 20 tests. 11/91 Test #11: NbLibIntegrationTests ........................ Passed 0.34 sec test 12 Start 12: NbLibIntegratorTests 12: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/nblib-integrator-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/NbLibIntegratorTests.xml" 12: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests 12: Test timeout computed to be: 600 12: [==========] Running 1 test from 1 test suite. 12: [----------] Global test environment set-up. 12: [----------] 1 test from NBlibTest 12: [ RUN ] NBlibTest.IntegratorWorks 12: [ OK ] NBlibTest.IntegratorWorks (0 ms) 12: [----------] 1 test from NBlibTest (0 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 1 test from 1 test suite ran. (0 ms total) 12: [ PASSED ] 1 test. 12/91 Test #12: NbLibIntegratorTests ......................... Passed 0.35 sec test 13 Start 13: TestUtilsUnitTests 13: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/testutils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/TestUtilsUnitTests.xml" 13: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/testutils/tests 13: Test timeout computed to be: 30 13: [==========] Running 59 tests from 5 test suites. 13: [----------] Global test environment set-up. 13: [----------] 10 tests from InteractiveTestHelperTest 13: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 13: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (1 ms) 13: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 13: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (0 ms) 13: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 13: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (0 ms) 13: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 13: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (0 ms) 13: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 13: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (0 ms) 13: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 13: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (0 ms) 13: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 13: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (0 ms) 13: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 13: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (0 ms) 13: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 13: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (0 ms) 13: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 13: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (0 ms) 13: [----------] 10 tests from InteractiveTestHelperTest (7 ms total) 13: 13: [----------] 34 tests from ReferenceDataTest 13: [ RUN ] ReferenceDataTest.HandlesSimpleData 13: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 13: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 13: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesStringBlockData 13: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesVectorData 13: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesSequenceData 13: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 13: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesIncorrectData 13: [ OK ] ReferenceDataTest.HandlesIncorrectData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 13: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesMissingData 13: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesUncheckedData 13: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 13: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 13: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesAnys 13: [ OK ] ReferenceDataTest.HandlesAnys (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 13: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 13: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 13: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue 13: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType 13: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 13: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 13: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 13: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 13: [ OK ] ReferenceDataTest.HandlesEmptyStrings (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 13: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 13: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 13: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (2 ms) 13: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 13: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 13: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesReadingValues 13: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 13: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 13: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 13: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 13: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 13: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (0 ms) 13: [----------] 34 tests from ReferenceDataTest (12 ms total) 13: 13: [----------] 7 tests from FloatingPointDifferenceTest 13: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 13: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 13: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 13: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 13: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 13: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 13: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 13: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 13: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 13: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 13: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 13: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 13: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 13: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 13: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 13: 13: [----------] 4 tests from FloatingPointToleranceTest 13: [ RUN ] FloatingPointToleranceTest.UlpTolerance 13: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 13: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 13: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 13: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 13: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 13: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 13: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 13: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 13: 13: [----------] 4 tests from XvgTests 13: [ RUN ] XvgTests.CreateFile 13: [ OK ] XvgTests.CreateFile (0 ms) 13: [ RUN ] XvgTests.CheckMissing 13: [ OK ] XvgTests.CheckMissing (0 ms) 13: [ RUN ] XvgTests.CheckExtra 13: [ OK ] XvgTests.CheckExtra (0 ms) 13: [ RUN ] XvgTests.ReadIncorrect 13: [ OK ] XvgTests.ReadIncorrect (0 ms) 13: [----------] 4 tests from XvgTests (1 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 59 tests from 5 test suites ran. (21 ms total) 13: [ PASSED ] 59 tests. 13/91 Test #13: TestUtilsUnitTests ........................... Passed 0.36 sec test 14 Start 14: TestUtilsMpiUnitTests 14: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/testutils-mpi-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/TestUtilsMpiUnitTests.xml" 14: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/testutils/tests 14: Test timeout computed to be: 30 14: [==========] Running 1 test from 1 test suite. 14: [----------] Global test environment set-up. 14: [----------] 1 test from MpiSelfTest 14: [ RUN ] MpiSelfTest.Runs 14: [ OK ] MpiSelfTest.Runs (2 ms) 14: [----------] 1 test from MpiSelfTest (2 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 1 test from 1 test suite ran. (2 ms total) 14: [ PASSED ] 1 test. 14/91 Test #14: TestUtilsMpiUnitTests ........................ Passed 0.48 sec test 15 Start 15: UtilityUnitTests 15: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/utility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/UtilityUnitTests.xml" 15: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests 15: Test timeout computed to be: 30 15: [==========] Running 400 tests from 62 test suites. 15: [----------] Global test environment set-up. 15: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 15: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 15: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 15: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 15: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/0.Move 15: [ OK ] AllocatorTest/0.Move (0 ms) 15: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 15: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 15: [----------] 5 tests from AllocatorTest/0 (0 ms total) 15: 15: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 15: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 15: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 15: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 15: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/1.Move 15: [ OK ] AllocatorTest/1.Move (0 ms) 15: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 15: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 15: [----------] 5 tests from AllocatorTest/1 (0 ms total) 15: 15: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 15: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 15: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 15: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 15: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/2.Move 15: [ OK ] AllocatorTest/2.Move (0 ms) 15: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 15: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 15: [----------] 5 tests from AllocatorTest/2 (0 ms total) 15: 15: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 15: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 15: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 15: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 15: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/3.Move 15: [ OK ] AllocatorTest/3.Move (0 ms) 15: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 15: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 15: [----------] 5 tests from AllocatorTest/3 (0 ms total) 15: 15: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 15: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 15: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 15: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 15: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/4.Move 15: [ OK ] AllocatorTest/4.Move (0 ms) 15: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 15: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 15: [----------] 5 tests from AllocatorTest/4 (0 ms total) 15: 15: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> 15: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 15: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 15: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 15: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/5.Move 15: [ OK ] AllocatorTest/5.Move (0 ms) 15: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 15: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 15: [----------] 5 tests from AllocatorTest/5 (0 ms total) 15: 15: [----------] 1 test from AllocatorUntypedTest 15: [ RUN ] AllocatorUntypedTest.Comparison 15: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 15: [----------] 1 test from AllocatorUntypedTest (0 ms total) 15: 15: [----------] 4 tests from EmptyArrayRefTest 15: [ RUN ] EmptyArrayRefTest.IsEmpty 15: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 15: [ RUN ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty 15: [ OK ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty (0 ms) 15: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr 15: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr (0 ms) 15: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull 15: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull (0 ms) 15: [----------] 4 tests from EmptyArrayRefTest (0 ms total) 15: 15: [----------] 1 test from EmptyConstArrayRefTest 15: [ RUN ] EmptyConstArrayRefTest.IsEmpty 15: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 15: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/8 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/14 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 15: 15: [----------] 8 tests from BoolType 15: [ RUN ] BoolType.ImplicitConversion 15: [ OK ] BoolType.ImplicitConversion (0 ms) 15: [ RUN ] BoolType.FalseByDefault 15: [ OK ] BoolType.FalseByDefault (0 ms) 15: [ RUN ] BoolType.Assignment 15: [ OK ] BoolType.Assignment (0 ms) 15: [ RUN ] BoolType.Copy 15: [ OK ] BoolType.Copy (0 ms) 15: [ RUN ] BoolType.ArrayRefCanBeCreated 15: [ OK ] BoolType.ArrayRefCanBeCreated (0 ms) 15: [ RUN ] BoolType.CanBeCastToBool 15: [ OK ] BoolType.CanBeCastToBool (0 ms) 15: [ RUN ] BoolType.HasSizeOfBool 15: [ OK ] BoolType.HasSizeOfBool (0 ms) 15: [ RUN ] BoolType.HasAlignmentOfBool 15: [ OK ] BoolType.HasAlignmentOfBool (0 ms) 15: [----------] 8 tests from BoolType (0 ms total) 15: 15: [----------] 4 tests from ArrayRefFromBoolTypeVector 15: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructEmpty 15: [ OK ] ArrayRefFromBoolTypeVector.CanConstructEmpty (0 ms) 15: [ RUN ] ArrayRefFromBoolTypeVector.Works 15: [ OK ] ArrayRefFromBoolTypeVector.Works (0 ms) 15: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty 15: [ OK ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty (0 ms) 15: [ RUN ] ArrayRefFromBoolTypeVector.ConstWorks 15: [ OK ] ArrayRefFromBoolTypeVector.ConstWorks (0 ms) 15: [----------] 4 tests from ArrayRefFromBoolTypeVector (0 ms total) 15: 15: [----------] 7 tests from CStringUtilityTest 15: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison 15: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms) 15: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength 15: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms) 15: [ RUN ] CStringUtilityTest.strip_comment 15: [ OK ] CStringUtilityTest.strip_comment (0 ms) 15: [ RUN ] CStringUtilityTest.upstring 15: [ OK ] CStringUtilityTest.upstring (0 ms) 15: [ RUN ] CStringUtilityTest.ltrim 15: [ OK ] CStringUtilityTest.ltrim (0 ms) 15: [ RUN ] CStringUtilityTest.rtrim 15: [ OK ] CStringUtilityTest.rtrim (0 ms) 15: [ RUN ] CStringUtilityTest.trim 15: [ OK ] CStringUtilityTest.trim (0 ms) 15: [----------] 7 tests from CStringUtilityTest (0 ms total) 15: 15: [----------] 2 tests from DefaultInitializationAllocator 15: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization 15: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms) 15: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization 15: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms) 15: [----------] 2 tests from DefaultInitializationAllocator (0 ms total) 15: 15: [----------] 4 tests from EnumerationHelpersTest 15: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks 15: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms) 15: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks 15: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms) 15: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe 15: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms) 15: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks 15: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms) 15: [----------] 4 tests from EnumerationHelpersTest (0 ms total) 15: 15: [----------] 9 tests from FixedCapacityVectorTest 15: [ RUN ] FixedCapacityVectorTest.IsEmpty 15: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms) 15: [ RUN ] FixedCapacityVectorTest.PushWorks 15: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.PopWorks 15: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.ClearWorks 15: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks 15: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.AtThrows 15: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms) 15: [ RUN ] FixedCapacityVectorTest.IteratorWorks 15: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks 15: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks 15: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms) 15: [----------] 9 tests from FixedCapacityVectorTest (0 ms total) 15: 15: [----------] 5 tests from InMemorySerializerTest 15: [ RUN ] InMemorySerializerTest.Roundtrip 15: [ OK ] InMemorySerializerTest.Roundtrip (0 ms) 15: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap 15: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms) 15: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap 15: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms) 15: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap 15: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms) 15: [ RUN ] InMemorySerializerTest.SizeIsCorrect 15: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms) 15: [----------] 5 tests from InMemorySerializerTest (0 ms total) 15: 15: [----------] 4 tests from KeyValueTreeSerializerTest 15: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 15: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms) 15: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 15: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms) 15: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 15: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms) 15: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 15: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms) 15: [----------] 4 tests from KeyValueTreeSerializerTest (0 ms total) 15: 15: [----------] 7 tests from TreeValueTransformTest 15: [ RUN ] TreeValueTransformTest.SimpleTransforms 15: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms) 15: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 15: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms) 15: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 15: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms) 15: [ RUN ] TreeValueTransformTest.ObjectFromString 15: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms) 15: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 15: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms) 15: [ RUN ] TreeValueTransformTest.ScopedTransformRules 15: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) 15: [ RUN ] TreeValueTransformTest.CanAssignUserMultiValue 15: [ OK ] TreeValueTransformTest.CanAssignUserMultiValue (0 ms) 15: [----------] 7 tests from TreeValueTransformTest (0 ms total) 15: 15: [----------] 1 test from TreeValueTransformErrorTest 15: [ RUN ] TreeValueTransformErrorTest.ConversionError 15: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms) 15: [----------] 1 test from TreeValueTransformErrorTest (0 ms total) 15: 15: [----------] 9 tests from ListOfLists 15: [ RUN ] ListOfLists.EmptyListOfListsWorks 15: [ OK ] ListOfLists.EmptyListOfListsWorks (0 ms) 15: [ RUN ] ListOfLists.AppendWorks 15: [ OK ] ListOfLists.AppendWorks (0 ms) 15: [ RUN ] ListOfLists.EmptyListWorks 15: [ OK ] ListOfLists.EmptyListWorks (0 ms) 15: [ RUN ] ListOfLists.AppendAccessWorks 15: [ OK ] ListOfLists.AppendAccessWorks (0 ms) 15: [ RUN ] ListOfLists.ClearWorks 15: [ OK ] ListOfLists.ClearWorks (0 ms) 15: [ RUN ] ListOfLists.OutOfRangeAccessThrows 15: [ OK ] ListOfLists.OutOfRangeAccessThrows (0 ms) 15: [ RUN ] ListOfLists.FrontAndBackWork 15: [ OK ] ListOfLists.FrontAndBackWork (0 ms) 15: [ RUN ] ListOfLists.ExtractsAndRestores 15: [ OK ] ListOfLists.ExtractsAndRestores (0 ms) 15: [ RUN ] ListOfLists.AppendsListOfListsWithOffset 15: [ OK ] ListOfLists.AppendsListOfListsWithOffset (0 ms) 15: [----------] 9 tests from ListOfLists (0 ms total) 15: 15: [----------] 7 tests from LoggerTest 15: [ RUN ] LoggerTest.EmptyLoggerWorks 15: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 15: [ RUN ] LoggerTest.LogsToStream 15: [ OK ] LoggerTest.LogsToStream (0 ms) 15: [ RUN ] LoggerTest.LogsToFile 15: [ OK ] LoggerTest.LogsToFile (0 ms) 15: [ RUN ] LoggerTest.LevelFilteringWorks 15: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) 15: [ RUN ] LoggerTest.LogsToMultipleStreams 15: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) 15: [ RUN ] LoggerTest.LogsToMultipleFiles 15: [ OK ] LoggerTest.LogsToMultipleFiles (0 ms) 15: [ RUN ] LoggerTest.LogsToStreamAndFile 15: [ OK ] LoggerTest.LogsToStreamAndFile (0 ms) 15: [----------] 7 tests from LoggerTest (1 ms total) 15: 15: [----------] 7 tests from MessageStringCollectorTest 15: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext 15: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext (0 ms) 15: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext 15: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext (0 ms) 15: [ RUN ] MessageStringCollectorTest.CanAddStringMessages 15: [ OK ] MessageStringCollectorTest.CanAddStringMessages (0 ms) 15: [ RUN ] MessageStringCollectorTest.CanAddCharMessagesConditionally 15: [ OK ] MessageStringCollectorTest.CanAddCharMessagesConditionally (0 ms) 15: [ RUN ] MessageStringCollectorTest.CanAddStringMessagesConditionally 15: [ OK ] MessageStringCollectorTest.CanAddStringMessagesConditionally (0 ms) 15: [ RUN ] MessageStringCollectorTest.CanMoveConstruct 15: [ OK ] MessageStringCollectorTest.CanMoveConstruct (0 ms) 15: [ RUN ] MessageStringCollectorTest.CanMoveAssign 15: [ OK ] MessageStringCollectorTest.CanMoveAssign (0 ms) 15: [----------] 7 tests from MessageStringCollectorTest (0 ms total) 15: 15: [----------] 1 test from PathTest 15: [ RUN ] PathTest.StripSourcePrefixWorks 15: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 15: [----------] 1 test from PathTest (0 ms total) 15: 15: [----------] 2 tests from PhysicalNodeCommunicatorTest 15: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 15: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 15: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 15: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 15: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 15: 15: [----------] 5 tests from Range 15: [ RUN ] Range.EmptyRangeWorks 15: [ OK ] Range.EmptyRangeWorks (0 ms) 15: [ RUN ] Range.NonEmptyRangeWorks 15: [ OK ] Range.NonEmptyRangeWorks (0 ms) 15: [ RUN ] Range.BeginEnd 15: [ OK ] Range.BeginEnd (0 ms) 15: [ RUN ] Range.IsInRangeWorks 15: [ OK ] Range.IsInRangeWorks (0 ms) 15: [ RUN ] Range.IteratorWorks 15: [ OK ] Range.IteratorWorks (0 ms) 15: [----------] 5 tests from Range (0 ms total) 15: 15: [----------] 7 tests from StringConvert 15: [ RUN ] StringConvert.NoResultFromEptyString 15: [ OK ] StringConvert.NoResultFromEptyString (0 ms) 15: [ RUN ] StringConvert.ThreeFloatsSuccessfully 15: [ OK ] StringConvert.ThreeFloatsSuccessfully (0 ms) 15: [ RUN ] StringConvert.OneIntSucessfully 15: [ OK ] StringConvert.OneIntSucessfully (0 ms) 15: [ RUN ] StringConvert.FloatAsStringToIntArrayThrows 15: [ OK ] StringConvert.FloatAsStringToIntArrayThrows (0 ms) 15: [ RUN ] StringConvert.ThrowsWhenWrongSize 15: [ OK ] StringConvert.ThrowsWhenWrongSize (0 ms) 15: [ RUN ] StringConvert.StringIdentityTransformWithArrayThrows 15: [ OK ] StringConvert.StringIdentityTransformWithArrayThrows (0 ms) 15: [ RUN ] StringConvert.StringIdentityTransformWithArrayOkay 15: [ OK ] StringConvert.StringIdentityTransformWithArrayOkay (0 ms) 15: [----------] 7 tests from StringConvert (0 ms total) 15: 15: [----------] 7 tests from StringToEnumValueConverterTest 15: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping 15: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping (0 ms) 15: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping 15: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping (0 ms) 15: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping 15: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping (0 ms) 15: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping 15: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping (0 ms) 15: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping 15: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping (0 ms) 15: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping 15: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping (0 ms) 15: [ RUN ] StringToEnumValueConverterTest.CustomConverterWorks 15: [ OK ] StringToEnumValueConverterTest.CustomConverterWorks (0 ms) 15: [----------] 7 tests from StringToEnumValueConverterTest (0 ms total) 15: 15: [----------] 9 tests from StringUtilityTest 15: [ RUN ] StringUtilityTest.StartsWith 15: [ OK ] StringUtilityTest.StartsWith (0 ms) 15: [ RUN ] StringUtilityTest.EndsWith 15: [ OK ] StringUtilityTest.EndsWith (0 ms) 15: [ RUN ] StringUtilityTest.StripSuffixIfPresent 15: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 15: [ RUN ] StringUtilityTest.StripString 15: [ OK ] StringUtilityTest.StripString (0 ms) 15: [ RUN ] StringUtilityTest.SplitString 15: [ OK ] StringUtilityTest.SplitString (0 ms) 15: [ RUN ] StringUtilityTest.SplitDelimitedString 15: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 15: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 15: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) 15: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive 15: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms) 15: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength 15: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms) 15: [----------] 9 tests from StringUtilityTest (0 ms total) 15: 15: [----------] 2 tests from FormatStringTest 15: [ RUN ] FormatStringTest.HandlesBasicFormatting 15: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 15: [ RUN ] FormatStringTest.HandlesLongStrings 15: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 15: [----------] 2 tests from FormatStringTest (0 ms total) 15: 15: [----------] 1 test from StringFormatterTest 15: [ RUN ] StringFormatterTest.HandlesBasicFormatting 15: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 15: [----------] 1 test from StringFormatterTest (0 ms total) 15: 15: [----------] 1 test from formatAndJoinTest 15: [ RUN ] formatAndJoinTest.Works 15: [ OK ] formatAndJoinTest.Works (0 ms) 15: [----------] 1 test from formatAndJoinTest (0 ms total) 15: 15: [----------] 1 test from JoinStringsTest 15: [ RUN ] JoinStringsTest.Works 15: [ OK ] JoinStringsTest.Works (0 ms) 15: [----------] 1 test from JoinStringsTest (0 ms total) 15: 15: [----------] 6 tests from ReplaceAllTest 15: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 15: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 15: [ RUN ] ReplaceAllTest.HandlesNoMatches 15: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 15: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 15: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 15: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 15: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 15: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 15: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 15: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 15: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 15: [----------] 6 tests from ReplaceAllTest (0 ms total) 15: 15: [----------] 10 tests from TextLineWrapperTest 15: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 15: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 15: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 15: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 15: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 15: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 15: [ RUN ] TextLineWrapperTest.WrapsCorrectly 15: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms) 15: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 15: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms) 15: [ RUN ] TextLineWrapperTest.HandlesIndent 15: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) 15: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 15: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) 15: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 15: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms) 15: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 15: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) 15: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 15: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) 15: [----------] 10 tests from TextLineWrapperTest (0 ms total) 15: 15: [----------] 3 tests from TemplateMPTest 15: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnum 15: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnum (0 ms) 15: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionBool 15: [ OK ] TemplateMPTest.DispatchTemplatedFunctionBool (0 ms) 15: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnumBool 15: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnumBool (0 ms) 15: [----------] 3 tests from TemplateMPTest (0 ms total) 15: 15: [----------] 6 tests from TextWriterTest 15: [ RUN ] TextWriterTest.WritesLines 15: [ OK ] TextWriterTest.WritesLines (0 ms) 15: [ RUN ] TextWriterTest.WritesLinesInParts 15: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) 15: [ RUN ] TextWriterTest.WritesWrappedLines 15: [ OK ] TextWriterTest.WritesWrappedLines (0 ms) 15: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 15: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) 15: [ RUN ] TextWriterTest.TracksNewlines 15: [ OK ] TextWriterTest.TracksNewlines (0 ms) 15: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 15: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) 15: [----------] 6 tests from TextWriterTest (0 ms total) 15: 15: [----------] 1 test from TypeTraitsTest 15: [ RUN ] TypeTraitsTest.IsIntegralConstant 15: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 15: [----------] 1 test from TypeTraitsTest (0 ms total) 15: 15: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 15: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 15: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 15: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 15: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 15: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 15: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 15: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 15: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 15: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 15: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 15: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 15: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 15: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 15: 15: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 15: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 15: 15: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 15: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) 15: 15: [----------] 11 tests from WithInputPaths/PathSearchTest 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 (0 ms) 15: [----------] 11 tests from WithInputPaths/PathSearchTest (0 ms total) 15: 15: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) 15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) 15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 15: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (0 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 400 tests from 62 test suites ran. (6 ms total) 15: [ PASSED ] 400 tests. 15: 15: YOU HAVE 1 DISABLED TEST 15: 15/91 Test #15: UtilityUnitTests ............................. Passed 0.41 sec test 16 Start 16: UtilityMpiUnitTests 16: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/utility-mpi-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/UtilityMpiUnitTests.xml" 16: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests 16: Test timeout computed to be: 30 16: [==========] Running 2 tests from 1 test suite. 16: [----------] Global test environment set-up. 16: [----------] 2 tests from PhysicalNodeCommunicatorTest 16: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 16: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (35 ms) 16: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 16: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (31 ms) 16: [----------] 2 tests from PhysicalNodeCommunicatorTest (87 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 2 tests from 1 test suite ran. (87 ms total) 16: [ PASSED ] 2 tests. 16/91 Test #16: UtilityMpiUnitTests .......................... Passed 0.53 sec test 17 Start 17: GmxlibTests 17: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/nonbonded-fep-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/GmxlibTests.xml" 17: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxlib/nonbonded/tests 17: Test timeout computed to be: 30 17: [==========] Running 78 tests from 2 test suites. 17: [----------] Global test environment set-up. 17: [----------] 72 tests from NBInteraction/NonbondedFepTest 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/0 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/0 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/1 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/1 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/2 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/2 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/3 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/3 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/4 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/4 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/5 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/5 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/6 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/6 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/7 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/7 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/8 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/8 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/9 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/9 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/10 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/10 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/11 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/11 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/12 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/12 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/13 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/13 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/14 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/14 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/15 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/15 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/16 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/16 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/17 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/17 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/18 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/18 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/19 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/19 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/20 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/20 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/21 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/21 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/22 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/22 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/23 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/23 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/24 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/24 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/25 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/25 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/26 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/26 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/27 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/27 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/28 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/28 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/29 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/29 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/30 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/30 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/31 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/31 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/32 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/32 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/33 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/33 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/34 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/34 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/35 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/35 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/36 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/36 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/37 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/37 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/38 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/38 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/39 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/39 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/40 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/40 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/41 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/41 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/42 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/42 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/43 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/43 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/44 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/44 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/45 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/45 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/46 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/46 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/47 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/47 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/48 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/48 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/49 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/49 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/50 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/50 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/51 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/51 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/52 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/52 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/53 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/53 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/54 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/54 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/55 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/55 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/56 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/56 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/57 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/57 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/58 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/58 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/59 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/59 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/60 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/60 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/61 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/61 (4 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/62 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/62 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/63 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/63 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/64 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/64 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/65 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/65 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/66 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/66 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/67 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/67 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/68 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/68 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/69 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/69 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/70 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/70 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/71 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/71 (0 ms) 17: [----------] 72 tests from NBInteraction/NonbondedFepTest (8 ms total) 17: 17: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest 17: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 17: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 (0 ms) 17: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 17: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 (0 ms) 17: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 17: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 (0 ms) 17: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 17: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 (0 ms) 17: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 17: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 (0 ms) 17: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 17: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 (0 ms) 17: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest (0 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 78 tests from 2 test suites ran. (9 ms total) 17: [ PASSED ] 78 tests. 17/91 Test #17: GmxlibTests .................................. Passed 0.36 sec test 18 Start 18: MdlibUnitTest 18: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdlib-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdlibUnitTest.xml" 18: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests 18: Test timeout computed to be: 30 18: [==========] Running 999 tests from 25 test suites. 18: [----------] Global test environment set-up. 18: [----------] 2 tests from EffectiveAtomDensity 18: [ RUN ] EffectiveAtomDensity.VolumeIndependence 18: [ OK ] EffectiveAtomDensity.VolumeIndependence (0 ms) 18: [ RUN ] EffectiveAtomDensity.WeightingWorks 18: [ OK ] EffectiveAtomDensity.WeightingWorks (0 ms) 18: [----------] 2 tests from EffectiveAtomDensity (0 ms total) 18: 18: [----------] 2 tests from AtomNonbondedAndKineticProperties 18: [ RUN ] AtomNonbondedAndKineticProperties.IsAccurate 18: [ OK ] AtomNonbondedAndKineticProperties.IsAccurate (0 ms) 18: [ RUN ] AtomNonbondedAndKineticProperties.ConstraintsWork 18: [ OK ] AtomNonbondedAndKineticProperties.ConstraintsWork (0 ms) 18: [----------] 2 tests from AtomNonbondedAndKineticProperties (0 ms total) 18: 18: [----------] 1 test from VerletBufferConstraintTest 18: [ RUN ] VerletBufferConstraintTest.EqualMasses 18: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) 18: [----------] 1 test from VerletBufferConstraintTest (0 ms total) 18: 18: [----------] 6 tests from CalcvirTest 18: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBox 18: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBox (0 ms) 18: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew 18: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew (0 ms) 18: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX 18: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX (0 ms) 18: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY 18: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY (0 ms) 18: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ 18: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ (0 ms) 18: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ 18: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ (0 ms) 18: [----------] 6 tests from CalcvirTest (0 ms total) 18: 18: [----------] 2 tests from PrEbinTest 18: [ RUN ] PrEbinTest.HandlesAverages 18: [ OK ] PrEbinTest.HandlesAverages (1 ms) 18: [ RUN ] PrEbinTest.HandlesEmptyAverages 18: [ OK ] PrEbinTest.HandlesEmptyAverages (0 ms) 18: [----------] 2 tests from PrEbinTest (1 ms total) 18: 18: [----------] 3 tests from EnergyDriftTracker 18: [ RUN ] EnergyDriftTracker.emptyWorks 18: [ OK ] EnergyDriftTracker.emptyWorks (0 ms) 18: [ RUN ] EnergyDriftTracker.onePointWorks 18: [ OK ] EnergyDriftTracker.onePointWorks (0 ms) 18: [ RUN ] EnergyDriftTracker.manyPointsWorks 18: [ OK ] EnergyDriftTracker.manyPointsWorks (0 ms) 18: [----------] 3 tests from EnergyDriftTracker (0 ms total) 18: 18: [----------] 4 tests from ShakeTest 18: [ RUN ] ShakeTest.ConstrainsOneBond 18: [ OK ] ShakeTest.ConstrainsOneBond (0 ms) 18: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 18: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 18: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 18: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 18: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 18: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 18: [----------] 4 tests from ShakeTest (0 ms total) 18: 18: [----------] 1 test from NullSignalTest 18: [ RUN ] NullSignalTest.NullSignallerWorks 18: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) 18: [----------] 1 test from NullSignalTest (0 ms total) 18: 18: [----------] 7 tests from SignalTest 18: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 18: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 18: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 18: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 18: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 18: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 18: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 18: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 18: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 18: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 18: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 18: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 18: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 18: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 18: [----------] 7 tests from SignalTest (0 ms total) 18: 18: [----------] 13 tests from UpdateGroupsTest 18: [ RUN ] UpdateGroupsTest.WithEthaneUA 18: [ OK ] UpdateGroupsTest.WithEthaneUA (0 ms) 18: [ RUN ] UpdateGroupsTest.WithMethane 18: [ OK ] UpdateGroupsTest.WithMethane (0 ms) 18: [ RUN ] UpdateGroupsTest.WithEthane 18: [ OK ] UpdateGroupsTest.WithEthane (0 ms) 18: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane 18: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane (0 ms) 18: [ RUN ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups 18: [ OK ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups (0 ms) 18: [ RUN ] UpdateGroupsTest.WithWaterThreeSite 18: [ OK ] UpdateGroupsTest.WithWaterThreeSite (0 ms) 18: [ RUN ] UpdateGroupsTest.WithWaterFourSite 18: [ OK ] UpdateGroupsTest.WithWaterFourSite (0 ms) 18: [ RUN ] UpdateGroupsTest.WithFourAtomsWithSettle 18: [ OK ] UpdateGroupsTest.WithFourAtomsWithSettle (0 ms) 18: [ RUN ] UpdateGroupsTest.WithWaterFlexAngle 18: [ OK ] UpdateGroupsTest.WithWaterFlexAngle (0 ms) 18: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle 18: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle (0 ms) 18: [ RUN ] UpdateGroupsTest.WithTwoMoltypes 18: [ OK ] UpdateGroupsTest.WithTwoMoltypes (0 ms) 18: [ RUN ] UpdateGroupsTest.LogsWhenSizesAreInvalid 18: [ OK ] UpdateGroupsTest.LogsWhenSizesAreInvalid (0 ms) 18: [ RUN ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful 18: [ OK ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful (0 ms) 18: [----------] 13 tests from UpdateGroupsTest (1 ms total) 18: 18: [----------] 1 test from UpdateGroupsCog 18: [ RUN ] UpdateGroupsCog.ComputesCogs 18: [ OK ] UpdateGroupsCog.ComputesCogs (0 ms) 18: [----------] 1 test from UpdateGroupsCog (0 ms total) 18: 18: [----------] 2 tests from WholeMoleculeTransform 18: [ RUN ] WholeMoleculeTransform.MakesMoleculesWhole 18: [ OK ] WholeMoleculeTransform.MakesMoleculesWhole (0 ms) 18: [ RUN ] WholeMoleculeTransform.HandlesReordering 18: [ OK ] WholeMoleculeTransform.HandlesReordering (0 ms) 18: [----------] 2 tests from WholeMoleculeTransform (0 ms total) 18: 18: [----------] 14 tests from WithParameters/ConstraintsTest 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 (4 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 (3 ms) 18: [----------] 14 tests from WithParameters/ConstraintsTest (21 ms total) 18: 18: [----------] 11 tests from WithParameters/EnergyOutputTest 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0 18: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (0 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1 18: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (0 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2 18: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (0 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3 18: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (0 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4 18: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as single precision energy file 18: Reading energy frame 0 time 10.100 Reading energy frame 1 time 27.500 Reading energy frame 2 time 44.900 Reading energy frame 3 time 62.300 Reading energy frame 4 time 79.700 Reading energy frame 5 time 97.100 Reading energy frame 6 time 114.500 Reading energy frame 7 time 131.900 Reading energy frame 8 time 149.300 Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (7 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5 18: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (0 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6 18: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (0 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7 18: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (0 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8 18: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (1 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9 18: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (7 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10 18: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (0 ms) 18: [----------] 11 tests from WithParameters/EnergyOutputTest (22 ms total) 18: 18: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms) 18: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (0 ms total) 18: 18: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms) 18: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (0 ms total) 18: 18: [----------] 23 tests from WithParameters/FreeEnergyParameterTest 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 (0 ms) 18: [----------] 23 tests from WithParameters/FreeEnergyParameterTest (0 ms total) 18: 18: [----------] 16 tests from WithParameters/LeapFrogTest 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (4 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (0 ms) 18: [----------] 16 tests from WithParameters/LeapFrogTest (16 ms total) 18: 18: [----------] 140 tests from Cubic/ParrRahmTest 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 18: [----------] 140 tests from Cubic/ParrRahmTest (17 ms total) 18: 18: [----------] 140 tests from Rectilinear/ParrRahmTest 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 (2 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 18: [----------] 140 tests from Rectilinear/ParrRahmTest (13 ms total) 18: 18: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (3 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 18: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest (14 ms total) 18: 18: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 18: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest (13 ms total) 18: 18: [----------] 140 tests from TruncOct/ParrRahmTest 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 18: [----------] 140 tests from TruncOct/ParrRahmTest (17 ms total) 18: 18: [----------] 140 tests from Other/ParrRahmTest 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (2 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 18: [----------] 140 tests from Other/ParrRahmTest (7 ms total) 18: 18: [----------] 13 tests from WithParameters/SettleTest 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (0 ms) 18: [----------] 13 tests from WithParameters/SettleTest (6 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 999 tests from 25 test suites ran. (160 ms total) 18: [ PASSED ] 999 tests. 18/91 Test #18: MdlibUnitTest ................................ Passed 0.62 sec test 19 Start 19: AwhTest 19: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/awh-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/AwhTest.xml" 19: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/awh/tests 19: Test timeout computed to be: 30 19: [==========] Running 25 tests from 9 test suites. 19: [----------] Global test environment set-up. 19: [----------] 3 tests from SerializationTest 19: [ RUN ] SerializationTest.CanSerializeDimParams 19: [ OK ] SerializationTest.CanSerializeDimParams (0 ms) 19: [ RUN ] SerializationTest.CanSerializeBiasParams 19: [ OK ] SerializationTest.CanSerializeBiasParams (0 ms) 19: [ RUN ] SerializationTest.CanSerializeAwhParams 19: [ OK ] SerializationTest.CanSerializeAwhParams (0 ms) 19: [----------] 3 tests from SerializationTest (0 ms total) 19: 19: [----------] 1 test from BiasTest 19: [ RUN ] BiasTest.DetectsCovering 19: [ OK ] BiasTest.DetectsCovering (0 ms) 19: [----------] 1 test from BiasTest (0 ms total) 19: 19: [----------] 1 test from biasGridTest 19: [ RUN ] biasGridTest.neighborhood 19: [ OK ] biasGridTest.neighborhood (0 ms) 19: [----------] 1 test from biasGridTest (0 ms total) 19: 19: [----------] 2 tests from BiasFepLambdaStateTest 19: [ RUN ] BiasFepLambdaStateTest.DetectsCovering 19: [ OK ] BiasFepLambdaStateTest.DetectsCovering (1 ms) 19: [ RUN ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy 19: [ OK ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy (0 ms) 19: [----------] 2 tests from BiasFepLambdaStateTest (1 ms total) 19: 19: [----------] 8 tests from WithParameters/BiasTest 19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 (0 ms) 19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 (0 ms) 19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 (0 ms) 19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 (0 ms) 19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 (0 ms) 19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 (0 ms) 19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 (0 ms) 19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 (0 ms) 19: [----------] 8 tests from WithParameters/BiasTest (2 ms total) 19: 19: [----------] 2 tests from WithParameters/BiasStateTest 19: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 19: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms) 19: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 19: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (0 ms) 19: [----------] 2 tests from WithParameters/BiasStateTest (0 ms total) 19: 19: [----------] 1 test from WithParameters/UserInputTest 19: [ RUN ] WithParameters/UserInputTest.ParsesUser3DInput/0 19: [ OK ] WithParameters/UserInputTest.ParsesUser3DInput/0 (0 ms) 19: [----------] 1 test from WithParameters/UserInputTest (0 ms total) 19: 19: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest 19: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 19: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 (7 ms) 19: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 19: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 (2 ms) 19: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 19: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 (6 ms) 19: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 19: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 (6 ms) 19: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest (30 ms total) 19: 19: [----------] 3 tests from WithParameters/FrictionMetricTest 19: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/0 19: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/0 (0 ms) 19: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/1 19: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/1 (0 ms) 19: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/2 19: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/2 (21 ms) 19: [----------] 3 tests from WithParameters/FrictionMetricTest (31 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 25 tests from 9 test suites ran. (68 ms total) 19: [ PASSED ] 25 tests. 19/91 Test #19: AwhTest ...................................... Passed 0.40 sec test 20 Start 20: DensityFittingAppliedForcesUnitTest 20: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/density_fitting_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/DensityFittingAppliedForcesUnitTest.xml" 20: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/densityfitting/tests 20: Test timeout computed to be: 30 20: [==========] Running 18 tests from 4 test suites. 20: [----------] Global test environment set-up. 20: [----------] 2 tests from DensityFittingTest 20: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows 20: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (0 ms) 20: [ RUN ] DensityFittingTest.SingleAtom 20: [ OK ] DensityFittingTest.SingleAtom (0 ms) 20: [----------] 2 tests from DensityFittingTest (0 ms total) 20: 20: [----------] 7 tests from DensityFittingAmplitudeLookupTest 20: [ RUN ] DensityFittingAmplitudeLookupTest.Unity 20: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms) 20: [ RUN ] DensityFittingAmplitudeLookupTest.Charge 20: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms) 20: [ RUN ] DensityFittingAmplitudeLookupTest.Masses 20: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms) 20: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign 20: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms) 20: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct 20: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms) 20: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign 20: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms) 20: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct 20: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms) 20: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total) 20: 20: [----------] 1 test from DensityFittingForceProviderState 20: [ RUN ] DensityFittingForceProviderState.RoundTripSaving 20: [ OK ] DensityFittingForceProviderState.RoundTripSaving (0 ms) 20: [----------] 1 test from DensityFittingForceProviderState (0 ms total) 20: 20: [----------] 8 tests from DensityFittingOptionsTest 20: [ RUN ] DensityFittingOptionsTest.DefaultParameters 20: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms) 20: [ RUN ] DensityFittingOptionsTest.OptionSetsActive 20: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms) 20: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive 20: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 20: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive 20: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (0 ms) 20: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup 20: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 20: [ RUN ] DensityFittingOptionsTest.InternalsToKvt 20: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms) 20: [ RUN ] DensityFittingOptionsTest.KvtToInternal 20: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms) 20: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent 20: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms) 20: [----------] 8 tests from DensityFittingOptionsTest (0 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 18 tests from 4 test suites ran. (0 ms total) 20: [ PASSED ] 18 tests. 20/91 Test #20: DensityFittingAppliedForcesUnitTest .......... Passed 0.36 sec test 21 Start 21: QMMMAppliedForcesUnitTest 21: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/qmmm_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/QMMMAppliedForcesUnitTest.xml" 21: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests 21: Test timeout computed to be: 30 21: [==========] Running 21 tests from 5 test suites. 21: [----------] Global test environment set-up. 21: [----------] 3 tests from QMMMInputGeneratorTest 21: [ RUN ] QMMMInputGeneratorTest.CanConstruct 21: [ OK ] QMMMInputGeneratorTest.CanConstruct (0 ms) 21: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBENoLink 21: [ OK ] QMMMInputGeneratorTest.TwoWatersPBENoLink (0 ms) 21: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBEWithLink 21: [ OK ] QMMMInputGeneratorTest.TwoWatersPBEWithLink (0 ms) 21: [----------] 3 tests from QMMMInputGeneratorTest (0 ms total) 21: 21: [----------] 7 tests from QMMMTopologyPreprocessorTest 21: [ RUN ] QMMMTopologyPreprocessorTest.CanConstruct 21: [ OK ] QMMMTopologyPreprocessorTest.CanConstruct (0 ms) 21: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: Number of degrees of freedom in T-Coupling group rest is 21.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 21: NVE simulation with an initial temperature of zero: will use a Verlet 21: buffer of 10%. Check your energy drift! 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 21: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 21: Setting the LD random seed to -1778516774 21: 21: Generated 10 of the 10 non-bonded parameter combinations 21: 21: Generated 10 of the 10 1-4 parameter combinations 21: 21: Excluding 2 bonded neighbours molecule type 'SOL' 21: Analysing residue names: 21: There are: 4 Water residues 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink (5 ms) 21: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: Number of degrees of freedom in T-Coupling group rest is 21.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 21: NVE simulation with an initial temperature of zero: will use a Verlet 21: buffer of 10%. Check your energy drift! 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 21: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 21: Setting the LD random seed to -1234184329 21: 21: Generated 10 of the 10 non-bonded parameter combinations 21: 21: Generated 10 of the 10 1-4 parameter combinations 21: 21: Excluding 2 bonded neighbours molecule type 'SOL' 21: Analysing residue names: 21: There are: 4 Water residues 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink (2 ms) 21: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: Number of degrees of freedom in T-Coupling group rest is 21.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 21: NVE simulation with an initial temperature of zero: will use a Verlet 21: buffer of 10%. Check your energy drift! 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 21: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 21: Setting the LD random seed to 2054158316 21: 21: Generated 10 of the 10 non-bonded parameter combinations 21: 21: Generated 10 of the 10 1-4 parameter combinations 21: 21: Excluding 2 bonded neighbours molecule type 'SOL' 21: Analysing residue names: 21: There are: 4 Water residues 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink (2 ms) 21: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: Number of degrees of freedom in T-Coupling group rest is 63.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 21: NVE simulation: will use the initial temperature of 129.093 K for 21: determining the Verlet buffer size 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 21: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 21: Setting the LD random seed to -302268449 21: 21: Generated 2145 of the 2145 non-bonded parameter combinations 21: 21: Generated 2145 of the 2145 1-4 parameter combinations 21: 21: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 21: Analysing residue names: 21: There are: 3 Protein residues 21: Analysing Protein... 21: 21: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 21: 21: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 21: 21: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 21: 21: Note that mdrun will redetermine rlist based on the actual pair-list setup 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints (9 ms) 21: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: 21: NOTE 2 [file unknown]: 21: You are using constraints on all bonds, whereas the forcefield has been 21: parametrized only with constraints involving hydrogen atoms. We suggest 21: using constraints = h-bonds instead, this will also improve performance. 21: 21: 21: NOTE 3 [file unknown]: 21: For energy conservation with LINCS, lincs_iter should be 2 or larger. 21: 21: 21: Number of degrees of freedom in T-Coupling group rest is 42.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 21: NVE simulation: will use the initial temperature of 193.640 K for 21: determining the Verlet buffer size 21: 21: 21: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 5 NOTEs 21: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 21: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 21: Setting the LD random seed to -82003 21: 21: Generated 2145 of the 2145 non-bonded parameter combinations 21: 21: Generated 2145 of the 2145 1-4 parameter combinations 21: 21: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 21: 21: turning all bonds into constraints... 21: Analysing residue names: 21: There are: 3 Protein residues 21: Analysing Protein... 21: 21: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 21: 21: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 21: 21: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 21: 21: Note that mdrun will redetermine rlist based on the actual pair-list setup 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints (17 ms) 21: [ RUN ] QMMMTopologyPreprocessorTest.RemovingQMVsites 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Number of degrees of freedom in T-Coupling group rest is 45.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 21: NVE simulation with an initial temperature of zero: will use a Verlet 21: buffer of 10%. Check your energy drift! 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 21: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 21: Setting the LD random seed to -537144145 21: 21: Generated 3 of the 6 non-bonded parameter combinations 21: 21: Excluding 3 bonded neighbours molecule type 'VSTEST' 21: 21: Cleaning up constraints and constant bonded interactions with virtual sites 21: Analysing residue names: 21: There are: 1 Other residues 21: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] QMMMTopologyPreprocessorTest.RemovingQMVsites (2 ms) 21: [----------] 7 tests from QMMMTopologyPreprocessorTest (44 ms total) 21: 21: [----------] 9 tests from QMMMOptionsTest 21: [ RUN ] QMMMOptionsTest.DefaultParameters 21: [ OK ] QMMMOptionsTest.DefaultParameters (0 ms) 21: [ RUN ] QMMMOptionsTest.OptionSetsActive 21: [ OK ] QMMMOptionsTest.OptionSetsActive (0 ms) 21: [ RUN ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive 21: [ OK ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 21: [ RUN ] QMMMOptionsTest.OutputDefaultValuesWhenActive 21: [ OK ] QMMMOptionsTest.OutputDefaultValuesWhenActive (0 ms) 21: [ RUN ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup 21: [ OK ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 21: [ RUN ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup 21: [ OK ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup (0 ms) 21: [ RUN ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup 21: [ OK ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup (0 ms) 21: [ RUN ] QMMMOptionsTest.InternalsToKvtAndBack 21: [ OK ] QMMMOptionsTest.InternalsToKvtAndBack (0 ms) 21: [ RUN ] QMMMOptionsTest.CP2KInputProcessing 21: [ OK ] QMMMOptionsTest.CP2KInputProcessing (0 ms) 21: [----------] 9 tests from QMMMOptionsTest (1 ms total) 21: 21: [----------] 1 test from QMMMForceProviderTest 21: [ RUN ] QMMMForceProviderTest.CanConstructOrNot 21: [ OK ] QMMMForceProviderTest.CanConstructOrNot (0 ms) 21: [----------] 1 test from QMMMForceProviderTest (0 ms total) 21: 21: [----------] 1 test from QMMMTest 21: [ RUN ] QMMMTest.ForceProviderLackingInputThrows 21: [ OK ] QMMMTest.ForceProviderLackingInputThrows (0 ms) 21: [----------] 1 test from QMMMTest (0 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 21 tests from 5 test suites ran. (46 ms total) 21: [ PASSED ] 21 tests. 21/91 Test #21: QMMMAppliedForcesUnitTest .................... Passed 0.42 sec test 22 Start 22: ColvarsAppliedForcesUnitTest 22: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/colvars_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/ColvarsAppliedForcesUnitTest.xml" 22: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests 22: Test timeout computed to be: 30 22: [==========] Running 16 tests from 4 test suites. 22: [----------] Global test environment set-up. 22: [----------] 1 test from ColvarsTest 22: [ RUN ] ColvarsTest.ForceProviderLackingInputThrows 22: [ OK ] ColvarsTest.ForceProviderLackingInputThrows (0 ms) 22: [----------] 1 test from ColvarsTest (0 ms total) 22: 22: [----------] 6 tests from ColvarsOptionsTest 22: [ RUN ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive 22: [ OK ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 22: [ RUN ] ColvarsOptionsTest.OutputDefaultValuesWhenActive 22: [ OK ] ColvarsOptionsTest.OutputDefaultValuesWhenActive (0 ms) 22: [ RUN ] ColvarsOptionsTest.OutputValuesWhenActive 22: [ OK ] ColvarsOptionsTest.OutputValuesWhenActive (0 ms) 22: [ RUN ] ColvarsOptionsTest.OptionSetsActive 22: [ OK ] ColvarsOptionsTest.OptionSetsActive (0 ms) 22: [ RUN ] ColvarsOptionsTest.InternalsToKvtAndBack 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 21.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 22: NVE simulation with an initial temperature of zero: will use a Verlet 22: buffer of 10%. Check your energy drift! 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 22: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 22: Setting the LD random seed to -538843425 22: 22: Generated 10 of the 10 non-bonded parameter combinations 22: 22: Generated 10 of the 10 1-4 parameter combinations 22: 22: Excluding 2 bonded neighbours molecule type 'SOL' 22: Analysing residue names: 22: There are: 4 Water residues 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsOptionsTest.InternalsToKvtAndBack (4 ms) 22: [ RUN ] ColvarsOptionsTest.RetrieveEdrFilename 22: [ OK ] ColvarsOptionsTest.RetrieveEdrFilename (0 ms) 22: [----------] 6 tests from ColvarsOptionsTest (4 ms total) 22: 22: [----------] 4 tests from ColvarsPreProcessorTest 22: [ RUN ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 21.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 22: NVE simulation with an initial temperature of zero: will use a Verlet 22: buffer of 10%. Check your energy drift! 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 22: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 22: Setting the LD random seed to 1845460991 22: 22: Generated 10 of the 10 non-bonded parameter combinations 22: 22: Generated 10 of the 10 1-4 parameter combinations 22: 22: Excluding 2 bonded neighbours molecule type 'SOL' 22: Analysing residue names: 22: There are: 4 Water residues 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess (2 ms) 22: [ RUN ] ColvarsPreProcessorTest.CheckValuesFourWaters 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 21.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 22: NVE simulation with an initial temperature of zero: will use a Verlet 22: buffer of 10%. Check your energy drift! 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 22: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 22: Setting the LD random seed to 536018043 22: 22: Generated 10 of the 10 non-bonded parameter combinations 22: 22: Generated 10 of the 10 1-4 parameter combinations 22: 22: Excluding 2 bonded neighbours molecule type 'SOL' 22: Analysing residue names: 22: There are: 4 Water residues 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsPreProcessorTest.CheckValuesFourWaters (16 ms) 22: [ RUN ] ColvarsPreProcessorTest.CheckNestedInputFiles 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 21.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 22: NVE simulation with an initial temperature of zero: will use a Verlet 22: buffer of 10%. Check your energy drift! 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 22: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 22: Setting the LD random seed to -1346519042 22: 22: Generated 10 of the 10 non-bonded parameter combinations 22: 22: Generated 10 of the 10 1-4 parameter combinations 22: 22: Excluding 2 bonded neighbours molecule type 'SOL' 22: Analysing residue names: 22: There are: 4 Water residues 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsPreProcessorTest.CheckNestedInputFiles (8 ms) 22: [ RUN ] ColvarsPreProcessorTest.WrongColvarsInput 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 21.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 22: NVE simulation with an initial temperature of zero: will use a Verlet 22: buffer of 10%. Check your energy drift! 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 22: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 22: Setting the LD random seed to -1023492353 22: 22: Generated 10 of the 10 non-bonded parameter combinations 22: 22: Generated 10 of the 10 1-4 parameter combinations 22: 22: Excluding 2 bonded neighbours molecule type 'SOL' 22: Analysing residue names: 22: There are: 4 Water residues 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsPreProcessorTest.WrongColvarsInput (7 ms) 22: [----------] 4 tests from ColvarsPreProcessorTest (38 ms total) 22: 22: [----------] 5 tests from ColvarsForceProviderTest 22: [ RUN ] ColvarsForceProviderTest.CanConstructOrNot 22: [ OK ] ColvarsForceProviderTest.CanConstructOrNot (0 ms) 22: [ RUN ] ColvarsForceProviderTest.SimpleInputs 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 21.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 22: NVE simulation with an initial temperature of zero: will use a Verlet 22: buffer of 10%. Check your energy drift! 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 22: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 22: Setting the LD random seed to -675680785 22: 22: Generated 10 of the 10 non-bonded parameter combinations 22: 22: Generated 10 of the 10 1-4 parameter combinations 22: 22: Excluding 2 bonded neighbours molecule type 'SOL' 22: Analysing residue names: 22: There are: 4 Water residues 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsForceProviderTest.SimpleInputs (7 ms) 22: [ RUN ] ColvarsForceProviderTest.WrongColvarsInput 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 21.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 22: NVE simulation with an initial temperature of zero: will use a Verlet 22: buffer of 10%. Check your energy drift! 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 22: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 22: Setting the LD random seed to -105168906 22: 22: Generated 10 of the 10 non-bonded parameter combinations 22: 22: Generated 10 of the 10 1-4 parameter combinations 22: 22: Excluding 2 bonded neighbours molecule type 'SOL' 22: Analysing residue names: 22: There are: 4 Water residues 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsForceProviderTest.WrongColvarsInput (3 ms) 22: [ RUN ] ColvarsForceProviderTest.CalculateForces4water 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 21.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 22: NVE simulation with an initial temperature of zero: will use a Verlet 22: buffer of 10%. Check your energy drift! 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 22: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 22: Setting the LD random seed to -287590657 22: 22: Generated 10 of the 10 non-bonded parameter combinations 22: 22: Generated 10 of the 10 1-4 parameter combinations 22: 22: Excluding 2 bonded neighbours molecule type 'SOL' 22: Analysing residue names: 22: There are: 4 Water residues 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsForceProviderTest.CalculateForces4water (64 ms) 22: [ RUN ] ColvarsForceProviderTest.CalculateForcesAlanine 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 66.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 22: NVE simulation: will use the initial temperature of 300.368 K for 22: determining the Verlet buffer size 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 22: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 22: Setting the LD random seed to 624360758 22: 22: Generated 2211 of the 2211 non-bonded parameter combinations 22: 22: Generated 2211 of the 2211 1-4 parameter combinations 22: 22: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 22: Analysing residue names: 22: There are: 2 Protein residues 22: Analysing Protein... 22: 22: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 22: 22: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 22: 22: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 22: 22: Note that mdrun will redetermine rlist based on the actual pair-list setup 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsForceProviderTest.CalculateForcesAlanine (75 ms) 22: [----------] 5 tests from ColvarsForceProviderTest (156 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 16 tests from 4 test suites ran. (199 ms total) 22: [ PASSED ] 16 tests. 22/91 Test #22: ColvarsAppliedForcesUnitTest ................. Passed 0.55 sec test 23 Start 23: AppliedForcesUnitTest 23: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/AppliedForcesUnitTest.xml" 23: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/tests 23: Test timeout computed to be: 30 23: [==========] Running 3 tests from 1 test suite. 23: [----------] Global test environment set-up. 23: [----------] 3 tests from ElectricFieldTest 23: [ RUN ] ElectricFieldTest.Static 23: [ OK ] ElectricFieldTest.Static (0 ms) 23: [ RUN ] ElectricFieldTest.Oscillating 23: [ OK ] ElectricFieldTest.Oscillating (0 ms) 23: [ RUN ] ElectricFieldTest.Pulsed 23: [ OK ] ElectricFieldTest.Pulsed (0 ms) 23: [----------] 3 tests from ElectricFieldTest (0 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 3 tests from 1 test suite ran. (0 ms total) 23: [ PASSED ] 3 tests. 23/91 Test #23: AppliedForcesUnitTest ........................ Passed 0.32 sec test 24 Start 24: ListedForcesTest 24: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/listed_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/ListedForcesTest.xml" 24: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/listed_forces/tests 24: Test timeout computed to be: 30 24: [==========] Running 132 tests from 9 test suites. 24: [----------] Global test environment set-up. 24: [----------] 24 tests from Bond/ListedForcesTest 24: [ RUN ] Bond/ListedForcesTest.Ifunc/0 24: [ OK ] Bond/ListedForcesTest.Ifunc/0 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/1 24: [ OK ] Bond/ListedForcesTest.Ifunc/1 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/2 24: [ OK ] Bond/ListedForcesTest.Ifunc/2 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/3 24: [ OK ] Bond/ListedForcesTest.Ifunc/3 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/4 24: [ OK ] Bond/ListedForcesTest.Ifunc/4 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/5 24: [ OK ] Bond/ListedForcesTest.Ifunc/5 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/6 24: [ OK ] Bond/ListedForcesTest.Ifunc/6 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/7 24: [ OK ] Bond/ListedForcesTest.Ifunc/7 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/8 24: [ OK ] Bond/ListedForcesTest.Ifunc/8 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/9 24: [ OK ] Bond/ListedForcesTest.Ifunc/9 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/10 24: [ OK ] Bond/ListedForcesTest.Ifunc/10 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/11 24: [ OK ] Bond/ListedForcesTest.Ifunc/11 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/12 24: [ OK ] Bond/ListedForcesTest.Ifunc/12 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/13 24: [ OK ] Bond/ListedForcesTest.Ifunc/13 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/14 24: [ OK ] Bond/ListedForcesTest.Ifunc/14 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/15 24: [ OK ] Bond/ListedForcesTest.Ifunc/15 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/16 24: [ OK ] Bond/ListedForcesTest.Ifunc/16 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/17 24: [ OK ] Bond/ListedForcesTest.Ifunc/17 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/18 24: [ OK ] Bond/ListedForcesTest.Ifunc/18 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/19 24: [ OK ] Bond/ListedForcesTest.Ifunc/19 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/20 24: [ OK ] Bond/ListedForcesTest.Ifunc/20 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/21 24: [ OK ] Bond/ListedForcesTest.Ifunc/21 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/22 24: [ OK ] Bond/ListedForcesTest.Ifunc/22 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/23 24: [ OK ] Bond/ListedForcesTest.Ifunc/23 (0 ms) 24: [----------] 24 tests from Bond/ListedForcesTest (5 ms total) 24: 24: [----------] 33 tests from Angle/ListedForcesTest 24: [ RUN ] Angle/ListedForcesTest.Ifunc/0 24: [ OK ] Angle/ListedForcesTest.Ifunc/0 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/1 24: [ OK ] Angle/ListedForcesTest.Ifunc/1 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/2 24: [ OK ] Angle/ListedForcesTest.Ifunc/2 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/3 24: [ OK ] Angle/ListedForcesTest.Ifunc/3 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/4 24: [ OK ] Angle/ListedForcesTest.Ifunc/4 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/5 24: [ OK ] Angle/ListedForcesTest.Ifunc/5 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/6 24: [ OK ] Angle/ListedForcesTest.Ifunc/6 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/7 24: [ OK ] Angle/ListedForcesTest.Ifunc/7 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/8 24: [ OK ] Angle/ListedForcesTest.Ifunc/8 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/9 24: [ OK ] Angle/ListedForcesTest.Ifunc/9 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/10 24: [ OK ] Angle/ListedForcesTest.Ifunc/10 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/11 24: [ OK ] Angle/ListedForcesTest.Ifunc/11 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/12 24: [ OK ] Angle/ListedForcesTest.Ifunc/12 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/13 24: [ OK ] Angle/ListedForcesTest.Ifunc/13 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/14 24: [ OK ] Angle/ListedForcesTest.Ifunc/14 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/15 24: [ OK ] Angle/ListedForcesTest.Ifunc/15 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/16 24: [ OK ] Angle/ListedForcesTest.Ifunc/16 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/17 24: [ OK ] Angle/ListedForcesTest.Ifunc/17 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/18 24: [ OK ] Angle/ListedForcesTest.Ifunc/18 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/19 24: [ OK ] Angle/ListedForcesTest.Ifunc/19 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/20 24: [ OK ] Angle/ListedForcesTest.Ifunc/20 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/21 24: [ OK ] Angle/ListedForcesTest.Ifunc/21 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/22 24: [ OK ] Angle/ListedForcesTest.Ifunc/22 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/23 24: [ OK ] Angle/ListedForcesTest.Ifunc/23 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/24 24: [ OK ] Angle/ListedForcesTest.Ifunc/24 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/25 24: [ OK ] Angle/ListedForcesTest.Ifunc/25 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/26 24: [ OK ] Angle/ListedForcesTest.Ifunc/26 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/27 24: [ OK ] Angle/ListedForcesTest.Ifunc/27 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/28 24: [ OK ] Angle/ListedForcesTest.Ifunc/28 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/29 24: [ OK ] Angle/ListedForcesTest.Ifunc/29 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/30 24: [ OK ] Angle/ListedForcesTest.Ifunc/30 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/31 24: [ OK ] Angle/ListedForcesTest.Ifunc/31 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/32 24: [ OK ] Angle/ListedForcesTest.Ifunc/32 (0 ms) 24: [----------] 33 tests from Angle/ListedForcesTest (7 ms total) 24: 24: [----------] 18 tests from Dihedral/ListedForcesTest 24: [ RUN ] Dihedral/ListedForcesTest.Ifunc/0 24: [ OK ] Dihedral/ListedForcesTest.Ifunc/0 (0 ms) 24: [ RUN ] Dihedral/ListedForcesTest.Ifunc/1 24: [ OK ] Dihedral/ListedForcesTest.Ifunc/1 (0 ms) 24: [ RUN ] Dihedral/ListedForcesTest.Ifunc/2 24: [ OK ] Dihedral/ListedForcesTest.Ifunc/2 (0 ms) 24: [ RUN ] Dihedral/ListedForcesTest.Ifunc/3 24: [ OK ] Dihedral/ListedForcesTest.Ifunc/3 (0 ms) 24: [ RUN ] Dihedral/ListedForcesTest.Ifunc/4 24: [ OK ] Dihedral/ListedForcesTest.Ifunc/4 (0 ms) 24: [ RUN ] Dihedral/ListedForcesTest.Ifunc/5 24: [ OK ] Dihedral/ListedForcesTest.Ifunc/5 (0 ms) 24: [ RUN ] Dihedral/ListedForcesTest.Ifunc/6 24: [ OK ] Dihedral/ListedForcesTest.Ifunc/6 (0 ms) 24: [ RUN ] Dihedral/ListedForcesTest.Ifunc/7 24: [ OK ] Dihedral/ListedForcesTest.Ifunc/7 (0 ms) 24: [ RUN ] Dihedral/ListedForcesTest.Ifunc/8 24: [ OK ] Dihedral/ListedForcesTest.Ifunc/8 (0 ms) 24: [ RUN ] Dihedral/ListedForcesTest.Ifunc/9 24: [ OK ] Dihedral/ListedForcesTest.Ifunc/9 (0 ms) 24: [ RUN ] Dihedral/ListedForcesTest.Ifunc/10 24: [ OK ] Dihedral/ListedForcesTest.Ifunc/10 (0 ms) 24: [ RUN ] Dihedral/ListedForcesTest.Ifunc/11 24: [ OK ] Dihedral/ListedForcesTest.Ifunc/11 (0 ms) 24: [ RUN ] Dihedral/ListedForcesTest.Ifunc/12 24: [ OK ] Dihedral/ListedForcesTest.Ifunc/12 (0 ms) 24: [ RUN ] Dihedral/ListedForcesTest.Ifunc/13 24: [ OK ] Dihedral/ListedForcesTest.Ifunc/13 (0 ms) 24: [ RUN ] Dihedral/ListedForcesTest.Ifunc/14 24: [ OK ] Dihedral/ListedForcesTest.Ifunc/14 (0 ms) 24: [ RUN ] Dihedral/ListedForcesTest.Ifunc/15 24: [ OK ] Dihedral/ListedForcesTest.Ifunc/15 (0 ms) 24: [ RUN ] Dihedral/ListedForcesTest.Ifunc/16 24: [ OK ] Dihedral/ListedForcesTest.Ifunc/16 (0 ms) 24: [ RUN ] Dihedral/ListedForcesTest.Ifunc/17 24: [ OK ] Dihedral/ListedForcesTest.Ifunc/17 (0 ms) 24: [----------] 18 tests from Dihedral/ListedForcesTest (5 ms total) 24: 24: [----------] 12 tests from Polarize/ListedForcesTest 24: [ RUN ] Polarize/ListedForcesTest.Ifunc/0 24: [ OK ] Polarize/ListedForcesTest.Ifunc/0 (0 ms) 24: [ RUN ] Polarize/ListedForcesTest.Ifunc/1 24: [ OK ] Polarize/ListedForcesTest.Ifunc/1 (0 ms) 24: [ RUN ] Polarize/ListedForcesTest.Ifunc/2 24: [ OK ] Polarize/ListedForcesTest.Ifunc/2 (0 ms) 24: [ RUN ] Polarize/ListedForcesTest.Ifunc/3 24: [ OK ] Polarize/ListedForcesTest.Ifunc/3 (0 ms) 24: [ RUN ] Polarize/ListedForcesTest.Ifunc/4 24: [ OK ] Polarize/ListedForcesTest.Ifunc/4 (0 ms) 24: [ RUN ] Polarize/ListedForcesTest.Ifunc/5 24: [ OK ] Polarize/ListedForcesTest.Ifunc/5 (0 ms) 24: [ RUN ] Polarize/ListedForcesTest.Ifunc/6 24: [ OK ] Polarize/ListedForcesTest.Ifunc/6 (0 ms) 24: [ RUN ] Polarize/ListedForcesTest.Ifunc/7 24: [ OK ] Polarize/ListedForcesTest.Ifunc/7 (0 ms) 24: [ RUN ] Polarize/ListedForcesTest.Ifunc/8 24: [ OK ] Polarize/ListedForcesTest.Ifunc/8 (0 ms) 24: [ RUN ] Polarize/ListedForcesTest.Ifunc/9 24: [ OK ] Polarize/ListedForcesTest.Ifunc/9 (0 ms) 24: [ RUN ] Polarize/ListedForcesTest.Ifunc/10 24: [ OK ] Polarize/ListedForcesTest.Ifunc/10 (0 ms) 24: [ RUN ] Polarize/ListedForcesTest.Ifunc/11 24: [ OK ] Polarize/ListedForcesTest.Ifunc/11 (0 ms) 24: [----------] 12 tests from Polarize/ListedForcesTest (2 ms total) 24: 24: [----------] 18 tests from Restraints/ListedForcesTest 24: [ RUN ] Restraints/ListedForcesTest.Ifunc/0 24: [ OK ] Restraints/ListedForcesTest.Ifunc/0 (0 ms) 24: [ RUN ] Restraints/ListedForcesTest.Ifunc/1 24: [ OK ] Restraints/ListedForcesTest.Ifunc/1 (0 ms) 24: [ RUN ] Restraints/ListedForcesTest.Ifunc/2 24: [ OK ] Restraints/ListedForcesTest.Ifunc/2 (0 ms) 24: [ RUN ] Restraints/ListedForcesTest.Ifunc/3 24: [ OK ] Restraints/ListedForcesTest.Ifunc/3 (0 ms) 24: [ RUN ] Restraints/ListedForcesTest.Ifunc/4 24: [ OK ] Restraints/ListedForcesTest.Ifunc/4 (0 ms) 24: [ RUN ] Restraints/ListedForcesTest.Ifunc/5 24: [ OK ] Restraints/ListedForcesTest.Ifunc/5 (0 ms) 24: [ RUN ] Restraints/ListedForcesTest.Ifunc/6 24: [ OK ] Restraints/ListedForcesTest.Ifunc/6 (0 ms) 24: [ RUN ] Restraints/ListedForcesTest.Ifunc/7 24: [ OK ] Restraints/ListedForcesTest.Ifunc/7 (0 ms) 24: [ RUN ] Restraints/ListedForcesTest.Ifunc/8 24: [ OK ] Restraints/ListedForcesTest.Ifunc/8 (0 ms) 24: [ RUN ] Restraints/ListedForcesTest.Ifunc/9 24: [ OK ] Restraints/ListedForcesTest.Ifunc/9 (0 ms) 24: [ RUN ] Restraints/ListedForcesTest.Ifunc/10 24: [ OK ] Restraints/ListedForcesTest.Ifunc/10 (0 ms) 24: [ RUN ] Restraints/ListedForcesTest.Ifunc/11 24: [ OK ] Restraints/ListedForcesTest.Ifunc/11 (0 ms) 24: [ RUN ] Restraints/ListedForcesTest.Ifunc/12 24: [ OK ] Restraints/ListedForcesTest.Ifunc/12 (0 ms) 24: [ RUN ] Restraints/ListedForcesTest.Ifunc/13 24: [ OK ] Restraints/ListedForcesTest.Ifunc/13 (0 ms) 24: [ RUN ] Restraints/ListedForcesTest.Ifunc/14 24: [ OK ] Restraints/ListedForcesTest.Ifunc/14 (0 ms) 24: [ RUN ] Restraints/ListedForcesTest.Ifunc/15 24: [ OK ] Restraints/ListedForcesTest.Ifunc/15 (0 ms) 24: [ RUN ] Restraints/ListedForcesTest.Ifunc/16 24: [ OK ] Restraints/ListedForcesTest.Ifunc/16 (0 ms) 24: [ RUN ] Restraints/ListedForcesTest.Ifunc/17 24: [ OK ] Restraints/ListedForcesTest.Ifunc/17 (0 ms) 24: [----------] 18 tests from Restraints/ListedForcesTest (4 ms total) 24: 24: [----------] 3 tests from BondZeroLength/ListedForcesTest 24: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/0 24: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/0 (0 ms) 24: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/1 24: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/1 (0 ms) 24: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/2 24: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/2 (0 ms) 24: [----------] 3 tests from BondZeroLength/ListedForcesTest (0 ms total) 24: 24: [----------] 3 tests from AngleZero/ListedForcesTest 24: [ RUN ] AngleZero/ListedForcesTest.Ifunc/0 24: [ OK ] AngleZero/ListedForcesTest.Ifunc/0 (0 ms) 24: [ RUN ] AngleZero/ListedForcesTest.Ifunc/1 24: [ OK ] AngleZero/ListedForcesTest.Ifunc/1 (0 ms) 24: [ RUN ] AngleZero/ListedForcesTest.Ifunc/2 24: [ OK ] AngleZero/ListedForcesTest.Ifunc/2 (0 ms) 24: [----------] 3 tests from AngleZero/ListedForcesTest (0 ms total) 24: 24: [----------] 12 tests from 14Interaction/ListedForcesPairsTest 24: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/0 24: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/0 (0 ms) 24: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/1 24: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/1 (0 ms) 24: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/2 24: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/2 (0 ms) 24: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/3 24: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/3 (0 ms) 24: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/4 24: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/4 (0 ms) 24: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/5 24: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/5 (0 ms) 24: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/6 24: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/6 (0 ms) 24: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/7 24: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/7 (0 ms) 24: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/8 24: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/8 (0 ms) 24: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/9 24: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/9 (0 ms) 24: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/10 24: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/10 (0 ms) 24: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/11 24: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/11 (0 ms) 24: [----------] 12 tests from 14Interaction/ListedForcesPairsTest (2 ms total) 24: 24: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest 24: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 24: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 (0 ms) 24: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 24: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 (0 ms) 24: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 24: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 (0 ms) 24: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 24: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 (0 ms) 24: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 24: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 (0 ms) 24: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 24: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 (0 ms) 24: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 24: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 (0 ms) 24: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 24: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 (0 ms) 24: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 24: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 (0 ms) 24: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest (0 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 132 tests from 9 test suites ran. (27 ms total) 24: [ PASSED ] 132 tests. 24/91 Test #24: ListedForcesTest ............................. Passed 0.40 sec test 25 Start 25: NbnxmTests 25: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/nbnxm-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/NbnxmTests.xml" 25: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/nbnxm/tests 25: Test timeout computed to be: 30 25: [==========] Running 80 tests from 3 test suites. 25: [----------] Global test environment set-up. 25: [----------] 18 tests from KernelSetupTest 25: [ RUN ] KernelSetupTest.getCoulombKernelTypeRF 25: [ OK ] KernelSetupTest.getCoulombKernelTypeRF (0 ms) 25: [ RUN ] KernelSetupTest.getCoulombKernelTypeCut 25: [ OK ] KernelSetupTest.getCoulombKernelTypeCut (0 ms) 25: [ RUN ] KernelSetupTest.getCoulombKernelTypeTable 25: [ OK ] KernelSetupTest.getCoulombKernelTypeTable (0 ms) 25: [ RUN ] KernelSetupTest.getCoulombKernelTypeTableTwin 25: [ OK ] KernelSetupTest.getCoulombKernelTypeTableTwin (0 ms) 25: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwald 25: [ OK ] KernelSetupTest.getCoulombKernelTypeEwald (0 ms) 25: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwaldTwin 25: [ OK ] KernelSetupTest.getCoulombKernelTypeEwaldTwin (0 ms) 25: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone 25: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone (0 ms) 25: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift 25: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift (0 ms) 25: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone 25: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone (0 ms) 25: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift 25: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift (0 ms) 25: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone 25: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone (0 ms) 25: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift 25: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift (0 ms) 25: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutThrows 25: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutThrows (0 ms) 25: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch 25: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch (0 ms) 25: [ RUN ] KernelSetupTest.getVdwKernelTypePmeGeom 25: [ OK ] KernelSetupTest.getVdwKernelTypePmeGeom (0 ms) 25: [ RUN ] KernelSetupTest.getVdwKernelTypePmeNone 25: [ OK ] KernelSetupTest.getVdwKernelTypePmeNone (0 ms) 25: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch 25: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch (0 ms) 25: [ RUN ] KernelSetupTest.getVdwKernelTypeAllCountThrows 25: [ OK ] KernelSetupTest.getVdwKernelTypeAllCountThrows (0 ms) 25: [----------] 18 tests from KernelSetupTest (0 ms total) 25: 25: [----------] 60 tests from NbnxmKernelTest 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwCutCombGeom 25: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwCutCombGeom (0 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwCutCombLB 25: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwCutCombLB (0 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwCutCombNone 25: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwCutCombNone (9 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwForceSwitch 25: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwForceSwitch (4 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwPotSwitch 25: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwPotSwitch (4 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwEwaldCombGeom 25: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwEwaldCombGeom (4 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwCutCombGeom 25: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwCutCombGeom (0 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwCutCombLB 25: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwCutCombLB (0 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwCutCombNone 25: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwCutCombNone (0 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwForceSwitch 25: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwForceSwitch (0 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwPotSwitch 25: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwPotSwitch (0 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwEwaldCombGeom 25: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwEwaldCombGeom (0 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwCutCombGeom 25: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwCutCombLB 25: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwCutCombLB (0 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwCutCombNone 25: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwCutCombNone (0 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwForceSwitch 25: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwForceSwitch (0 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwPotSwitch 25: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwPotSwitch (0 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwEwaldCombGeom 25: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwCutCombGeom 25: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwCutCombGeom (0 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwCutCombLB 25: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwCutCombLB (0 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwCutCombNone 25: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwCutCombNone (4 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwForceSwitch 25: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwForceSwitch (9 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwPotSwitch 25: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwPotSwitch (8 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwEwaldCombGeom 25: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwEwaldCombGeom (5 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwCutCombGeom 25: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwCutCombLB 25: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwCutCombLB (0 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwCutCombNone 25: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwCutCombNone (4 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwForceSwitch 25: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwForceSwitch (8 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwPotSwitch 25: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwPotSwitch (8 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwEwaldCombGeom 25: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwEwaldCombGeom (5 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwCutCombGeom 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwCutCombGeom (1 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwCutCombLB 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwCutCombLB (1 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwCutCombNone 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwCutCombNone (1 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwForceSwitch 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwForceSwitch (2 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwPotSwitch 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwPotSwitch (1 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwEwaldCombGeom 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwEwaldCombGeom (2 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwCutCombGeom 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwCutCombGeom (2 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwCutCombLB 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwCutCombLB (2 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwCutCombNone 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwCutCombNone (2 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwForceSwitch 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwForceSwitch (3 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwPotSwitch 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwPotSwitch (2 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwEwaldCombGeom 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwEwaldCombGeom (3 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwCutCombGeom 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwCutCombGeom (2 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwCutCombLB 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwCutCombLB (2 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwCutCombNone 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwCutCombNone (2 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwForceSwitch 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwForceSwitch (2 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwPotSwitch 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwPotSwitch (2 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwEwaldCombGeom 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwCutCombGeom 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwCutCombGeom (2 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwCutCombLB 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwCutCombLB (2 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwCutCombNone 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwCutCombNone (2 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwForceSwitch 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwForceSwitch (2 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwPotSwitch 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwPotSwitch (2 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwEwaldCombGeom 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwEwaldCombGeom (2 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwCutCombGeom 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwCutCombGeom (2 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwCutCombLB 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwCutCombLB (2 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwCutCombNone 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwCutCombNone (2 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwForceSwitch 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwForceSwitch (2 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwPotSwitch 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwPotSwitch (2 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwEwaldCombGeom 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 25: [----------] 60 tests from NbnxmKernelTest (222 ms total) 25: 25: [----------] 2 tests from WithParameters/CpuListDiagonalExclusionsTest 25: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 25: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 (0 ms) 25: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 25: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 (0 ms) 25: [----------] 2 tests from WithParameters/CpuListDiagonalExclusionsTest (0 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 80 tests from 3 test suites ran. (223 ms total) 25: [ PASSED ] 80 tests. 25/91 Test #25: NbnxmTests ................................... Passed 0.68 sec test 26 Start 26: CommandLineUnitTests 26: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/commandline-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/CommandLineUnitTests.xml" 26: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/commandline/tests 26: Test timeout computed to be: 30 26: [==========] Running 60 tests from 7 test suites. 26: [----------] Global test environment set-up. 26: [----------] 3 tests from CommandLineHelpModuleTest 26: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 26: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (0 ms) 26: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 26: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (0 ms) 26: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 26: [ OK ] CommandLineHelpModuleTest.ExportsHelp (0 ms) 26: [----------] 3 tests from CommandLineHelpModuleTest (0 ms total) 26: 26: [----------] 7 tests from CommandLineHelpWriterTest 26: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 26: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (0 ms) 26: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 26: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms) 26: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 26: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms) 26: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 26: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms) 26: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 26: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) 26: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 26: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms) 26: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues 26: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms) 26: [----------] 7 tests from CommandLineHelpWriterTest (0 ms total) 26: 26: [----------] 6 tests from CommandLineModuleManagerTest 26: [ RUN ] CommandLineModuleManagerTest.RunsModule 26: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms) 26: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 26: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 26: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 26: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 26: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 26: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) 26: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 26: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 26: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 26: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 26: [----------] 6 tests from CommandLineModuleManagerTest (0 ms total) 26: 26: [----------] 13 tests from CommandLineParserTest 26: [ RUN ] CommandLineParserTest.HandlesSingleValues 26: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 26: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 26: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 26: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 26: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 26: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesString 26: [ OK ] CommandLineParserTest.HandlesString (0 ms) 26: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 26: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 26: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 26: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 26: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 26: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 26: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 26: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 26: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 26: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 26: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 26: [----------] 13 tests from CommandLineParserTest (0 ms total) 26: 26: [----------] 6 tests from CommandLineProgramContextTest 26: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 26: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (4 ms) 26: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 26: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 26: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 26: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 26: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 26: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 26: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 26: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (2 ms) 26: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 26: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 26: [----------] 6 tests from CommandLineProgramContextTest (8 ms total) 26: 26: [----------] 3 tests from OutputNamesTest 26: [ RUN ] OutputNamesTest.CanBeSuffixed 26: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms) 26: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend 26: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms) 26: [ RUN ] OutputNamesTest.CanHavePartNumberAdded 26: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms) 26: [----------] 3 tests from OutputNamesTest (0 ms total) 26: 26: [----------] 22 tests from ParseCommonArgsTest 26: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 26: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 26: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 26: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 26: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 26: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum 26: [ OK ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 26: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 26: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 26: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 26: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 26: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 26: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 26: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 26: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 26: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 26: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 26: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 26: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 26: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 26: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 26: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 26: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (1 ms) 26: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 26: Value is /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/commandline/tests/Testing/Temporary/ParseCommonArgsTest_AcceptsUnknownTrajectoryExtension.foo 26: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) 26: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 26: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (0 ms) 26: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 26: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (6 ms) 26: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 26: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 26: [----------] 22 tests from ParseCommonArgsTest (11 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 60 tests from 7 test suites ran. (23 ms total) 26: [ PASSED ] 60 tests. 26/91 Test #26: CommandLineUnitTests ......................... Passed 0.43 sec test 27 Start 27: DomDecTests 27: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/domdec-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/DomDecTests.xml" 27: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/domdec/tests 27: Test timeout computed to be: 30 27: [==========] Running 9 tests from 2 test suites. 27: [----------] Global test environment set-up. 27: [----------] 7 tests from HashedMap 27: [ RUN ] HashedMap.InsertsFinds 27: [ OK ] HashedMap.InsertsFinds (0 ms) 27: [ RUN ] HashedMap.NegativeKeysWork 27: [ OK ] HashedMap.NegativeKeysWork (0 ms) 27: [ RUN ] HashedMap.InsertsErases 27: [ OK ] HashedMap.InsertsErases (0 ms) 27: [ RUN ] HashedMap.InsertsOrAssigns 27: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 27: [ RUN ] HashedMap.Clears 27: [ OK ] HashedMap.Clears (0 ms) 27: [ RUN ] HashedMap.LinkedEntries 27: [ OK ] HashedMap.LinkedEntries (0 ms) 27: [ RUN ] HashedMap.ResizesTable 27: [ OK ] HashedMap.ResizesTable (0 ms) 27: [----------] 7 tests from HashedMap (0 ms total) 27: 27: [----------] 2 tests from LocalAtomSetManager 27: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 27: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 27: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 27: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 27: [----------] 2 tests from LocalAtomSetManager (0 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 9 tests from 2 test suites ran. (0 ms total) 27: [ PASSED ] 9 tests. 27/91 Test #27: DomDecTests .................................. Passed 0.33 sec test 28 Start 28: DomDecMpiTests 28: Test command: /usr/bin/mpiexec "-n" "4" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/domdec-mpi-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/DomDecMpiTests.xml" 28: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/domdec/tests 28: Test timeout computed to be: 30 28: [==========] Running 4 tests from 1 test suite. 28: [----------] Global test environment set-up. 28: [----------] 4 tests from HaloExchangeTest 28: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith1Pulse 28: [ OK ] HaloExchangeTest.Coordinates1dHaloWith1Pulse (0 ms) 28: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith2Pulses 28: [ OK ] HaloExchangeTest.Coordinates1dHaloWith2Pulses (19 ms) 28: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim 28: [ OK ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim (0 ms) 28: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 28: [ OK ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 (4 ms) 28: [----------] 4 tests from HaloExchangeTest (135 ms total) 28: 28: [----------] Global test environment tear-down 28: [==========] 4 tests from 1 test suite ran. (135 ms total) 28: [ PASSED ] 4 tests. 28/91 Test #28: DomDecMpiTests ............................... Passed 0.76 sec test 29 Start 29: EwaldUnitTests 29: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/ewald-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/EwaldUnitTests.xml" 29: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/ewald/tests 29: Test timeout computed to be: 30 29: [==========] Running 407 tests from 9 test suites. 29: [----------] Global test environment set-up. 29: [----------] 6 tests from SeparatePmeRanksPermittedTest 29: [ RUN ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons 29: [ OK ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons (0 ms) 29: [ RUN ] SeparatePmeRanksPermittedTest.CanBeDisabled 29: [ OK ] SeparatePmeRanksPermittedTest.CanBeDisabled (0 ms) 29: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag 29: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag (0 ms) 29: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonText 29: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonText (0 ms) 29: [ RUN ] SeparatePmeRanksPermittedTest.TwoDisableReasonText 29: [ OK ] SeparatePmeRanksPermittedTest.TwoDisableReasonText (0 ms) 29: [ RUN ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText 29: [ OK ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText (0 ms) 29: [----------] 6 tests from SeparatePmeRanksPermittedTest (0 ms total) 29: 29: [----------] 108 tests from Pme_SplineAndSpreadTest 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline (22 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline (8 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline (4 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline (4 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread (5 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline (5 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (5 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread (5 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 29: [----------] 108 tests from Pme_SplineAndSpreadTest (145 ms total) 29: 29: [----------] 64 tests from Pme_SolveTest 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (4 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [----------] 64 tests from Pme_SolveTest (24 ms total) 29: 29: [----------] 32 tests from PmeDiffEwaldQ_SolveTest 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (4 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [----------] 32 tests from PmeDiffEwaldQ_SolveTest (13 ms total) 29: 29: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (4 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest (8 ms total) 29: 29: [----------] 64 tests from PmeDiffEps_SolveTest 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [----------] 64 tests from PmeDiffEps_SolveTest (22 ms total) 29: 29: [----------] 72 tests from Pme_GatherTest 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 29: [----------] 72 tests from Pme_GatherTest (17 ms total) 29: 29: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 29: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 29: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms) 29: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 29: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 29: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 29: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 29: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 29: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (1 ms) 29: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 29: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 29: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (1 ms total) 29: 29: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (1 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (0 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (1 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (1 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (1 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (1 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (1 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (1 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (1 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (1 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (1 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (1 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (5 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (0 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (0 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (1 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (0 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (0 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (1 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (0 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (1 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (0 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (0 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (0 ms) 29: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (54 ms total) 29: 29: [----------] Global test environment tear-down 29: [==========] 407 tests from 9 test suites ran. (289 ms total) 29: [ PASSED ] 311 tests. 29: [ SKIPPED ] 96 tests, listed below: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29/91 Test #29: EwaldUnitTests ............................... Passed 0.68 sec test 30 Start 30: FFTUnitTests 30: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/fft-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/FFTUnitTests.xml" 30: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fft/tests 30: Test timeout computed to be: 1920 30: [==========] Running 15 tests from 4 test suites. 30: [----------] Global test environment set-up. 30: [----------] 2 tests from ManyFFTTest 30: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 30: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (3 ms) 30: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 30: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (17 ms) 30: [----------] 2 tests from ManyFFTTest (20 ms total) 30: 30: [----------] 1 test from FFTTest 30: [ RUN ] FFTTest.Real2DLength18_15Test 30: [ OK ] FFTTest.Real2DLength18_15Test (2 ms) 30: [----------] 1 test from FFTTest (7 ms total) 30: 30: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 30: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (0 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 30: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (0 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 30: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (0 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 30: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (1 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 30: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (0 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 30: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (0 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 30: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (0 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 30: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (0 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 30: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (9 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 30: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (11 ms) 30: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (31 ms total) 30: 30: [----------] 2 tests from Works/ParameterizedFFTTest3D 30: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 30: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 (0 ms) 30: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 30: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 (0 ms) 30: [----------] 2 tests from Works/ParameterizedFFTTest3D (3 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 15 tests from 4 test suites ran. (63 ms total) 30: [ PASSED ] 15 tests. 30/91 Test #30: FFTUnitTests ................................. Passed 0.44 sec test 31 Start 31: GpuUtilsUnitTests 31: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/gpu_utils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/GpuUtilsUnitTests.xml" 31: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gpu_utils/tests 31: Test timeout computed to be: 30 31: [==========] Running 64 tests from 22 test suites. 31: [----------] Global test environment set-up. 31: [----------] 2 tests from ClfftInitializer 31: [ RUN ] ClfftInitializer.SingleInitializationWorks 31: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms) 31: [ RUN ] ClfftInitializer.TwoInitializationsWork 31: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms) 31: [----------] 2 tests from ClfftInitializer (0 ms total) 31: 31: [----------] 1 test from DevicesAvailable 31: [ RUN ] DevicesAvailable.ShouldBeAbleToRunOnDevice 31: [ OK ] DevicesAvailable.ShouldBeAbleToRunOnDevice (0 ms) 31: [----------] 1 test from DevicesAvailable (0 ms total) 31: 31: [----------] 1 test from DeviceStreamManagerTest 31: [ RUN ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice 31: [ OK ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice (0 ms) 31: [----------] 1 test from DeviceStreamManagerTest (0 ms total) 31: 31: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 31: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 31: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 31: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 31: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 31: 31: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float 31: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 31: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 31: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 31: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 31: 31: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 31: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 31: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 31: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 31: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 31: 31: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 31: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 31: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 31: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 31: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 31: 31: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 31: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 31: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 31: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 31: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 31: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 31: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 31: 31: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float 31: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 31: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 31: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 31: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 31: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 31: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 31: 31: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 31: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 31: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 31: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 31: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 31: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 31: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 31: 31: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 31: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 31: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 31: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 31: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/0.Swap 31: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/0.Comparison 31: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 31: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 31: 31: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float 31: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 31: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 31: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 31: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/1.Swap 31: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/1.Comparison 31: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 31: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 31: 31: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 31: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 31: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 31: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 31: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/2.Swap 31: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/2.Comparison 31: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 31: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 31: 31: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 31: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 31: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 31: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 31: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/3.Swap 31: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/3.Comparison 31: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 31: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 31: 31: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 31: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 31: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 31: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 31: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 31: 31: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float 31: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 31: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 31: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 31: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 31: 31: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 31: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 31: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 31: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 31: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 31: 31: [----------] 1 test from HostAllocatorUntypedTest 31: [ RUN ] HostAllocatorUntypedTest.Comparison 31: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 31: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 31: 31: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 31: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 31: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 31: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 31: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/0.Move 31: [ OK ] AllocatorTest/0.Move (0 ms) 31: [----------] 4 tests from AllocatorTest/0 (0 ms total) 31: 31: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 31: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 31: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 31: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 31: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/1.Move 31: [ OK ] AllocatorTest/1.Move (0 ms) 31: [----------] 4 tests from AllocatorTest/1 (0 ms total) 31: 31: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> 31: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 31: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 31: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 31: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/2.Move 31: [ OK ] AllocatorTest/2.Move (0 ms) 31: [----------] 4 tests from AllocatorTest/2 (0 ms total) 31: 31: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 31: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 31: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 31: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 31: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/3.Move 31: [ OK ] AllocatorTest/3.Move (0 ms) 31: [----------] 4 tests from AllocatorTest/3 (0 ms total) 31: 31: [----------] Global test environment tear-down 31: [==========] 64 tests from 22 test suites ran. (0 ms total) 31: [ PASSED ] 64 tests. 31/91 Test #31: GpuUtilsUnitTests ............................ Passed 0.38 sec test 32 Start 32: HardwareUnitTests 32: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/hardware-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/HardwareUnitTests.xml" 32: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/hardware/tests 32: Test timeout computed to be: 30 32: [==========] Running 21 tests from 9 test suites. 32: [----------] Global test environment set-up. 32: [----------] 1 test from CpuInfoTest 32: [ RUN ] CpuInfoTest.SupportLevel 32: [ OK ] CpuInfoTest.SupportLevel (0 ms) 32: [----------] 1 test from CpuInfoTest (0 ms total) 32: 32: [----------] 4 tests from HardwareTopologyTest 32: [ RUN ] HardwareTopologyTest.Execute 32: [ OK ] HardwareTopologyTest.Execute (22 ms) 32: [ RUN ] HardwareTopologyTest.HwlocExecute 32: [ OK ] HardwareTopologyTest.HwlocExecute (23 ms) 32: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 32: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (20 ms) 32: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 32: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (31 ms) 32: [----------] 4 tests from HardwareTopologyTest (98 ms total) 32: 32: [----------] 1 test from DevicesManagerTest 32: [ RUN ] DevicesManagerTest.Serialization 32: [ OK ] DevicesManagerTest.Serialization (0 ms) 32: [----------] 1 test from DevicesManagerTest (0 ms total) 32: 32: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest 32: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 32: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 (0 ms) 32: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 32: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 32: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 32: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) 32: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 32: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) 32: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 32: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) 32: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest (1 ms total) 32: 32: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest 32: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 32: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 (1 ms) 32: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 32: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 32: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 32: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) 32: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 32: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) 32: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 32: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) 32: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest (5 ms total) 32: 32: [----------] 2 tests from Core12900K/MockHardwareTopologyTest 32: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 32: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 (0 ms) 32: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 32: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 32: [----------] 2 tests from Core12900K/MockHardwareTopologyTest (1 ms total) 32: 32: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest 32: [ RUN ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 32: [ OK ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (0 ms) 32: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest (5 ms total) 32: 32: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest 32: [ RUN ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 32: [ OK ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (0 ms) 32: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest (0 ms total) 32: 32: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest 32: [ RUN ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 32: [ OK ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (1 ms) 32: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest (1 ms total) 32: 32: [----------] Global test environment tear-down 32: [==========] 21 tests from 9 test suites ran. (115 ms total) 32: [ PASSED ] 21 tests. 32/91 Test #32: HardwareUnitTests ............................ Passed 0.47 sec test 33 Start 33: MathUnitTests 33: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/math-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MathUnitTests.xml" 33: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests 33: Test timeout computed to be: 30 33: [==========] Running 304 tests from 38 test suites. 33: [----------] Global test environment set-up. 33: [----------] 1 test from EmptyArrayRefWithPaddingTest 33: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 33: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 33: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 33: 33: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 33: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 33: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 33: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 33: 33: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 33: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 33: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 33: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 33: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 33: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 33: 33: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 33: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 33: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 33: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 33: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 33: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 33: 33: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 33: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 33: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 33: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 33: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 33: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 33: 33: [----------] 2 tests from InvertBoxMatrixTest 33: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 33: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 33: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 33: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 33: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 33: 33: [----------] 11 tests from TranslateAndScaleTest 33: [ RUN ] TranslateAndScaleTest.identityTransformation 33: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms) 33: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling 33: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation 33: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms) 33: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial 33: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms) 33: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector 33: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingIdentity 33: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingNonTrivial 33: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingNonTrivialSingleVector 33: [ OK ] TranslateAndScaleTest.scalingNonTrivialSingleVector (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero 33: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero 33: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector 33: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector (0 ms) 33: [----------] 11 tests from TranslateAndScaleTest (0 ms total) 33: 33: [----------] 3 tests from AffineTransformationTest 33: [ RUN ] AffineTransformationTest.identityTransformYieldsSameVectors 33: [ OK ] AffineTransformationTest.identityTransformYieldsSameVectors (0 ms) 33: [ RUN ] AffineTransformationTest.applyTransformationToVectors 33: [ OK ] AffineTransformationTest.applyTransformationToVectors (0 ms) 33: [ RUN ] AffineTransformationTest.retrieveGradient 33: [ OK ] AffineTransformationTest.retrieveGradient (0 ms) 33: [----------] 3 tests from AffineTransformationTest (0 ms total) 33: 33: [----------] 14 tests from DensitySimilarityTest 33: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect 33: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect 33: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch 33: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms) 33: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch 33: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms) 33: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect 33: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero 33: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms) 33: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect 33: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect 33: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne 33: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (29 ms) 33: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated 33: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (22 ms) 33: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated 33: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (1 ms) 33: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect 33: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.NormalizationCorrect 33: [ OK ] DensitySimilarityTest.NormalizationCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.NormalizationAllNonPositive 33: [ OK ] DensitySimilarityTest.NormalizationAllNonPositive (0 ms) 33: [----------] 14 tests from DensitySimilarityTest (59 ms total) 33: 33: [----------] 6 tests from StructureSimilarityTest 33: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 33: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 33: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 33: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 33: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 33: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 33: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 33: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 33: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 33: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 33: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 33: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 33: [----------] 6 tests from StructureSimilarityTest (0 ms total) 33: 33: [----------] 8 tests from ExponentialMovingAverage 33: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero 33: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms) 33: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative 33: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms) 33: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue 33: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms) 33: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue 33: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms) 33: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly 33: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms) 33: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing 33: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms) 33: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect 33: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms) 33: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree 33: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms) 33: [----------] 8 tests from ExponentialMovingAverage (0 ms total) 33: 33: [----------] 21 tests from FunctionTest 33: [ RUN ] FunctionTest.StaticLog2 33: [ OK ] FunctionTest.StaticLog2 (0 ms) 33: [ RUN ] FunctionTest.Log2I32Bit 33: [ OK ] FunctionTest.Log2I32Bit (0 ms) 33: [ RUN ] FunctionTest.Log2I64Bit 33: [ OK ] FunctionTest.Log2I64Bit (0 ms) 33: [ RUN ] FunctionTest.GreatestCommonDivisor 33: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 33: [ RUN ] FunctionTest.InvsqrtFloat 33: [ OK ] FunctionTest.InvsqrtFloat (0 ms) 33: [ RUN ] FunctionTest.InvsqrtDouble 33: [ OK ] FunctionTest.InvsqrtDouble (0 ms) 33: [ RUN ] FunctionTest.InvsqrtInteger 33: [ OK ] FunctionTest.InvsqrtInteger (0 ms) 33: [ RUN ] FunctionTest.InvcbrtFloat 33: [ OK ] FunctionTest.InvcbrtFloat (0 ms) 33: [ RUN ] FunctionTest.InvcbrtDouble 33: [ OK ] FunctionTest.InvcbrtDouble (0 ms) 33: [ RUN ] FunctionTest.InvcbrtInteger 33: [ OK ] FunctionTest.InvcbrtInteger (0 ms) 33: [ RUN ] FunctionTest.SixthrootFloat 33: [ OK ] FunctionTest.SixthrootFloat (0 ms) 33: [ RUN ] FunctionTest.SixthrootDouble 33: [ OK ] FunctionTest.SixthrootDouble (0 ms) 33: [ RUN ] FunctionTest.SixthrootInteger 33: [ OK ] FunctionTest.SixthrootInteger (0 ms) 33: [ RUN ] FunctionTest.InvsixthrootFloat 33: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) 33: [ RUN ] FunctionTest.InvsixthrootDouble 33: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) 33: [ RUN ] FunctionTest.InvsixthrootInteger 33: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) 33: [ RUN ] FunctionTest.Powers 33: [ OK ] FunctionTest.Powers (0 ms) 33: [ RUN ] FunctionTest.ErfInvFloat 33: [ OK ] FunctionTest.ErfInvFloat (0 ms) 33: [ RUN ] FunctionTest.ErfInvDouble 33: [ OK ] FunctionTest.ErfInvDouble (0 ms) 33: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 33: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) 33: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 33: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms) 33: [----------] 21 tests from FunctionTest (0 ms total) 33: 33: [----------] 1 test from FunctionTestIntegerTypes/0, where TypeParam = char 33: [ RUN ] FunctionTestIntegerTypes/0.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/0.IsPowerOfTwo (0 ms) 33: [----------] 1 test from FunctionTestIntegerTypes/0 (0 ms total) 33: 33: [----------] 1 test from FunctionTestIntegerTypes/1, where TypeParam = unsigned char 33: [ RUN ] FunctionTestIntegerTypes/1.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/1.IsPowerOfTwo (0 ms) 33: [----------] 1 test from FunctionTestIntegerTypes/1 (0 ms total) 33: 33: [----------] 1 test from FunctionTestIntegerTypes/2, where TypeParam = int 33: [ RUN ] FunctionTestIntegerTypes/2.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/2.IsPowerOfTwo (0 ms) 33: [----------] 1 test from FunctionTestIntegerTypes/2 (0 ms total) 33: 33: [----------] 1 test from FunctionTestIntegerTypes/3, where TypeParam = unsigned int 33: [ RUN ] FunctionTestIntegerTypes/3.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/3.IsPowerOfTwo (0 ms) 33: [----------] 1 test from FunctionTestIntegerTypes/3 (0 ms total) 33: 33: [----------] 1 test from FunctionTestIntegerTypes/4, where TypeParam = long 33: [ RUN ] FunctionTestIntegerTypes/4.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/4.IsPowerOfTwo (0 ms) 33: [----------] 1 test from FunctionTestIntegerTypes/4 (0 ms total) 33: 33: [----------] 1 test from FunctionTestIntegerTypes/5, where TypeParam = unsigned long 33: [ RUN ] FunctionTestIntegerTypes/5.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/5.IsPowerOfTwo (0 ms) 33: [----------] 1 test from FunctionTestIntegerTypes/5 (0 ms total) 33: 33: [----------] 4 tests from GaussianOn1DLattice 33: [ RUN ] GaussianOn1DLattice.sumsCloseToOne 33: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms) 33: [ RUN ] GaussianOn1DLattice.isCorrect 33: [ OK ] GaussianOn1DLattice.isCorrect (0 ms) 33: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero 33: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms) 33: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange 33: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms) 33: [----------] 4 tests from GaussianOn1DLattice (0 ms total) 33: 33: [----------] 9 tests from GaussTransformTest 33: [ RUN ] GaussTransformTest.isZeroUponConstruction 33: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms) 33: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss 33: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms) 33: [ RUN ] GaussTransformTest.isZeroAfterSettingZero 33: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms) 33: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX 33: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms) 33: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY 33: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms) 33: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ 33: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms) 33: [ RUN ] GaussTransformTest.complementaryGaussAddToZero 33: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms) 33: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues 33: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms) 33: [ RUN ] GaussTransformTest.view 33: [ OK ] GaussTransformTest.view (0 ms) 33: [----------] 9 tests from GaussTransformTest (0 ms total) 33: 33: [----------] 3 tests from DensityFittingForce 33: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity 33: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms) 33: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections 33: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms) 33: [ RUN ] DensityFittingForce.pullsTowardsDerivative 33: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms) 33: [----------] 3 tests from DensityFittingForce (0 ms total) 33: 33: [----------] 2 tests from InvertMatrixTest 33: [ RUN ] InvertMatrixTest.IdentityIsImpotent 33: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 33: [ RUN ] InvertMatrixTest.ComputesInverse 33: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 33: [----------] 2 tests from InvertMatrixTest (0 ms total) 33: 33: [----------] 17 tests from MatrixTest 33: [ RUN ] MatrixTest.canSetFromArray 33: [ OK ] MatrixTest.canSetFromArray (0 ms) 33: [ RUN ] MatrixTest.canSetStaticallyFromList 33: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms) 33: [ RUN ] MatrixTest.canConstructAndFill 33: [ OK ] MatrixTest.canConstructAndFill (0 ms) 33: [ RUN ] MatrixTest.canSetValues 33: [ OK ] MatrixTest.canSetValues (0 ms) 33: [ RUN ] MatrixTest.canCopyAssign 33: [ OK ] MatrixTest.canCopyAssign (0 ms) 33: [ RUN ] MatrixTest.canSwap 33: [ OK ] MatrixTest.canSwap (0 ms) 33: [ RUN ] MatrixTest.staticMultiDimArrayExtent 33: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms) 33: [ RUN ] MatrixTest.determinantWorks 33: [ OK ] MatrixTest.determinantWorks (0 ms) 33: [ RUN ] MatrixTest.noninvertableDeterminantIsZero 33: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms) 33: [ RUN ] MatrixTest.determinantOfDiagonalMatrix 33: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms) 33: [ RUN ] MatrixTest.traceWorks 33: [ OK ] MatrixTest.traceWorks (0 ms) 33: [ RUN ] MatrixTest.transposeWorks 33: [ OK ] MatrixTest.transposeWorks (0 ms) 33: [ RUN ] MatrixTest.transposeOfSymmetricMatrix 33: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms) 33: [ RUN ] MatrixTest.canCreateFromLegacyMatrix 33: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms) 33: [ RUN ] MatrixTest.canFillLegacyMatrix 33: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms) 33: [ RUN ] MatrixTest.IdentityMatrix 33: [ OK ] MatrixTest.IdentityMatrix (0 ms) 33: [ RUN ] MatrixTest.MatrixVectorMultiplication 33: [ OK ] MatrixTest.MatrixVectorMultiplication (0 ms) 33: [----------] 17 tests from MatrixTest (0 ms total) 33: 33: [----------] 25 tests from MultiDimArrayTest 33: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic 33: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic 33: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.canSetValuesInStatic 33: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic 33: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.canMoveConstructStatic 33: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic 33: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.canMoveAssignStatic 33: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic 33: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.canCopyConstructStatic 33: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic 33: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.canCopyAssignStatic 33: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic 33: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.canSwapStatic 33: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canSwapDynamic 33: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent 33: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms) 33: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent 33: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms) 33: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent 33: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms) 33: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue 33: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms) 33: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray 33: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms) 33: [ RUN ] MultiDimArrayTest.conversionToView 33: [ OK ] MultiDimArrayTest.conversionToView (0 ms) 33: [ RUN ] MultiDimArrayTest.conversionToConstView 33: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms) 33: [ RUN ] MultiDimArrayTest.viewBegin 33: [ OK ] MultiDimArrayTest.viewBegin (0 ms) 33: [ RUN ] MultiDimArrayTest.viewEnd 33: [ OK ] MultiDimArrayTest.viewEnd (0 ms) 33: [ RUN ] MultiDimArrayTest.constViewConstBegin 33: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms) 33: [ RUN ] MultiDimArrayTest.constViewConstEnd 33: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms) 33: [----------] 25 tests from MultiDimArrayTest (0 ms total) 33: 33: [----------] 4 tests from MultiDimArrayToMdSpanTest 33: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan 33: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms) 33: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan 33: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms) 33: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan 33: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms) 33: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan 33: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms) 33: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total) 33: 33: [----------] 9 tests from NelderMeadSimplexTest 33: [ RUN ] NelderMeadSimplexTest.BestVertex 33: [ OK ] NelderMeadSimplexTest.BestVertex (0 ms) 33: [ RUN ] NelderMeadSimplexTest.WorstVertex 33: [ OK ] NelderMeadSimplexTest.WorstVertex (0 ms) 33: [ RUN ] NelderMeadSimplexTest.SecondWorstValue 33: [ OK ] NelderMeadSimplexTest.SecondWorstValue (0 ms) 33: [ RUN ] NelderMeadSimplexTest.ReflectionPoint 33: [ OK ] NelderMeadSimplexTest.ReflectionPoint (0 ms) 33: [ RUN ] NelderMeadSimplexTest.EvaluateExpansionPoint 33: [ OK ] NelderMeadSimplexTest.EvaluateExpansionPoint (0 ms) 33: [ RUN ] NelderMeadSimplexTest.EvaluateContractionPoint 33: [ OK ] NelderMeadSimplexTest.EvaluateContractionPoint (0 ms) 33: [ RUN ] NelderMeadSimplexTest.SwapOutWorst 33: [ OK ] NelderMeadSimplexTest.SwapOutWorst (0 ms) 33: [ RUN ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest 33: [ OK ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest (0 ms) 33: [ RUN ] NelderMeadSimplexTest.OrientedLength 33: [ OK ] NelderMeadSimplexTest.OrientedLength (0 ms) 33: [----------] 9 tests from NelderMeadSimplexTest (0 ms total) 33: 33: [----------] 2 tests from NelderMead 33: [ RUN ] NelderMead.Optimizes2DFunctionCorrectly 33: [ OK ] NelderMead.Optimizes2DFunctionCorrectly (0 ms) 33: [ RUN ] NelderMead.Optimizes3DFunctorCorrectly 33: [ OK ] NelderMead.Optimizes3DFunctorCorrectly (0 ms) 33: [----------] 2 tests from NelderMead (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/0, where TypeParam = std::allocator 33: [ RUN ] PaddedVectorTest/0.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/0.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/0.ResizeWorks 33: [ OK ] PaddedVectorTest/0.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/0.ReserveWorks 33: [ OK ] PaddedVectorTest/0.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/0.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/0.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/0.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/0.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/0.CanCopyAssign 33: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/0.CanMoveAssign 33: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/0.CanSwap 33: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/0 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/1, where TypeParam = std::allocator 33: [ RUN ] PaddedVectorTest/1.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/1.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/1.ResizeWorks 33: [ OK ] PaddedVectorTest/1.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/1.ReserveWorks 33: [ OK ] PaddedVectorTest/1.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/1.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/1.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/1.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/1.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/1.CanCopyAssign 33: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/1.CanMoveAssign 33: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/1.CanSwap 33: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/1 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/2, where TypeParam = std::allocator 33: [ RUN ] PaddedVectorTest/2.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/2.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/2.ResizeWorks 33: [ OK ] PaddedVectorTest/2.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/2.ReserveWorks 33: [ OK ] PaddedVectorTest/2.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/2.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/2.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/2.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/2.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/2.CanCopyAssign 33: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/2.CanMoveAssign 33: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/2.CanSwap 33: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/2 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 33: [ RUN ] PaddedVectorTest/3.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/3.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/3.ResizeWorks 33: [ OK ] PaddedVectorTest/3.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/3.ReserveWorks 33: [ OK ] PaddedVectorTest/3.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/3.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/3.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/3.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/3.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/3.CanCopyAssign 33: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/3.CanMoveAssign 33: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/3.CanSwap 33: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/3 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 33: [ RUN ] PaddedVectorTest/4.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/4.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/4.ResizeWorks 33: [ OK ] PaddedVectorTest/4.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/4.ReserveWorks 33: [ OK ] PaddedVectorTest/4.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/4.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/4.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/4.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/4.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/4.CanCopyAssign 33: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/4.CanMoveAssign 33: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/4.CanSwap 33: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/4 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 33: [ RUN ] PaddedVectorTest/5.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/5.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/5.ResizeWorks 33: [ OK ] PaddedVectorTest/5.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/5.ReserveWorks 33: [ OK ] PaddedVectorTest/5.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/5.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/5.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/5.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/5.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/5.CanCopyAssign 33: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/5.CanMoveAssign 33: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/5.CanSwap 33: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/5 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 33: [ RUN ] PaddedVectorTest/6.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/6.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/6.ResizeWorks 33: [ OK ] PaddedVectorTest/6.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/6.ReserveWorks 33: [ OK ] PaddedVectorTest/6.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/6.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/6.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/6.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/6.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/6.CanCopyAssign 33: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/6.CanMoveAssign 33: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/6.CanSwap 33: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/6 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 33: [ RUN ] PaddedVectorTest/7.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/7.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/7.ResizeWorks 33: [ OK ] PaddedVectorTest/7.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/7.ReserveWorks 33: [ OK ] PaddedVectorTest/7.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/7.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/7.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/7.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/7.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/7.CanCopyAssign 33: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/7.CanMoveAssign 33: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/7.CanSwap 33: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/7 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 33: [ RUN ] PaddedVectorTest/8.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/8.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/8.ResizeWorks 33: [ OK ] PaddedVectorTest/8.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/8.ReserveWorks 33: [ OK ] PaddedVectorTest/8.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/8.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/8.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/8.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/8.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/8.CanCopyAssign 33: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/8.CanMoveAssign 33: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/8.CanSwap 33: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/8 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 33: [ RUN ] PaddedVectorTest/9.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/9.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/9.ResizeWorks 33: [ OK ] PaddedVectorTest/9.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/9.ReserveWorks 33: [ OK ] PaddedVectorTest/9.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/9.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/9.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/9.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/9.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/9.CanCopyAssign 33: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/9.CanMoveAssign 33: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/9.CanSwap 33: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/9 (0 ms total) 33: 33: [----------] 40 tests from RVecTest 33: [ RUN ] RVecTest.CanBeStoredInVector 33: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 33: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 33: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 33: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 33: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 33: [ RUN ] RVecTest.WorksAsMutable_rvec 33: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 33: [ RUN ] RVecTest.WorksAs_rvec_Array 33: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 33: [ RUN ] RVecTest.ComparesEqual 33: [ OK ] RVecTest.ComparesEqual (0 ms) 33: [ RUN ] RVecTest.ComparesUnequal 33: [ OK ] RVecTest.ComparesUnequal (0 ms) 33: [ RUN ] RVecTest.CanAddRVecToRvec 33: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 33: [ RUN ] RVecTest.CanAddAssignRVecToRvec 33: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 33: [ RUN ] RVecTest.CanSubtractRVecFromRvec 33: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 33: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 33: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 33: [ RUN ] RVecTest.CanDotProductRVecByRvec 33: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 33: [ RUN ] RVecTest.CanCrossProductRVecByRvec 33: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 33: [ RUN ] RVecTest.CanDivideRVecInplace 33: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 33: [ RUN ] RVecTest.CanScaleRVec 33: [ OK ] RVecTest.CanScaleRVec (0 ms) 33: [ RUN ] RVecTest.CanDivideRVec 33: [ OK ] RVecTest.CanDivideRVec (0 ms) 33: [ RUN ] RVecTest.CanDoUnitvFromRVec 33: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 33: [ RUN ] RVecTest.CanSqLengthOfRVec 33: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 33: [ RUN ] RVecTest.CanLengthOfRVec 33: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 33: [ RUN ] RVecTest.CanCastToRVec 33: [ OK ] RVecTest.CanCastToRVec (0 ms) 33: [ RUN ] RVecTest.CanCastToDVec 33: [ OK ] RVecTest.CanCastToDVec (0 ms) 33: [ RUN ] RVecTest.CanLeftScalarMultiply 33: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 33: [ RUN ] RVecTest.CanRightScalarMultiply 33: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 33: [ RUN ] RVecTest.CanGetUnitvFromRVec 33: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 33: [ RUN ] RVecTest.CanGetSqLengthOfRVec 33: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 33: [ RUN ] RVecTest.CanGetLengthOfRVec 33: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 33: [ RUN ] RVecTest.CanDoCrossProductOfRVec 33: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 33: [ RUN ] RVecTest.CanDoDotProductOfRVec 33: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 33: [ RUN ] RVecTest.CanScaleByVector 33: [ OK ] RVecTest.CanScaleByVector (0 ms) 33: [ RUN ] RVecTest.CanNegate 33: [ OK ] RVecTest.CanNegate (0 ms) 33: [ RUN ] RVecTest.asIVec 33: [ OK ] RVecTest.asIVec (0 ms) 33: [ RUN ] RVecTest.elementWiseMin 33: [ OK ] RVecTest.elementWiseMin (0 ms) 33: [ RUN ] RVecTest.elementWiseMax 33: [ OK ] RVecTest.elementWiseMax (0 ms) 33: [ RUN ] RVecTest.WorksAs_dvec_Reference 33: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 33: [ RUN ] RVecTest.WorksAs_ivec_Reference 33: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 33: [ RUN ] RVecTest.WorksAs_rvec_Reference 33: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 33: [ RUN ] RVecTest.CopyConstructorWorks 33: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 33: [ RUN ] RVecTest.CopyAssignmentWorks 33: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 33: [ RUN ] RVecTest.MoveConstructorWorks 33: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 33: [ RUN ] RVecTest.MoveAssignmentWorks 33: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 33: [----------] 40 tests from RVecTest (0 ms total) 33: 33: [----------] Global test environment tear-down 33: [==========] 304 tests from 38 test suites ran. (61 ms total) 33: [ PASSED ] 304 tests. 33/91 Test #33: MathUnitTests ................................ Passed 0.43 sec test 34 Start 34: MdrunUtilityUnitTests 34: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrunutility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunUtilityUnitTests.xml" 34: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdrunutility/tests 34: Test timeout computed to be: 30 34: [==========] Running 21 tests from 2 test suites. 34: [----------] Global test environment set-up. 34: [----------] 4 tests from MDModulesNotifierTest 34: [ RUN ] MDModulesNotifierTest.AddConsumer 34: [ OK ] MDModulesNotifierTest.AddConsumer (0 ms) 34: [ RUN ] MDModulesNotifierTest.AddConsumerWithPointerParameter 34: [ OK ] MDModulesNotifierTest.AddConsumerWithPointerParameter (0 ms) 34: [ RUN ] MDModulesNotifierTest.AddTwoDifferentConsumers 34: [ OK ] MDModulesNotifierTest.AddTwoDifferentConsumers (0 ms) 34: [ RUN ] MDModulesNotifierTest.AddConsumerOfTwoResources 34: [ OK ] MDModulesNotifierTest.AddConsumerOfTwoResources (0 ms) 34: [----------] 4 tests from MDModulesNotifierTest (0 ms total) 34: 34: [----------] 17 tests from ThreadAffinityTest 34: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 34: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 34: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 34: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 34: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 34: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 34: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 34: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 34: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 34: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 34: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 34: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms) 34: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 34: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) 34: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 34: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (0 ms) 34: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 34: NOTE: Affinity setting failed. 34: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) 34: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 34: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (6 ms) 34: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 34: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (7 ms) 34: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 34: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (4 ms) 34: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 34: NOTE: Affinity setting for 1/2 threads failed. 34: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (0 ms) 34: [----------] 17 tests from ThreadAffinityTest (20 ms total) 34: 34: [----------] Global test environment tear-down 34: [==========] 21 tests from 2 test suites ran. (20 ms total) 34: [ PASSED ] 21 tests. 34/91 Test #34: MdrunUtilityUnitTests ........................ Passed 0.42 sec test 35 Start 35: MdrunUtilityMpiUnitTests 35: Test command: /usr/bin/mpiexec "-n" "4" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrunutility-mpi-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 35: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdrunutility/tests 35: Test timeout computed to be: 30 35: [==========] Running 13 tests from 2 test suites. 35: [----------] Global test environment set-up. 35: [----------] 6 tests from ThreadAffinityMultiRankTest 35: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 35: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (63 ms) 35: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 35: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (56 ms) 35: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 35: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (44 ms) 35: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 35: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (39 ms) 35: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 35: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (32 ms) 35: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 35: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (40 ms) 35: [----------] 6 tests from ThreadAffinityMultiRankTest (359 ms total) 35: 35: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly (32 ms) 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly (40 ms) 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain (44 ms) 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly (40 ms) 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly (40 ms) 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly (40 ms) 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly (59 ms) 35: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (375 ms total) 35: 35: [----------] Global test environment tear-down 35: [==========] 13 tests from 2 test suites ran. (735 ms total) 35: [ PASSED ] 13 tests. 35/91 Test #35: MdrunUtilityMpiUnitTests ..................... Passed 1.32 sec test 36 Start 36: MDSpanTests 36: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdspan-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MDSpanTests.xml" 36: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdspan/tests 36: Test timeout computed to be: 30 36: [==========] Running 32 tests from 7 test suites. 36: [----------] Global test environment set-up. 36: [----------] 4 tests from BasicAccessorPolicy 36: [ RUN ] BasicAccessorPolicy.Decay 36: [ OK ] BasicAccessorPolicy.Decay (0 ms) 36: [ RUN ] BasicAccessorPolicy.Access 36: [ OK ] BasicAccessorPolicy.Access (0 ms) 36: [ RUN ] BasicAccessorPolicy.Offset 36: [ OK ] BasicAccessorPolicy.Offset (0 ms) 36: [ RUN ] BasicAccessorPolicy.CopyAccessor 36: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms) 36: [----------] 4 tests from BasicAccessorPolicy (0 ms total) 36: 36: [----------] 4 tests from ExtentsTest 36: [ RUN ] ExtentsTest.Construction 36: [ OK ] ExtentsTest.Construction (0 ms) 36: [ RUN ] ExtentsTest.PurelyStatic 36: [ OK ] ExtentsTest.PurelyStatic (0 ms) 36: [ RUN ] ExtentsTest.RankNought 36: [ OK ] ExtentsTest.RankNought (0 ms) 36: [ RUN ] ExtentsTest.Assignment 36: [ OK ] ExtentsTest.Assignment (0 ms) 36: [----------] 4 tests from ExtentsTest (0 ms total) 36: 36: [----------] 8 tests from MdSpanExtension 36: [ RUN ] MdSpanExtension.SlicingAllStatic 36: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms) 36: [ RUN ] MdSpanExtension.SlicingDynamic 36: [ OK ] MdSpanExtension.SlicingDynamic (0 ms) 36: [ RUN ] MdSpanExtension.SlicingAllStatic3D 36: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms) 36: [ RUN ] MdSpanExtension.SlicingEqualsView3D 36: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms) 36: [ RUN ] MdSpanExtension.additionWorks 36: [ OK ] MdSpanExtension.additionWorks (0 ms) 36: [ RUN ] MdSpanExtension.subtractionWorks 36: [ OK ] MdSpanExtension.subtractionWorks (0 ms) 36: [ RUN ] MdSpanExtension.multiplicationWorks 36: [ OK ] MdSpanExtension.multiplicationWorks (0 ms) 36: [ RUN ] MdSpanExtension.divisionWorks 36: [ OK ] MdSpanExtension.divisionWorks (0 ms) 36: [----------] 8 tests from MdSpanExtension (0 ms total) 36: 36: [----------] 3 tests from LayoutTests 36: [ RUN ] LayoutTests.LayoutRightConstruction 36: [ OK ] LayoutTests.LayoutRightConstruction (0 ms) 36: [ RUN ] LayoutTests.LayoutRightProperties 36: [ OK ] LayoutTests.LayoutRightProperties (0 ms) 36: [ RUN ] LayoutTests.LayoutRightOperator 36: [ OK ] LayoutTests.LayoutRightOperator (0 ms) 36: [----------] 3 tests from LayoutTests (0 ms total) 36: 36: [----------] 1 test from MdSpanTest 36: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly 36: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms) 36: [----------] 1 test from MdSpanTest (0 ms total) 36: 36: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 36: [ RUN ] MdSpanTest/0.Rank 36: [ OK ] MdSpanTest/0.Rank (0 ms) 36: [ RUN ] MdSpanTest/0.DynamicRank 36: [ OK ] MdSpanTest/0.DynamicRank (0 ms) 36: [ RUN ] MdSpanTest/0.Extents 36: [ OK ] MdSpanTest/0.Extents (0 ms) 36: [ RUN ] MdSpanTest/0.Strides 36: [ OK ] MdSpanTest/0.Strides (0 ms) 36: [ RUN ] MdSpanTest/0.Properties 36: [ OK ] MdSpanTest/0.Properties (0 ms) 36: [ RUN ] MdSpanTest/0.Operator 36: [ OK ] MdSpanTest/0.Operator (0 ms) 36: [----------] 6 tests from MdSpanTest/0 (0 ms total) 36: 36: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 36: [ RUN ] MdSpanTest/1.Rank 36: [ OK ] MdSpanTest/1.Rank (0 ms) 36: [ RUN ] MdSpanTest/1.DynamicRank 36: [ OK ] MdSpanTest/1.DynamicRank (0 ms) 36: [ RUN ] MdSpanTest/1.Extents 36: [ OK ] MdSpanTest/1.Extents (0 ms) 36: [ RUN ] MdSpanTest/1.Strides 36: [ OK ] MdSpanTest/1.Strides (0 ms) 36: [ RUN ] MdSpanTest/1.Properties 36: [ OK ] MdSpanTest/1.Properties (0 ms) 36: [ RUN ] MdSpanTest/1.Operator 36: [ OK ] MdSpanTest/1.Operator (0 ms) 36: [----------] 6 tests from MdSpanTest/1 (0 ms total) 36: 36: [----------] Global test environment tear-down 36: [==========] 32 tests from 7 test suites ran. (0 ms total) 36: [ PASSED ] 32 tests. 36/91 Test #36: MDSpanTests .................................. Passed 0.41 sec test 37 Start 37: MdtypesUnitTest 37: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdtypes-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdtypesUnitTest.xml" 37: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdtypes/tests 37: Test timeout computed to be: 30 37: [==========] Running 97 tests from 7 test suites. 37: [----------] Global test environment set-up. 37: [----------] 4 tests from ForeingLambdaTermsDhdl 37: [ RUN ] ForeingLambdaTermsDhdl.RateCheckWorks 37: [ OK ] ForeingLambdaTermsDhdl.RateCheckWorks (0 ms) 37: [ RUN ] ForeingLambdaTermsDhdl.AllLinear 37: [ OK ] ForeingLambdaTermsDhdl.AllLinear (0 ms) 37: [ RUN ] ForeingLambdaTermsDhdl.AllLinearNegative 37: [ OK ] ForeingLambdaTermsDhdl.AllLinearNegative (0 ms) 37: [ RUN ] ForeingLambdaTermsDhdl.SeparateVdwCoul 37: [ OK ] ForeingLambdaTermsDhdl.SeparateVdwCoul (0 ms) 37: [----------] 4 tests from ForeingLambdaTermsDhdl (0 ms total) 37: 37: [----------] 4 tests from ObservablesReducerTest 37: [ RUN ] ObservablesReducerTest.CanMoveAssign 37: [ OK ] ObservablesReducerTest.CanMoveAssign (0 ms) 37: [ RUN ] ObservablesReducerTest.CanMoveConstruct 37: [ OK ] ObservablesReducerTest.CanMoveConstruct (0 ms) 37: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers 37: [ OK ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers (0 ms) 37: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber 37: [ OK ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber (0 ms) 37: [----------] 4 tests from ObservablesReducerTest (0 ms total) 37: 37: [----------] 2 tests from CheckpointDataTest 37: [ RUN ] CheckpointDataTest.SingleDataTest 37: [ OK ] CheckpointDataTest.SingleDataTest (22 ms) 37: [ RUN ] CheckpointDataTest.MultiDataTest 37: [ OK ] CheckpointDataTest.MultiDataTest (92 ms) 37: [----------] 2 tests from CheckpointDataTest (115 ms total) 37: 37: [----------] 7 tests from ForceBuffers 37: [ RUN ] ForceBuffers.ConstructsUnpinned 37: [ OK ] ForceBuffers.ConstructsUnpinned (0 ms) 37: [ RUN ] ForceBuffers.ConstructsPinned 37: [ OK ] ForceBuffers.ConstructsPinned (0 ms) 37: [ RUN ] ForceBuffers.ConstructsEmpty 37: [ OK ] ForceBuffers.ConstructsEmpty (0 ms) 37: [ RUN ] ForceBuffers.ResizeWorks 37: [ OK ] ForceBuffers.ResizeWorks (0 ms) 37: [ RUN ] ForceBuffers.PaddingWorks 37: [ OK ] ForceBuffers.PaddingWorks (0 ms) 37: [ RUN ] ForceBuffers.CopyWorks 37: [ OK ] ForceBuffers.CopyWorks (0 ms) 37: [ RUN ] ForceBuffers.CopyDoesNotPin 37: [ OK ] ForceBuffers.CopyDoesNotPin (0 ms) 37: [----------] 7 tests from ForceBuffers (0 ms total) 37: 37: [----------] 5 tests from MultipleTimeStepping 37: [ RUN ] MultipleTimeStepping.ChecksNumLevels 37: [ OK ] MultipleTimeStepping.ChecksNumLevels (0 ms) 37: [ RUN ] MultipleTimeStepping.SelectsForceGroups 37: [ OK ] MultipleTimeStepping.SelectsForceGroups (0 ms) 37: [ RUN ] MultipleTimeStepping.ChecksStepFactor 37: [ OK ] MultipleTimeStepping.ChecksStepFactor (0 ms) 37: [ RUN ] MultipleTimeStepping.ChecksPmeIsAtLastLevel 37: [ OK ] MultipleTimeStepping.ChecksPmeIsAtLastLevel (0 ms) 37: [ RUN ] MultipleTimeStepping.ChecksIntegrator 37: [ OK ] MultipleTimeStepping.ChecksIntegrator (0 ms) 37: [----------] 5 tests from MultipleTimeStepping (0 ms total) 37: 37: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 (0 ms) 37: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest (0 ms total) 37: 37: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/0 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/0 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/1 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/1 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/2 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/2 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/3 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/3 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/4 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/4 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/5 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/5 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/6 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/6 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/7 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/7 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/8 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/8 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/9 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/9 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/10 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/10 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/11 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/11 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/12 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/12 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/13 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/13 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/14 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/14 (0 ms) 37: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest (0 ms total) 37: 37: [----------] Global test environment tear-down 37: [==========] 97 tests from 7 test suites ran. (116 ms total) 37: [ PASSED ] 97 tests. 37/91 Test #37: MdtypesUnitTest .............................. Passed 0.50 sec test 38 Start 38: OnlineHelpUnitTests 38: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/onlinehelp-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/OnlineHelpUnitTests.xml" 38: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/onlinehelp/tests 38: Test timeout computed to be: 30 38: [==========] Running 22 tests from 4 test suites. 38: [----------] Global test environment set-up. 38: [----------] 6 tests from TextTableFormatterTest 38: [ RUN ] TextTableFormatterTest.HandlesBasicCase 38: [ OK ] TextTableFormatterTest.HandlesBasicCase (0 ms) 38: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 38: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms) 38: [ RUN ] TextTableFormatterTest.HandlesIndentation 38: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) 38: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 38: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms) 38: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 38: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms) 38: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 38: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) 38: [----------] 6 tests from TextTableFormatterTest (0 ms total) 38: 38: [----------] 3 tests from HelpManagerTest 38: [ RUN ] HelpManagerTest.HandlesRootTopic 38: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) 38: [ RUN ] HelpManagerTest.HandlesSubTopics 38: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 38: [ RUN ] HelpManagerTest.HandlesInvalidTopics 38: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) 38: [----------] 3 tests from HelpManagerTest (0 ms total) 38: 38: [----------] 2 tests from HelpTopicFormattingTest 38: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 38: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms) 38: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 38: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) 38: [----------] 2 tests from HelpTopicFormattingTest (0 ms total) 38: 38: [----------] 11 tests from HelpWriterContextTest 38: [ RUN ] HelpWriterContextTest.FormatsParagraphs 38: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 38: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) 38: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 38: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsLiteralText 38: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 38: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 38: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsBulletList 38: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 38: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 38: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsGridTable 38: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsTitles 38: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms) 38: [----------] 11 tests from HelpWriterContextTest (0 ms total) 38: 38: [----------] Global test environment tear-down 38: [==========] 22 tests from 4 test suites ran. (4 ms total) 38: [ PASSED ] 22 tests. 38/91 Test #38: OnlineHelpUnitTests .......................... Passed 0.34 sec test 39 Start 39: OptionsUnitTests 39: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/options-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/OptionsUnitTests.xml" 39: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options/tests 39: Test timeout computed to be: 30 39: [==========] Running 111 tests from 18 test suites. 39: [----------] Global test environment set-up. 39: [----------] 5 tests from AbstractOptionStorageTest 39: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 39: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 39: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 39: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) 39: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 39: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 39: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 39: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) 39: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 39: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 39: [----------] 5 tests from AbstractOptionStorageTest (0 ms total) 39: 39: [----------] 10 tests from FileNameOptionTest 39: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 39: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 39: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 39: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 39: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 39: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 39: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 39: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 39: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 39: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 39: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension 39: [ OK ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue 39: [ OK ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue (0 ms) 39: [----------] 10 tests from FileNameOptionTest (0 ms total) 39: 39: [----------] 15 tests from FileNameOptionManagerTest 39: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 39: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 39: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 39: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 39: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 39: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 39: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 39: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 39: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 39: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 39: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 39: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 39: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 39: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 39: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 39: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 39: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 39: [----------] 15 tests from FileNameOptionManagerTest (0 ms total) 39: 39: [----------] 1 test from OptionsTest 39: [ RUN ] OptionsTest.FailsOnNonsafeStorage 39: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 39: [----------] 1 test from OptionsTest (0 ms total) 39: 39: [----------] 9 tests from OptionsAssignerTest 39: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 39: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 39: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 39: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 39: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesMissingValue 39: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesExtraValue 39: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesGroups 39: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesSections 39: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 39: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 39: [----------] 9 tests from OptionsAssignerTest (0 ms total) 39: 39: [----------] 4 tests from OptionsAssignerBooleanTest 39: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 39: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 39: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 39: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 39: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 39: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 39: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 39: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 39: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 39: 39: [----------] 13 tests from OptionsAssignerIntegerTest 39: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 39: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 39: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 39: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 39: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 39: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 39: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 39: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 39: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 39: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 39: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 39: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 39: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 39: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 39: [----------] 13 tests from OptionsAssignerIntegerTest (0 ms total) 39: 39: [----------] 5 tests from OptionsAssignerDoubleTest 39: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 39: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 39: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 39: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 39: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 39: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 39: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 39: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 39: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 39: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 39: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) 39: 39: [----------] 9 tests from OptionsAssignerStringTest 39: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 39: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 39: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 39: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 39: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 39: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 39: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 39: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 39: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 39: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 39: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 39: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) 39: 39: [----------] 6 tests from OptionsAssignerEnumTest 39: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 39: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 39: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 39: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 39: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 39: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 39: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 39: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 39: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 39: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 39: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 39: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 39: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) 39: 39: [----------] 8 tests from RepeatingOptionSectionTest 39: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 39: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 39: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 39: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 39: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 39: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 39: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 39: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 39: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 39: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) 39: 39: [----------] 1 test from TimeUnitManagerTest 39: [ RUN ] TimeUnitManagerTest.BasicOperations 39: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 39: [----------] 1 test from TimeUnitManagerTest (0 ms total) 39: 39: [----------] 4 tests from TimeUnitBehaviorTest 39: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 39: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 39: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 39: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 39: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 39: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 39: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 39: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 39: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 39: 39: [----------] 2 tests from TreeValueSupportAssignTest 39: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 39: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 39: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 39: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 39: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) 39: 39: [----------] 1 test from TreeValueSupportAssignErrorTest 39: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 39: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 39: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 39: 39: [----------] 5 tests from TreeValueSupportCheckTest 39: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 39: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 39: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 39: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 39: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 39: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 39: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 39: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 39: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 39: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 39: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 39: 39: [----------] 6 tests from TreeValueSupportAdjustTest 39: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 39: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms) 39: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 39: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms) 39: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 39: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms) 39: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 39: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) 39: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 39: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) 39: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 39: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) 39: [----------] 6 tests from TreeValueSupportAdjustTest (0 ms total) 39: 39: [----------] 7 tests from TreeValueSupportTest 39: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 39: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms) 39: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 39: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms) 39: [ RUN ] TreeValueSupportTest.SupportsInt64Option 39: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms) 39: [ RUN ] TreeValueSupportTest.SupportsStringOption 39: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) 39: [ RUN ] TreeValueSupportTest.SupportsFloatOption 39: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) 39: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 39: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) 39: [ RUN ] TreeValueSupportTest.SupportsEnumOption 39: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) 39: [----------] 7 tests from TreeValueSupportTest (0 ms total) 39: 39: [----------] Global test environment tear-down 39: [==========] 111 tests from 18 test suites ran. (2 ms total) 39: [ PASSED ] 111 tests. 39/91 Test #39: OptionsUnitTests ............................. Passed 0.38 sec test 40 Start 40: PbcutilUnitTest 40: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/pbcutil-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/PbcutilUnitTest.xml" 40: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/pbcutil/tests 40: Test timeout computed to be: 30 40: [==========] Running 37 tests from 5 test suites. 40: [----------] Global test environment set-up. 40: [----------] 1 test from ShiftTest 40: [ RUN ] ShiftTest.CoordinateShiftWorks 40: [ OK ] ShiftTest.CoordinateShiftWorks (0 ms) 40: [----------] 1 test from ShiftTest (0 ms total) 40: 40: [----------] 2 tests from MShift 40: [ RUN ] MShift.shiftsAndUnshifts 40: [ OK ] MShift.shiftsAndUnshifts (0 ms) 40: [ RUN ] MShift.shiftsAndUnshiftsSelf 40: [ OK ] MShift.shiftsAndUnshiftsSelf (0 ms) 40: [----------] 2 tests from MShift (0 ms total) 40: 40: [----------] 5 tests from PbcTest 40: [ RUN ] PbcTest.CalcShiftsWorks 40: [ OK ] PbcTest.CalcShiftsWorks (0 ms) 40: [ RUN ] PbcTest.PutAtomsInCubicBoxAlreadyInBox 40: [ OK ] PbcTest.PutAtomsInCubicBoxAlreadyInBox (0 ms) 40: [ RUN ] PbcTest.PutAtomsInCubicBoxFromOutsideBox 40: [ OK ] PbcTest.PutAtomsInCubicBoxFromOutsideBox (0 ms) 40: [ RUN ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox 40: [ OK ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox (0 ms) 40: [ RUN ] PbcTest.PutAtomsInBoxHandlesInf 40: [ OK ] PbcTest.PutAtomsInBoxHandlesInf (0 ms) 40: [----------] 5 tests from PbcTest (0 ms total) 40: 40: [----------] 2 tests from PbcEnumsTest 40: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect 40: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms) 40: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect 40: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms) 40: [----------] 2 tests from PbcEnumsTest (0 ms total) 40: 40: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 (0 ms) 40: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest (2 ms total) 40: 40: [----------] Global test environment tear-down 40: [==========] 37 tests from 5 test suites ran. (3 ms total) 40: [ PASSED ] 37 tests. 40/91 Test #40: PbcutilUnitTest .............................. Passed 0.35 sec test 41 Start 41: RandomUnitTests 41: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/random-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/RandomUnitTests.xml" 41: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/random/tests 41: Test timeout computed to be: 30 41: [==========] Running 44 tests from 10 test suites. 41: [----------] Global test environment set-up. 41: [----------] 4 tests from ExponentialDistributionTest 41: [ RUN ] ExponentialDistributionTest.Output 41: [ OK ] ExponentialDistributionTest.Output (0 ms) 41: [ RUN ] ExponentialDistributionTest.Logical 41: [ OK ] ExponentialDistributionTest.Logical (0 ms) 41: [ RUN ] ExponentialDistributionTest.Reset 41: [ OK ] ExponentialDistributionTest.Reset (0 ms) 41: [ RUN ] ExponentialDistributionTest.AltParam 41: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 41: [----------] 4 tests from ExponentialDistributionTest (0 ms total) 41: 41: [----------] 4 tests from GammaDistributionTest 41: [ RUN ] GammaDistributionTest.Output 41: [ OK ] GammaDistributionTest.Output (0 ms) 41: [ RUN ] GammaDistributionTest.Logical 41: [ OK ] GammaDistributionTest.Logical (0 ms) 41: [ RUN ] GammaDistributionTest.Reset 41: [ OK ] GammaDistributionTest.Reset (0 ms) 41: [ RUN ] GammaDistributionTest.AltParam 41: [ OK ] GammaDistributionTest.AltParam (0 ms) 41: [----------] 4 tests from GammaDistributionTest (0 ms total) 41: 41: [----------] 4 tests from NormalDistributionTest 41: [ RUN ] NormalDistributionTest.Output 41: [ OK ] NormalDistributionTest.Output (0 ms) 41: [ RUN ] NormalDistributionTest.Logical 41: [ OK ] NormalDistributionTest.Logical (0 ms) 41: [ RUN ] NormalDistributionTest.Reset 41: [ OK ] NormalDistributionTest.Reset (0 ms) 41: [ RUN ] NormalDistributionTest.AltParam 41: [ OK ] NormalDistributionTest.AltParam (0 ms) 41: [----------] 4 tests from NormalDistributionTest (0 ms total) 41: 41: [----------] 1 test from SeedTest 41: [ RUN ] SeedTest.makeRandomSeed 41: [ OK ] SeedTest.makeRandomSeed (0 ms) 41: [----------] 1 test from SeedTest (0 ms total) 41: 41: [----------] 6 tests from TabulatedNormalDistributionTest 41: [ RUN ] TabulatedNormalDistributionTest.Output14 41: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) 41: [ RUN ] TabulatedNormalDistributionTest.Output16 41: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms) 41: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 41: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms) 41: [ RUN ] TabulatedNormalDistributionTest.Logical 41: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 41: [ RUN ] TabulatedNormalDistributionTest.Reset 41: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 41: [ RUN ] TabulatedNormalDistributionTest.AltParam 41: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 41: [----------] 6 tests from TabulatedNormalDistributionTest (0 ms total) 41: 41: [----------] 1 test from TabulatedNormalDistributionTableTest 41: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 41: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (0 ms) 41: [----------] 1 test from TabulatedNormalDistributionTableTest (0 ms total) 41: 41: [----------] 6 tests from ThreeFry2x64Test 41: [ RUN ] ThreeFry2x64Test.Logical 41: [ OK ] ThreeFry2x64Test.Logical (0 ms) 41: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 41: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms) 41: [ RUN ] ThreeFry2x64Test.Reseed 41: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 41: [ RUN ] ThreeFry2x64Test.Discard 41: [ OK ] ThreeFry2x64Test.Discard (0 ms) 41: [ RUN ] ThreeFry2x64Test.InvalidCounter 41: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) 41: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 41: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 41: [----------] 6 tests from ThreeFry2x64Test (0 ms total) 41: 41: [----------] 4 tests from UniformIntDistributionTest 41: [ RUN ] UniformIntDistributionTest.Output 41: [ OK ] UniformIntDistributionTest.Output (0 ms) 41: [ RUN ] UniformIntDistributionTest.Logical 41: [ OK ] UniformIntDistributionTest.Logical (0 ms) 41: [ RUN ] UniformIntDistributionTest.Reset 41: [ OK ] UniformIntDistributionTest.Reset (0 ms) 41: [ RUN ] UniformIntDistributionTest.AltParam 41: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 41: [----------] 4 tests from UniformIntDistributionTest (0 ms total) 41: 41: [----------] 5 tests from UniformRealDistributionTest 41: [ RUN ] UniformRealDistributionTest.GenerateCanonical 41: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) 41: [ RUN ] UniformRealDistributionTest.Output 41: [ OK ] UniformRealDistributionTest.Output (0 ms) 41: [ RUN ] UniformRealDistributionTest.Logical 41: [ OK ] UniformRealDistributionTest.Logical (0 ms) 41: [ RUN ] UniformRealDistributionTest.Reset 41: [ OK ] UniformRealDistributionTest.Reset (0 ms) 41: [ RUN ] UniformRealDistributionTest.AltParam 41: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 41: [----------] 5 tests from UniformRealDistributionTest (0 ms total) 41: 41: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) 41: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (0 ms total) 41: 41: [----------] Global test environment tear-down 41: [==========] 44 tests from 10 test suites ran. (1 ms total) 41: [ PASSED ] 44 tests. 41/91 Test #41: RandomUnitTests .............................. Passed 0.38 sec test 42 Start 42: RestraintTests 42: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/restraintpotential-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/RestraintTests.xml" 42: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/restraint/tests 42: Test timeout computed to be: 30 42: [==========] Running 1 test from 1 test suite. 42: [----------] Global test environment set-up. 42: [----------] 1 test from RestraintManager 42: [ RUN ] RestraintManager.restraintList 42: [ OK ] RestraintManager.restraintList (0 ms) 42: [----------] 1 test from RestraintManager (0 ms total) 42: 42: [----------] Global test environment tear-down 42: [==========] 1 test from 1 test suite ran. (0 ms total) 42: [ PASSED ] 1 test. 42/91 Test #42: RestraintTests ............................... Passed 0.34 sec test 43 Start 43: TableUnitTests 43: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/table-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/TableUnitTests.xml" 43: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tables/tests 43: Test timeout computed to be: 30 43: [==========] Running 20 tests from 2 test suites. 43: [----------] Global test environment set-up. 43: [----------] 10 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 43: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 43: [ OK ] SplineTableTest/0.HandlesIncorrectInput (0 ms) 43: [ RUN ] SplineTableTest/0.Sinc 43: [ OK ] SplineTableTest/0.Sinc (0 ms) 43: [ RUN ] SplineTableTest/0.LJ12 43: [ OK ] SplineTableTest/0.LJ12 (6 ms) 43: [ RUN ] SplineTableTest/0.PmeCorrection 43: [ OK ] SplineTableTest/0.PmeCorrection (0 ms) 43: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 43: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (0 ms) 43: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 43: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (0 ms) 43: [ RUN ] SplineTableTest/0.TwoFunctions 43: [ OK ] SplineTableTest/0.TwoFunctions (14 ms) 43: [ RUN ] SplineTableTest/0.ThreeFunctions 43: [ OK ] SplineTableTest/0.ThreeFunctions (15 ms) 43: [ RUN ] SplineTableTest/0.Simd 43: [ OK ] SplineTableTest/0.Simd (2 ms) 43: [ RUN ] SplineTableTest/0.SimdTwoFunctions 43: [ OK ] SplineTableTest/0.SimdTwoFunctions (18 ms) 43: [----------] 10 tests from SplineTableTest/0 (72 ms total) 43: 43: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 43: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 43: [ OK ] SplineTableTest/1.HandlesIncorrectInput (0 ms) 43: [ RUN ] SplineTableTest/1.Sinc 43: [ OK ] SplineTableTest/1.Sinc (0 ms) 43: [ RUN ] SplineTableTest/1.LJ12 43: [ OK ] SplineTableTest/1.LJ12 (0 ms) 43: [ RUN ] SplineTableTest/1.PmeCorrection 43: [ OK ] SplineTableTest/1.PmeCorrection (0 ms) 43: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 43: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (0 ms) 43: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 43: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (0 ms) 43: [ RUN ] SplineTableTest/1.TwoFunctions 43: [ OK ] SplineTableTest/1.TwoFunctions (1 ms) 43: [ RUN ] SplineTableTest/1.ThreeFunctions 43: [ OK ] SplineTableTest/1.ThreeFunctions (1 ms) 43: [ RUN ] SplineTableTest/1.Simd 43: [ OK ] SplineTableTest/1.Simd (0 ms) 43: [ RUN ] SplineTableTest/1.SimdTwoFunctions 43: [ OK ] SplineTableTest/1.SimdTwoFunctions (1 ms) 43: [----------] 10 tests from SplineTableTest/1 (14 ms total) 43: 43: [----------] Global test environment tear-down 43: [==========] 20 tests from 2 test suites ran. (87 ms total) 43: [ PASSED ] 20 tests. 43/91 Test #43: TableUnitTests ............................... Passed 0.43 sec test 44 Start 44: TaskAssignmentUnitTests 44: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/taskassignment-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/TaskAssignmentUnitTests.xml" 44: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/taskassignment/tests 44: Test timeout computed to be: 30 44: [==========] Running 3 tests from 2 test suites. 44: [----------] Global test environment set-up. 44: [----------] 2 tests from UserTaskAssignmentStringHandlingTest 44: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork 44: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (0 ms) 44: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid 44: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms) 44: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (0 ms total) 44: 44: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest 44: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow 44: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (0 ms) 44: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (0 ms total) 44: 44: [----------] Global test environment tear-down 44: [==========] 3 tests from 2 test suites ran. (1 ms total) 44: [ PASSED ] 3 tests. 44/91 Test #44: TaskAssignmentUnitTests ...................... Passed 0.34 sec test 45 Start 45: GmxTimingTests 45: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/timing-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/GmxTimingTests.xml" 45: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/timing/tests 45: Test timeout computed to be: 30 45: [==========] Running 6 tests from 1 test suite. 45: [----------] Global test environment set-up. 45: [----------] 6 tests from TimingTest 45: [ RUN ] TimingTest.ElementCountingWorks 45: [ OK ] TimingTest.ElementCountingWorks (0 ms) 45: [ RUN ] TimingTest.ElementNoCountingWorks 45: [ OK ] TimingTest.ElementNoCountingWorks (0 ms) 45: [ RUN ] TimingTest.SubElementCountingWorks 45: [ OK ] TimingTest.SubElementCountingWorks (0 ms) 45: [ RUN ] TimingTest.SubElementNoCountingWorks 45: [ OK ] TimingTest.SubElementNoCountingWorks (0 ms) 45: [ RUN ] TimingTest.RunWallCycle 45: [ OK ] TimingTest.RunWallCycle (6 ms) 45: [ RUN ] TimingTest.RunWallCycleSub 45: [ OK ] TimingTest.RunWallCycleSub (0 ms) 45: [----------] 6 tests from TimingTest (6 ms total) 45: 45: [----------] Global test environment tear-down 45: [==========] 6 tests from 1 test suite ran. (6 ms total) 45: [ PASSED ] 6 tests. 45/91 Test #45: GmxTimingTests ............................... Passed 0.36 sec test 46 Start 46: TopologyTest 46: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/topology-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/TopologyTest.xml" 46: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/topology/tests 46: Test timeout computed to be: 30 46: [==========] Running 153 tests from 10 test suites. 46: [----------] Global test environment set-up. 46: [----------] 3 tests from PdbAtomEntryTest 46: [ RUN ] PdbAtomEntryTest.CanCreateBasicEntry 46: [ OK ] PdbAtomEntryTest.CanCreateBasicEntry (0 ms) 46: [ RUN ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac 46: [ OK ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac (0 ms) 46: [ RUN ] PdbAtomEntryTest.CanCreateFullEntry 46: [ OK ] PdbAtomEntryTest.CanCreateFullEntry (0 ms) 46: [----------] 3 tests from PdbAtomEntryTest (0 ms total) 46: 46: [----------] 3 tests from ExclusionBlockTest 46: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks 46: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms) 46: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka 46: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms) 46: [ RUN ] ExclusionBlockTest.MergeExclusions 46: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms) 46: [----------] 3 tests from ExclusionBlockTest (0 ms total) 46: 46: [----------] 6 tests from InteractionListTest 46: [ RUN ] InteractionListTest.EmptyWorks 46: [ OK ] InteractionListTest.EmptyWorks (0 ms) 46: [ RUN ] InteractionListTest.CanAddInteractionArray 46: [ OK ] InteractionListTest.CanAddInteractionArray (0 ms) 46: [ RUN ] InteractionListTest.CanAddInteractionArrayMultipleAtoms 46: [ OK ] InteractionListTest.CanAddInteractionArrayMultipleAtoms (0 ms) 46: [ RUN ] InteractionListTest.CanAddInteractionPointer 46: [ OK ] InteractionListTest.CanAddInteractionPointer (0 ms) 46: [ RUN ] InteractionListTest.CanAddListToOtherList 46: [ OK ] InteractionListTest.CanAddListToOtherList (0 ms) 46: [ RUN ] InteractionListTest.ClearingWorks 46: [ OK ] InteractionListTest.ClearingWorks (0 ms) 46: [----------] 6 tests from InteractionListTest (0 ms total) 46: 46: [----------] 3 tests from IndexTest 46: [ RUN ] IndexTest.AnalyseWorksDefaultGroups 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: [ OK ] IndexTest.AnalyseWorksDefaultGroups (2 ms) 46: [ RUN ] IndexTest.WriteIndexWorks 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: [ OK ] IndexTest.WriteIndexWorks (12 ms) 46: [ RUN ] IndexTest.WriteAndReadIndexWorks 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: [ OK ] IndexTest.WriteAndReadIndexWorks (1 ms) 46: [----------] 3 tests from IndexTest (24 ms total) 46: 46: [----------] 4 tests from MtopTest 46: [ RUN ] MtopTest.RangeBasedLoop 46: [ OK ] MtopTest.RangeBasedLoop (0 ms) 46: [ RUN ] MtopTest.Operators 46: [ OK ] MtopTest.Operators (0 ms) 46: [ RUN ] MtopTest.CanFindResidueStartAndEndAtoms 46: [ OK ] MtopTest.CanFindResidueStartAndEndAtoms (0 ms) 46: [ RUN ] MtopTest.CanSortPerturbedInteractionsCorrectly 46: [ OK ] MtopTest.CanSortPerturbedInteractionsCorrectly (0 ms) 46: [----------] 4 tests from MtopTest (0 ms total) 46: 46: [----------] 2 tests from IListRangeTest 46: [ RUN ] IListRangeTest.RangeBasedLoopWorks 46: [ OK ] IListRangeTest.RangeBasedLoopWorks (0 ms) 46: [ RUN ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction 46: [ OK ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction (0 ms) 46: [----------] 2 tests from IListRangeTest (0 ms total) 46: 46: [----------] 13 tests from StringTableTest 46: [ RUN ] StringTableTest.AddSingleEntry 46: [ OK ] StringTableTest.AddSingleEntry (0 ms) 46: [ RUN ] StringTableTest.CanAccessWithAt 46: [ OK ] StringTableTest.CanAccessWithAt (0 ms) 46: [ RUN ] StringTableTest.CanAccessWithBracket 46: [ OK ] StringTableTest.CanAccessWithBracket (0 ms) 46: [ RUN ] StringTableTest.ThrowsOutOfRange 46: [ OK ] StringTableTest.ThrowsOutOfRange (0 ms) 46: [ RUN ] StringTableTest.StringCompareIsCorrect 46: [ OK ] StringTableTest.StringCompareIsCorrect (0 ms) 46: [ RUN ] StringTableTest.AddTwoDistinctEntries 46: [ OK ] StringTableTest.AddTwoDistinctEntries (0 ms) 46: [ RUN ] StringTableTest.TryToAddDuplicates 46: [ OK ] StringTableTest.TryToAddDuplicates (0 ms) 46: [ RUN ] StringTableTest.AddLargeNumberOfEntries 46: [ OK ] StringTableTest.AddLargeNumberOfEntries (0 ms) 46: [ RUN ] StringTableTest.NoDuplicatesInLargeTable 46: [ OK ] StringTableTest.NoDuplicatesInLargeTable (0 ms) 46: [ RUN ] StringTableTest.CanWriteToBuffer 46: [ OK ] StringTableTest.CanWriteToBuffer (0 ms) 46: [ RUN ] StringTableTest.Roundtrip 46: [ OK ] StringTableTest.Roundtrip (0 ms) 46: [ RUN ] StringTableTest.RoundtripWithCorrectStringIndices 46: [ OK ] StringTableTest.RoundtripWithCorrectStringIndices (0 ms) 46: [ RUN ] StringTableTest.CanCopyToLegacyTable 46: [ OK ] StringTableTest.CanCopyToLegacyTable (0 ms) 46: [----------] 13 tests from StringTableTest (1 ms total) 46: 46: [----------] 6 tests from LegacySymtabTest 46: [ RUN ] LegacySymtabTest.EmptyOnOpen 46: [ OK ] LegacySymtabTest.EmptyOnOpen (0 ms) 46: [ RUN ] LegacySymtabTest.AddSingleEntry 46: [ OK ] LegacySymtabTest.AddSingleEntry (0 ms) 46: [ RUN ] LegacySymtabTest.AddTwoDistinctEntries 46: [ OK ] LegacySymtabTest.AddTwoDistinctEntries (0 ms) 46: [ RUN ] LegacySymtabTest.TryToAddDuplicates 46: [ OK ] LegacySymtabTest.TryToAddDuplicates (0 ms) 46: [ RUN ] LegacySymtabTest.AddLargeNumberOfEntries 46: [ OK ] LegacySymtabTest.AddLargeNumberOfEntries (0 ms) 46: [ RUN ] LegacySymtabTest.NoDuplicatesInLargeTable 46: [ OK ] LegacySymtabTest.NoDuplicatesInLargeTable (0 ms) 46: [----------] 6 tests from LegacySymtabTest (0 ms total) 46: 46: [----------] 5 tests from TopSortTest 46: [ RUN ] TopSortTest.WorksOnEmptyIdef 46: [ OK ] TopSortTest.WorksOnEmptyIdef (0 ms) 46: [ RUN ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction 46: [ OK ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction (0 ms) 46: [ RUN ] TopSortTest.WorksOnIdefWithPerturbedInteractions 46: [ OK ] TopSortTest.WorksOnIdefWithPerturbedInteractions (0 ms) 46: [ RUN ] TopSortTest.SortsIdefWithPerturbedInteractions 46: [ OK ] TopSortTest.SortsIdefWithPerturbedInteractions (0 ms) 46: [ RUN ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions 46: [ OK ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions (0 ms) 46: [----------] 5 tests from TopSortTest (0 ms total) 46: 46: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 (4 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 (0 ms) 46: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest (25 ms total) 46: 46: [----------] Global test environment tear-down 46: [==========] 153 tests from 10 test suites ran. (55 ms total) 46: [ PASSED ] 153 tests. 46: 46: YOU HAVE 1 DISABLED TEST 46: 46/91 Test #46: TopologyTest ................................. Passed 0.41 sec test 47 Start 47: PullTest 47: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/pull-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/PullTest.xml" 47: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/pulling/tests 47: Test timeout computed to be: 30 47: [==========] Running 10 tests from 1 test suite. 47: [----------] Global test environment set-up. 47: [----------] 10 tests from PullTest 47: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 47: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) 47: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 47: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 47: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 47: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 47: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 47: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 47: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 47: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 47: [ RUN ] PullTest.TransformationCoordSimple 47: [ OK ] PullTest.TransformationCoordSimple (0 ms) 47: [ RUN ] PullTest.TransformationCoordAdvanced 47: [ OK ] PullTest.TransformationCoordAdvanced (0 ms) 47: [ RUN ] PullTest.TransformationCoordTime 47: [ OK ] PullTest.TransformationCoordTime (0 ms) 47: [ RUN ] PullTest.TransformationCoordTimeNotAllowed 47: [ OK ] PullTest.TransformationCoordTimeNotAllowed (0 ms) 47: [ RUN ] PullTest.TransformationCoordDummyExpression 47: [ OK ] PullTest.TransformationCoordDummyExpression (0 ms) 47: [----------] 10 tests from PullTest (0 ms total) 47: 47: [----------] Global test environment tear-down 47: [==========] 10 tests from 1 test suite ran. (0 ms total) 47: [ PASSED ] 10 tests. 47/91 Test #47: PullTest ..................................... Passed 0.38 sec test 48 Start 48: SimdUnitTests 48: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/simd-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/SimdUnitTests.xml" 48: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/simd/tests 48: Test timeout computed to be: 30 48: [==========] Running 288 tests from 22 test suites. 48: [----------] Global test environment set-up. 48: [----------] 9 tests from SimdBootstrapTest 48: [ RUN ] SimdBootstrapTest.loadStore 48: [ OK ] SimdBootstrapTest.loadStore (0 ms) 48: [ RUN ] SimdBootstrapTest.loadU 48: [ OK ] SimdBootstrapTest.loadU (0 ms) 48: [ RUN ] SimdBootstrapTest.storeU 48: [ OK ] SimdBootstrapTest.storeU (0 ms) 48: [ RUN ] SimdBootstrapTest.loadStoreI 48: [ OK ] SimdBootstrapTest.loadStoreI (0 ms) 48: [ RUN ] SimdBootstrapTest.loadUI 48: [ OK ] SimdBootstrapTest.loadUI (0 ms) 48: [ RUN ] SimdBootstrapTest.storeUI 48: [ OK ] SimdBootstrapTest.storeUI (0 ms) 48: [ RUN ] SimdBootstrapTest.simd4LoadStore 48: [ OK ] SimdBootstrapTest.simd4LoadStore (0 ms) 48: [ RUN ] SimdBootstrapTest.simd4LoadU 48: [ OK ] SimdBootstrapTest.simd4LoadU (0 ms) 48: [ RUN ] SimdBootstrapTest.simd4StoreU 48: [ OK ] SimdBootstrapTest.simd4StoreU (0 ms) 48: [----------] 9 tests from SimdBootstrapTest (0 ms total) 48: 48: [----------] 41 tests from SimdScalarTest 48: [ RUN ] SimdScalarTest.load 48: [ OK ] SimdScalarTest.load (0 ms) 48: [ RUN ] SimdScalarTest.loadU 48: [ OK ] SimdScalarTest.loadU (0 ms) 48: [ RUN ] SimdScalarTest.store 48: [ OK ] SimdScalarTest.store (0 ms) 48: [ RUN ] SimdScalarTest.storeU 48: [ OK ] SimdScalarTest.storeU (0 ms) 48: [ RUN ] SimdScalarTest.setZero 48: [ OK ] SimdScalarTest.setZero (0 ms) 48: [ RUN ] SimdScalarTest.andNot 48: [ OK ] SimdScalarTest.andNot (0 ms) 48: [ RUN ] SimdScalarTest.fma 48: [ OK ] SimdScalarTest.fma (0 ms) 48: [ RUN ] SimdScalarTest.fms 48: [ OK ] SimdScalarTest.fms (0 ms) 48: [ RUN ] SimdScalarTest.fnma 48: [ OK ] SimdScalarTest.fnma (0 ms) 48: [ RUN ] SimdScalarTest.fnms 48: [ OK ] SimdScalarTest.fnms (0 ms) 48: [ RUN ] SimdScalarTest.maskAdd 48: [ OK ] SimdScalarTest.maskAdd (0 ms) 48: [ RUN ] SimdScalarTest.maskzMul 48: [ OK ] SimdScalarTest.maskzMul (0 ms) 48: [ RUN ] SimdScalarTest.maskzFma 48: [ OK ] SimdScalarTest.maskzFma (0 ms) 48: [ RUN ] SimdScalarTest.abs 48: [ OK ] SimdScalarTest.abs (0 ms) 48: [ RUN ] SimdScalarTest.max 48: [ OK ] SimdScalarTest.max (0 ms) 48: [ RUN ] SimdScalarTest.min 48: [ OK ] SimdScalarTest.min (0 ms) 48: [ RUN ] SimdScalarTest.round 48: [ OK ] SimdScalarTest.round (0 ms) 48: [ RUN ] SimdScalarTest.trunc 48: [ OK ] SimdScalarTest.trunc (0 ms) 48: [ RUN ] SimdScalarTest.reduce 48: [ OK ] SimdScalarTest.reduce (0 ms) 48: [ RUN ] SimdScalarTest.testBits 48: [ OK ] SimdScalarTest.testBits (0 ms) 48: [ RUN ] SimdScalarTest.anyTrue 48: [ OK ] SimdScalarTest.anyTrue (0 ms) 48: [ RUN ] SimdScalarTest.selectByMask 48: [ OK ] SimdScalarTest.selectByMask (0 ms) 48: [ RUN ] SimdScalarTest.selectByNotMask 48: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 48: [ RUN ] SimdScalarTest.blend 48: [ OK ] SimdScalarTest.blend (0 ms) 48: [ RUN ] SimdScalarTest.cvtR2I 48: [ OK ] SimdScalarTest.cvtR2I (0 ms) 48: [ RUN ] SimdScalarTest.cvttR2I 48: [ OK ] SimdScalarTest.cvttR2I (0 ms) 48: [ RUN ] SimdScalarTest.cvtI2R 48: [ OK ] SimdScalarTest.cvtI2R (0 ms) 48: [ RUN ] SimdScalarTest.cvtF2D 48: [ OK ] SimdScalarTest.cvtF2D (0 ms) 48: [ RUN ] SimdScalarTest.cvtD2D 48: [ OK ] SimdScalarTest.cvtD2D (0 ms) 48: [ RUN ] SimdScalarTest.loadI 48: [ OK ] SimdScalarTest.loadI (0 ms) 48: [ RUN ] SimdScalarTest.loadUI 48: [ OK ] SimdScalarTest.loadUI (0 ms) 48: [ RUN ] SimdScalarTest.storeI 48: [ OK ] SimdScalarTest.storeI (0 ms) 48: [ RUN ] SimdScalarTest.storeUI 48: [ OK ] SimdScalarTest.storeUI (0 ms) 48: [ RUN ] SimdScalarTest.andNotI 48: [ OK ] SimdScalarTest.andNotI (0 ms) 48: [ RUN ] SimdScalarTest.testBitsI 48: [ OK ] SimdScalarTest.testBitsI (0 ms) 48: [ RUN ] SimdScalarTest.selectByMaskI 48: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 48: [ RUN ] SimdScalarTest.selectByNotMaskI 48: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 48: [ RUN ] SimdScalarTest.blendI 48: [ OK ] SimdScalarTest.blendI (0 ms) 48: [ RUN ] SimdScalarTest.cvtB2IB 48: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 48: [ RUN ] SimdScalarTest.cvtIB2B 48: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 48: [ RUN ] SimdScalarTest.expandScalarsToTriplets 48: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 48: [----------] 41 tests from SimdScalarTest (1 ms total) 48: 48: [----------] 8 tests from SimdScalarUtilTest 48: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 48: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 48: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 48: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 48: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 48: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 48: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 48: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 48: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 48: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 48: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 48: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 48: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 48: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 48: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 48: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 48: [----------] 8 tests from SimdScalarUtilTest (3 ms total) 48: 48: [----------] 37 tests from SimdScalarMathTest 48: [ RUN ] SimdScalarMathTest.copysign 48: [ OK ] SimdScalarMathTest.copysign (0 ms) 48: [ RUN ] SimdScalarMathTest.invsqrtPair 48: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 48: [ RUN ] SimdScalarMathTest.inv 48: [ OK ] SimdScalarMathTest.inv (0 ms) 48: [ RUN ] SimdScalarMathTest.maskzInvsqrt 48: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 48: [ RUN ] SimdScalarMathTest.log 48: [ OK ] SimdScalarMathTest.log (0 ms) 48: [ RUN ] SimdScalarMathTest.exp2 48: [ OK ] SimdScalarMathTest.exp2 (0 ms) 48: [ RUN ] SimdScalarMathTest.exp 48: [ OK ] SimdScalarMathTest.exp (0 ms) 48: [ RUN ] SimdScalarMathTest.erf 48: [ OK ] SimdScalarMathTest.erf (0 ms) 48: [ RUN ] SimdScalarMathTest.erfc 48: [ OK ] SimdScalarMathTest.erfc (0 ms) 48: [ RUN ] SimdScalarMathTest.sincos 48: [ OK ] SimdScalarMathTest.sincos (0 ms) 48: [ RUN ] SimdScalarMathTest.sin 48: [ OK ] SimdScalarMathTest.sin (0 ms) 48: [ RUN ] SimdScalarMathTest.cos 48: [ OK ] SimdScalarMathTest.cos (0 ms) 48: [ RUN ] SimdScalarMathTest.tan 48: [ OK ] SimdScalarMathTest.tan (0 ms) 48: [ RUN ] SimdScalarMathTest.asin 48: [ OK ] SimdScalarMathTest.asin (0 ms) 48: [ RUN ] SimdScalarMathTest.acos 48: [ OK ] SimdScalarMathTest.acos (0 ms) 48: [ RUN ] SimdScalarMathTest.atan 48: [ OK ] SimdScalarMathTest.atan (0 ms) 48: [ RUN ] SimdScalarMathTest.atan2 48: [ OK ] SimdScalarMathTest.atan2 (0 ms) 48: [ RUN ] SimdScalarMathTest.pmeForceCorrection 48: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 48: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 48: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 48: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 48: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.invSingleAccuracy 48: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 48: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.logSingleAccuracy 48: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 48: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.expSingleAccuracy 48: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 48: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 48: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 48: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 48: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 48: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 48: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 48: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 48: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 48: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 48: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 48: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 48: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 48: [----------] 37 tests from SimdScalarMathTest (0 ms total) 48: 48: [----------] 1 test from SimdTest 48: [ RUN ] SimdTest.GmxAligned 48: [ OK ] SimdTest.GmxAligned (0 ms) 48: [----------] 1 test from SimdTest (0 ms total) 48: 48: [----------] 42 tests from SimdFloatingpointTest 48: [ RUN ] SimdFloatingpointTest.setZero 48: [ OK ] SimdFloatingpointTest.setZero (0 ms) 48: [ RUN ] SimdFloatingpointTest.set 48: [ OK ] SimdFloatingpointTest.set (0 ms) 48: [ RUN ] SimdFloatingpointTest.add 48: [ OK ] SimdFloatingpointTest.add (0 ms) 48: [ RUN ] SimdFloatingpointTest.maskAdd 48: [ OK ] SimdFloatingpointTest.maskAdd (0 ms) 48: [ RUN ] SimdFloatingpointTest.sub 48: [ OK ] SimdFloatingpointTest.sub (0 ms) 48: [ RUN ] SimdFloatingpointTest.mul 48: [ OK ] SimdFloatingpointTest.mul (0 ms) 48: [ RUN ] SimdFloatingpointTest.maskzMul 48: [ OK ] SimdFloatingpointTest.maskzMul (0 ms) 48: [ RUN ] SimdFloatingpointTest.fma 48: [ OK ] SimdFloatingpointTest.fma (0 ms) 48: [ RUN ] SimdFloatingpointTest.maskzFma 48: [ OK ] SimdFloatingpointTest.maskzFma (0 ms) 48: [ RUN ] SimdFloatingpointTest.fms 48: [ OK ] SimdFloatingpointTest.fms (0 ms) 48: [ RUN ] SimdFloatingpointTest.fnma 48: [ OK ] SimdFloatingpointTest.fnma (0 ms) 48: [ RUN ] SimdFloatingpointTest.fnms 48: [ OK ] SimdFloatingpointTest.fnms (0 ms) 48: [ RUN ] SimdFloatingpointTest.abs 48: [ OK ] SimdFloatingpointTest.abs (0 ms) 48: [ RUN ] SimdFloatingpointTest.neg 48: [ OK ] SimdFloatingpointTest.neg (0 ms) 48: [ RUN ] SimdFloatingpointTest.and 48: [ OK ] SimdFloatingpointTest.and (0 ms) 48: [ RUN ] SimdFloatingpointTest.or 48: [ OK ] SimdFloatingpointTest.or (0 ms) 48: [ RUN ] SimdFloatingpointTest.xor 48: [ OK ] SimdFloatingpointTest.xor (0 ms) 48: [ RUN ] SimdFloatingpointTest.andNot 48: [ OK ] SimdFloatingpointTest.andNot (0 ms) 48: [ RUN ] SimdFloatingpointTest.max 48: [ OK ] SimdFloatingpointTest.max (0 ms) 48: [ RUN ] SimdFloatingpointTest.min 48: [ OK ] SimdFloatingpointTest.min (0 ms) 48: [ RUN ] SimdFloatingpointTest.round 48: [ OK ] SimdFloatingpointTest.round (0 ms) 48: [ RUN ] SimdFloatingpointTest.roundMode 48: [ OK ] SimdFloatingpointTest.roundMode (0 ms) 48: [ RUN ] SimdFloatingpointTest.trunc 48: [ OK ] SimdFloatingpointTest.trunc (0 ms) 48: [ RUN ] SimdFloatingpointTest.frexp 48: [ OK ] SimdFloatingpointTest.frexp (0 ms) 48: [ RUN ] SimdFloatingpointTest.ldexp 48: [ OK ] SimdFloatingpointTest.ldexp (0 ms) 48: [ RUN ] SimdFloatingpointTest.rsqrt 48: [ OK ] SimdFloatingpointTest.rsqrt (0 ms) 48: [ RUN ] SimdFloatingpointTest.maskzRsqrt 48: [ OK ] SimdFloatingpointTest.maskzRsqrt (0 ms) 48: [ RUN ] SimdFloatingpointTest.rcp 48: [ OK ] SimdFloatingpointTest.rcp (0 ms) 48: [ RUN ] SimdFloatingpointTest.maskzRcp 48: [ OK ] SimdFloatingpointTest.maskzRcp (0 ms) 48: [ RUN ] SimdFloatingpointTest.cmpEqAndSelectByMask 48: [ OK ] SimdFloatingpointTest.cmpEqAndSelectByMask (0 ms) 48: [ RUN ] SimdFloatingpointTest.selectByNotMask 48: [ OK ] SimdFloatingpointTest.selectByNotMask (0 ms) 48: [ RUN ] SimdFloatingpointTest.cmpNe 48: [ OK ] SimdFloatingpointTest.cmpNe (0 ms) 48: [ RUN ] SimdFloatingpointTest.cmpLe 48: [ OK ] SimdFloatingpointTest.cmpLe (0 ms) 48: [ RUN ] SimdFloatingpointTest.cmpLt 48: [ OK ] SimdFloatingpointTest.cmpLt (0 ms) 48: [ RUN ] SimdFloatingpointTest.testBits 48: [ OK ] SimdFloatingpointTest.testBits (0 ms) 48: [ RUN ] SimdFloatingpointTest.andB 48: [ OK ] SimdFloatingpointTest.andB (0 ms) 48: [ RUN ] SimdFloatingpointTest.orB 48: [ OK ] SimdFloatingpointTest.orB (0 ms) 48: [ RUN ] SimdFloatingpointTest.anyTrueB 48: [ OK ] SimdFloatingpointTest.anyTrueB (0 ms) 48: [ RUN ] SimdFloatingpointTest.blend 48: [ OK ] SimdFloatingpointTest.blend (0 ms) 48: [ RUN ] SimdFloatingpointTest.reduce 48: [ OK ] SimdFloatingpointTest.reduce (0 ms) 48: [ RUN ] SimdFloatingpointTest.cvtFloat2Double 48: [ OK ] SimdFloatingpointTest.cvtFloat2Double (0 ms) 48: [ RUN ] SimdFloatingpointTest.cvtDouble2Float 48: [ OK ] SimdFloatingpointTest.cvtDouble2Float (0 ms) 48: [----------] 42 tests from SimdFloatingpointTest (0 ms total) 48: 48: [----------] 16 tests from SimdFloatingpointUtilTest 48: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose4 48: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose4 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose2 48: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose2 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 48: [ OK ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.transposeScatterStoreU3 48: [ OK ] SimdFloatingpointUtilTest.transposeScatterStoreU3 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3 48: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping 48: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3 48: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping 48: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.expandScalarsToTriplets 48: [ OK ] SimdFloatingpointUtilTest.expandScalarsToTriplets (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 48: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 48: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 48: [ OK ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.reduceIncr4Sum 48: [ OK ] SimdFloatingpointUtilTest.reduceIncr4Sum (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.loadUNDuplicate4 48: [ OK ] SimdFloatingpointUtilTest.loadUNDuplicate4 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.load4DuplicateN 48: [ OK ] SimdFloatingpointUtilTest.load4DuplicateN (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.loadU4NOffset 48: [ OK ] SimdFloatingpointUtilTest.loadU4NOffset (0 ms) 48: [----------] 16 tests from SimdFloatingpointUtilTest (0 ms total) 48: 48: [----------] 23 tests from SimdIntegerTest 48: [ RUN ] SimdIntegerTest.setZero 48: [ OK ] SimdIntegerTest.setZero (0 ms) 48: [ RUN ] SimdIntegerTest.set 48: [ OK ] SimdIntegerTest.set (0 ms) 48: [ RUN ] SimdIntegerTest.add 48: [ OK ] SimdIntegerTest.add (0 ms) 48: [ RUN ] SimdIntegerTest.sub 48: [ OK ] SimdIntegerTest.sub (0 ms) 48: [ RUN ] SimdIntegerTest.mul 48: [ OK ] SimdIntegerTest.mul (0 ms) 48: [ RUN ] SimdIntegerTest.and 48: [ OK ] SimdIntegerTest.and (0 ms) 48: [ RUN ] SimdIntegerTest.andNot 48: [ OK ] SimdIntegerTest.andNot (0 ms) 48: [ RUN ] SimdIntegerTest.or 48: [ OK ] SimdIntegerTest.or (0 ms) 48: [ RUN ] SimdIntegerTest.xor 48: [ OK ] SimdIntegerTest.xor (0 ms) 48: [ RUN ] SimdIntegerTest.extract 48: [ OK ] SimdIntegerTest.extract (0 ms) 48: [ RUN ] SimdIntegerTest.cvtR2I 48: [ OK ] SimdIntegerTest.cvtR2I (0 ms) 48: [ RUN ] SimdIntegerTest.cvttR2I 48: [ OK ] SimdIntegerTest.cvttR2I (0 ms) 48: [ RUN ] SimdIntegerTest.cvtI2R 48: [ OK ] SimdIntegerTest.cvtI2R (0 ms) 48: [ RUN ] SimdIntegerTest.cmpEqAndSelectMask 48: [ OK ] SimdIntegerTest.cmpEqAndSelectMask (0 ms) 48: [ RUN ] SimdIntegerTest.cmpEqAndSelectNotMask 48: [ OK ] SimdIntegerTest.cmpEqAndSelectNotMask (0 ms) 48: [ RUN ] SimdIntegerTest.cmpLt 48: [ OK ] SimdIntegerTest.cmpLt (0 ms) 48: [ RUN ] SimdIntegerTest.testBits 48: [ OK ] SimdIntegerTest.testBits (0 ms) 48: [ RUN ] SimdIntegerTest.andB 48: [ OK ] SimdIntegerTest.andB (0 ms) 48: [ RUN ] SimdIntegerTest.orB 48: [ OK ] SimdIntegerTest.orB (0 ms) 48: [ RUN ] SimdIntegerTest.anyTrue 48: [ OK ] SimdIntegerTest.anyTrue (0 ms) 48: [ RUN ] SimdIntegerTest.blend 48: [ OK ] SimdIntegerTest.blend (0 ms) 48: [ RUN ] SimdIntegerTest.cvtB2IB 48: [ OK ] SimdIntegerTest.cvtB2IB (0 ms) 48: [ RUN ] SimdIntegerTest.cvtIB2B 48: [ OK ] SimdIntegerTest.cvtIB2B (0 ms) 48: [----------] 23 tests from SimdIntegerTest (0 ms total) 48: 48: [----------] 56 tests from SimdMathTest 48: [ RUN ] SimdMathTest.generateTestPointsFloat 48: [ OK ] SimdMathTest.generateTestPointsFloat (4 ms) 48: [ RUN ] SimdMathTest.copysign 48: [ OK ] SimdMathTest.copysign (0 ms) 48: [ RUN ] SimdMathTest.invsqrt 48: [ OK ] SimdMathTest.invsqrt (0 ms) 48: [ RUN ] SimdMathTest.maskzInvsqrt 48: [ OK ] SimdMathTest.maskzInvsqrt (0 ms) 48: [ RUN ] SimdMathTest.invsqrtPair 48: [ OK ] SimdMathTest.invsqrtPair (0 ms) 48: [ RUN ] SimdMathTest.sqrt 48: [ OK ] SimdMathTest.sqrt (0 ms) 48: [ RUN ] SimdMathTest.sqrtUnsafe 48: [ OK ] SimdMathTest.sqrtUnsafe (0 ms) 48: [ RUN ] SimdMathTest.inv 48: [ OK ] SimdMathTest.inv (0 ms) 48: [ RUN ] SimdMathTest.maskzInv 48: [ OK ] SimdMathTest.maskzInv (0 ms) 48: [ RUN ] SimdMathTest.cbrt 48: [ OK ] SimdMathTest.cbrt (0 ms) 48: [ RUN ] SimdMathTest.invcbrt 48: [ OK ] SimdMathTest.invcbrt (0 ms) 48: [ RUN ] SimdMathTest.log2 48: [ OK ] SimdMathTest.log2 (8 ms) 48: [ RUN ] SimdMathTest.log 48: [ OK ] SimdMathTest.log (0 ms) 48: [ RUN ] SimdMathTest.exp2 48: [ OK ] SimdMathTest.exp2 (0 ms) 48: [ RUN ] SimdMathTest.exp2Unsafe 48: [ OK ] SimdMathTest.exp2Unsafe (0 ms) 48: [ RUN ] SimdMathTest.exp 48: [ OK ] SimdMathTest.exp (0 ms) 48: [ RUN ] SimdMathTest.expUnsafe 48: [ OK ] SimdMathTest.expUnsafe (0 ms) 48: [ RUN ] SimdMathTest.pow 48: [ OK ] SimdMathTest.pow (0 ms) 48: [ RUN ] SimdMathTest.powUnsafe 48: [ OK ] SimdMathTest.powUnsafe (0 ms) 48: [ RUN ] SimdMathTest.erf 48: [ OK ] SimdMathTest.erf (0 ms) 48: [ RUN ] SimdMathTest.erfc 48: [ OK ] SimdMathTest.erfc (0 ms) 48: [ RUN ] SimdMathTest.sin 48: [ OK ] SimdMathTest.sin (0 ms) 48: [ RUN ] SimdMathTest.cos 48: [ OK ] SimdMathTest.cos (4 ms) 48: [ RUN ] SimdMathTest.tan 48: [ OK ] SimdMathTest.tan (0 ms) 48: [ RUN ] SimdMathTest.asin 48: [ OK ] SimdMathTest.asin (0 ms) 48: [ RUN ] SimdMathTest.acos 48: [ OK ] SimdMathTest.acos (0 ms) 48: [ RUN ] SimdMathTest.atan 48: [ OK ] SimdMathTest.atan (0 ms) 48: [ RUN ] SimdMathTest.atan2 48: [ OK ] SimdMathTest.atan2 (0 ms) 48: [ RUN ] SimdMathTest.pmeForceCorrection 48: [ OK ] SimdMathTest.pmeForceCorrection (0 ms) 48: [ RUN ] SimdMathTest.pmePotentialCorrection 48: [ OK ] SimdMathTest.pmePotentialCorrection (0 ms) 48: [ RUN ] SimdMathTest.invsqrtSingleAccuracy 48: [ OK ] SimdMathTest.invsqrtSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.invsqrtPairSingleAccuracy 48: [ OK ] SimdMathTest.invsqrtPairSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.sqrtSingleAccuracy 48: [ OK ] SimdMathTest.sqrtSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.sqrtSingleAccuracyUnsafe 48: [ OK ] SimdMathTest.sqrtSingleAccuracyUnsafe (0 ms) 48: [ RUN ] SimdMathTest.invSingleAccuracy 48: [ OK ] SimdMathTest.invSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.cbrtSingleAccuracy 48: [ OK ] SimdMathTest.cbrtSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.invcbrtSingleAccuracy 48: [ OK ] SimdMathTest.invcbrtSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.log2SingleAccuracy 48: [ OK ] SimdMathTest.log2SingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.logSingleAccuracy 48: [ OK ] SimdMathTest.logSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.exp2SingleAccuracy 48: [ OK ] SimdMathTest.exp2SingleAccuracy (4 ms) 48: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe 48: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (0 ms) 48: [ RUN ] SimdMathTest.expSingleAccuracy 48: [ OK ] SimdMathTest.expSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.expSingleAccuracyUnsafe 48: [ OK ] SimdMathTest.expSingleAccuracyUnsafe (0 ms) 48: [ RUN ] SimdMathTest.powSingleAccuracy 48: [ OK ] SimdMathTest.powSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.powSingleAccuracyUnsafe 48: [ OK ] SimdMathTest.powSingleAccuracyUnsafe (0 ms) 48: [ RUN ] SimdMathTest.erfSingleAccuracy 48: [ OK ] SimdMathTest.erfSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.erfcSingleAccuracy 48: [ OK ] SimdMathTest.erfcSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.sinSingleAccuracy 48: [ OK ] SimdMathTest.sinSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.cosSingleAccuracy 48: [ OK ] SimdMathTest.cosSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.tanSingleAccuracy 48: [ OK ] SimdMathTest.tanSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.asinSingleAccuracy 48: [ OK ] SimdMathTest.asinSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.acosSingleAccuracy 48: [ OK ] SimdMathTest.acosSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.atanSingleAccuracy 48: [ OK ] SimdMathTest.atanSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.atan2SingleAccuracy 48: [ OK ] SimdMathTest.atan2SingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.pmeForceCorrectionSingleAccuracy 48: [ OK ] SimdMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy 48: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 48: [----------] 56 tests from SimdMathTest (52 ms total) 48: 48: [----------] 1 test from EmptyArrayRefTest 48: [ RUN ] EmptyArrayRefTest.IsEmpty 48: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 48: [----------] 1 test from EmptyArrayRefTest (0 ms total) 48: 48: [----------] 3 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 48: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 48: [ RUN ] ArrayRefTest/0.ConstructFromArrayRefWorks 48: [ OK ] ArrayRefTest/0.ConstructFromArrayRefWorks (0 ms) 48: [ RUN ] ArrayRefTest/0.ConstructFromArrayWorks 48: [ OK ] ArrayRefTest/0.ConstructFromArrayWorks (0 ms) 48: [----------] 3 tests from ArrayRefTest/0 (0 ms total) 48: 48: [----------] 3 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 48: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 48: [ RUN ] ArrayRefTest/1.ConstructFromArrayRefWorks 48: [ OK ] ArrayRefTest/1.ConstructFromArrayRefWorks (0 ms) 48: [ RUN ] ArrayRefTest/1.ConstructFromArrayWorks 48: [ OK ] ArrayRefTest/1.ConstructFromArrayWorks (0 ms) 48: [----------] 3 tests from ArrayRefTest/1 (0 ms total) 48: 48: [----------] 3 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 48: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 48: [ RUN ] ArrayRefTest/2.ConstructFromArrayRefWorks 48: [ OK ] ArrayRefTest/2.ConstructFromArrayRefWorks (0 ms) 48: [ RUN ] ArrayRefTest/2.ConstructFromArrayWorks 48: [ OK ] ArrayRefTest/2.ConstructFromArrayWorks (0 ms) 48: [----------] 3 tests from ArrayRefTest/2 (0 ms total) 48: 48: [----------] 3 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 48: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 48: [ RUN ] ArrayRefTest/3.ConstructFromArrayRefWorks 48: [ OK ] ArrayRefTest/3.ConstructFromArrayRefWorks (0 ms) 48: [ RUN ] ArrayRefTest/3.ConstructFromArrayWorks 48: [ OK ] ArrayRefTest/3.ConstructFromArrayWorks (0 ms) 48: [----------] 3 tests from ArrayRefTest/3 (0 ms total) 48: 48: [----------] 1 test from ArrayRefReadWriteTest/0, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefReadWriteTest/0.Assignment 48: [ OK ] ArrayRefReadWriteTest/0.Assignment (0 ms) 48: [----------] 1 test from ArrayRefReadWriteTest/0 (0 ms total) 48: 48: [----------] 1 test from ArrayRefReadWriteTest/1, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefReadWriteTest/1.Assignment 48: [ OK ] ArrayRefReadWriteTest/1.Assignment (0 ms) 48: [----------] 1 test from ArrayRefReadWriteTest/1 (0 ms total) 48: 48: [----------] 1 test from ArrayRefArithmeticTest/0, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefArithmeticTest/0.Basic 48: [ OK ] ArrayRefArithmeticTest/0.Basic (0 ms) 48: [----------] 1 test from ArrayRefArithmeticTest/0 (0 ms total) 48: 48: [----------] 1 test from ArrayRefArithmeticTest/1, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefArithmeticTest/1.Basic 48: [ OK ] ArrayRefArithmeticTest/1.Basic (0 ms) 48: [----------] 1 test from ArrayRefArithmeticTest/1 (0 ms total) 48: 48: [----------] 3 tests from SimdVectorOperationsTest 48: [ RUN ] SimdVectorOperationsTest.iprod 48: [ OK ] SimdVectorOperationsTest.iprod (0 ms) 48: [ RUN ] SimdVectorOperationsTest.norm2 48: [ OK ] SimdVectorOperationsTest.norm2 (0 ms) 48: [ RUN ] SimdVectorOperationsTest.cprod 48: [ OK ] SimdVectorOperationsTest.cprod (0 ms) 48: [----------] 3 tests from SimdVectorOperationsTest (0 ms total) 48: 48: [----------] 32 tests from Simd4FloatingpointTest 48: [ RUN ] Simd4FloatingpointTest.setZero 48: [ OK ] Simd4FloatingpointTest.setZero (0 ms) 48: [ RUN ] Simd4FloatingpointTest.set 48: [ OK ] Simd4FloatingpointTest.set (0 ms) 48: [ RUN ] Simd4FloatingpointTest.add 48: [ OK ] Simd4FloatingpointTest.add (0 ms) 48: [ RUN ] Simd4FloatingpointTest.sub 48: [ OK ] Simd4FloatingpointTest.sub (0 ms) 48: [ RUN ] Simd4FloatingpointTest.mul 48: [ OK ] Simd4FloatingpointTest.mul (0 ms) 48: [ RUN ] Simd4FloatingpointTest.fma 48: [ OK ] Simd4FloatingpointTest.fma (0 ms) 48: [ RUN ] Simd4FloatingpointTest.fms 48: [ OK ] Simd4FloatingpointTest.fms (0 ms) 48: [ RUN ] Simd4FloatingpointTest.fnma 48: [ OK ] Simd4FloatingpointTest.fnma (0 ms) 48: [ RUN ] Simd4FloatingpointTest.fnms 48: [ OK ] Simd4FloatingpointTest.fnms (0 ms) 48: [ RUN ] Simd4FloatingpointTest.abs 48: [ OK ] Simd4FloatingpointTest.abs (0 ms) 48: [ RUN ] Simd4FloatingpointTest.neg 48: [ OK ] Simd4FloatingpointTest.neg (0 ms) 48: [ RUN ] Simd4FloatingpointTest.and 48: [ OK ] Simd4FloatingpointTest.and (0 ms) 48: [ RUN ] Simd4FloatingpointTest.or 48: [ OK ] Simd4FloatingpointTest.or (0 ms) 48: [ RUN ] Simd4FloatingpointTest.xor 48: [ OK ] Simd4FloatingpointTest.xor (0 ms) 48: [ RUN ] Simd4FloatingpointTest.andNot 48: [ OK ] Simd4FloatingpointTest.andNot (0 ms) 48: [ RUN ] Simd4FloatingpointTest.max 48: [ OK ] Simd4FloatingpointTest.max (0 ms) 48: [ RUN ] Simd4FloatingpointTest.min 48: [ OK ] Simd4FloatingpointTest.min (0 ms) 48: [ RUN ] Simd4FloatingpointTest.round 48: [ OK ] Simd4FloatingpointTest.round (0 ms) 48: [ RUN ] Simd4FloatingpointTest.trunc 48: [ OK ] Simd4FloatingpointTest.trunc (0 ms) 48: [ RUN ] Simd4FloatingpointTest.gmxSimd4RsqrtR 48: [ OK ] Simd4FloatingpointTest.gmxSimd4RsqrtR (0 ms) 48: [ RUN ] Simd4FloatingpointTest.cmpEqAndSelectByMask 48: [ OK ] Simd4FloatingpointTest.cmpEqAndSelectByMask (0 ms) 48: [ RUN ] Simd4FloatingpointTest.selectByNotMask 48: [ OK ] Simd4FloatingpointTest.selectByNotMask (0 ms) 48: [ RUN ] Simd4FloatingpointTest.cmpNe 48: [ OK ] Simd4FloatingpointTest.cmpNe (0 ms) 48: [ RUN ] Simd4FloatingpointTest.cmpLe 48: [ OK ] Simd4FloatingpointTest.cmpLe (0 ms) 48: [ RUN ] Simd4FloatingpointTest.cmpLt 48: [ OK ] Simd4FloatingpointTest.cmpLt (0 ms) 48: [ RUN ] Simd4FloatingpointTest.andB 48: [ OK ] Simd4FloatingpointTest.andB (0 ms) 48: [ RUN ] Simd4FloatingpointTest.orB 48: [ OK ] Simd4FloatingpointTest.orB (0 ms) 48: [ RUN ] Simd4FloatingpointTest.anyTrue 48: [ OK ] Simd4FloatingpointTest.anyTrue (0 ms) 48: [ RUN ] Simd4FloatingpointTest.blend 48: [ OK ] Simd4FloatingpointTest.blend (0 ms) 48: [ RUN ] Simd4FloatingpointTest.reduce 48: [ OK ] Simd4FloatingpointTest.reduce (0 ms) 48: [ RUN ] Simd4FloatingpointTest.dotProduct 48: [ OK ] Simd4FloatingpointTest.dotProduct (0 ms) 48: [ RUN ] Simd4FloatingpointTest.transpose 48: [ OK ] Simd4FloatingpointTest.transpose (0 ms) 48: [----------] 32 tests from Simd4FloatingpointTest (5 ms total) 48: 48: [----------] 2 tests from Simd4MathTest 48: [ RUN ] Simd4MathTest.invsqrt 48: [ OK ] Simd4MathTest.invsqrt (0 ms) 48: [ RUN ] Simd4MathTest.invsqrtSingleAccuracy 48: [ OK ] Simd4MathTest.invsqrtSingleAccuracy (0 ms) 48: [----------] 2 tests from Simd4MathTest (0 ms total) 48: 48: [----------] 1 test from Simd4VectorOperationsTest 48: [ RUN ] Simd4VectorOperationsTest.norm2 48: [ OK ] Simd4VectorOperationsTest.norm2 (0 ms) 48: [----------] 1 test from Simd4VectorOperationsTest (0 ms total) 48: 48: [----------] Global test environment tear-down 48: [==========] 288 tests from 22 test suites ran. (68 ms total) 48: [ PASSED ] 288 tests. 48/91 Test #48: SimdUnitTests ................................ Passed 0.45 sec test 49 Start 49: CompatibilityHelpersTests 49: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/compat-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/CompatibilityHelpersTests.xml" 49: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/compat/tests 49: Test timeout computed to be: 30 49: [==========] Running 9 tests from 6 test suites. 49: [----------] Global test environment set-up. 49: [----------] 4 tests from TemplateMPTest 49: [ RUN ] TemplateMPTest.MpWithIndexInt 49: [ OK ] TemplateMPTest.MpWithIndexInt (0 ms) 49: [ RUN ] TemplateMPTest.MpWithIndexIntBad 49: [ OK ] TemplateMPTest.MpWithIndexIntBad (0 ms) 49: [ RUN ] TemplateMPTest.MpWithIndexBool 49: [ OK ] TemplateMPTest.MpWithIndexBool (0 ms) 49: [ RUN ] TemplateMPTest.MpWithIndexEnum 49: [ OK ] TemplateMPTest.MpWithIndexEnum (0 ms) 49: [----------] 4 tests from TemplateMPTest (0 ms total) 49: 49: [----------] 1 test from NotNullConstruction 49: [ RUN ] NotNullConstruction.Works 49: [ OK ] NotNullConstruction.Works (0 ms) 49: [----------] 1 test from NotNullConstruction (0 ms total) 49: 49: [----------] 1 test from NotNullCasting 49: [ RUN ] NotNullCasting.Works 49: [ OK ] NotNullCasting.Works (0 ms) 49: [----------] 1 test from NotNullCasting (0 ms total) 49: 49: [----------] 1 test from NotNullAssignment 49: [ RUN ] NotNullAssignment.Works 49: [ OK ] NotNullAssignment.Works (0 ms) 49: [----------] 1 test from NotNullAssignment (0 ms total) 49: 49: [----------] 1 test from MakeNotNull 49: [ RUN ] MakeNotNull.Works 49: [ OK ] MakeNotNull.Works (0 ms) 49: [----------] 1 test from MakeNotNull (0 ms total) 49: 49: [----------] 1 test from NotNull 49: [ RUN ] NotNull.WorksInContainers 49: [ OK ] NotNull.WorksInContainers (0 ms) 49: [----------] 1 test from NotNull (0 ms total) 49: 49: [----------] Global test environment tear-down 49: [==========] 9 tests from 6 test suites ran. (0 ms total) 49: [ PASSED ] 9 tests. 49/91 Test #49: CompatibilityHelpersTests .................... Passed 0.39 sec test 50 Start 50: GmxAnaTest 50: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/gmxana-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/GmxAnaTest.xml" 50: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxana/tests 50: Test timeout computed to be: 600 50: [==========] Running 31 tests from 4 test suites. 50: [----------] Global test environment set-up. 50: [----------] 7 tests from Entropy 50: [ RUN ] Entropy.Schlitter_300_NoLinear 50: [ OK ] Entropy.Schlitter_300_NoLinear (0 ms) 50: [ RUN ] Entropy.Schlitter_300_Linear 50: [ OK ] Entropy.Schlitter_300_Linear (0 ms) 50: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear 50: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms) 50: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear 50: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms) 50: [ RUN ] Entropy.QuasiHarmonic_200_Linear 50: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms) 50: [ RUN ] Entropy.EntropyCompare_200_Linear 50: [ OK ] Entropy.EntropyCompare_200_Linear (0 ms) 50: [ RUN ] Entropy.EntropyCompare_300_Linear 50: [ OK ] Entropy.EntropyCompare_300_Linear (0 ms) 50: [----------] 7 tests from Entropy (0 ms total) 50: 50: [----------] 2 tests from GmxChiTest 50: [ RUN ] GmxChiTest.gmxchiWorksWithAll 50: Analyzing from residue 1 to residue 11 50: 10 residues with dihedrals found 50: 46 dihedrals found 50: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 50: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 50: j after resetting (nr. active dihedrals) = 46 50: Printing phiLYS1.xvg Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing phiGLU7.xvg Printing phiLEU8.xvg Printing phiALA9.xvg Printing phiALA10.xvg Printing psiLYS1.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing psiGLU7.xvg Printing psiLEU8.xvg Printing psiALA9.xvg Printing psiALA10.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing omegaGLU7.xvg Printing omegaLEU8.xvg Printing omegaALA9.xvg Printing omegaALA10.xvg Printing chi1LYS1.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi1GLU7.xvg Printing chi1LEU8.xvg Printing chi2LYS1.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi2GLU7.xvg Printing chi2LEU8.xvg Printing chi3LYS1.xvg Printing chi3ARG5.xvg Printing chi3GLU7.xvg Printing chi4LYS1.xvg Printing chi4ARG5.xvg 50: Now calculating transitions... 50: Total number of transitions: 0 50: Now printing out transitions and OPs... 50: Now printing out rotamer occupancies... 50: Now calculating Chi product trajectories... 50: Printing chiproductLYS1.xvg and histo-chiprodLYS1.xvg Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg Printing chiproductGLU7.xvg and histo-chiprodGLU7.xvg Printing chiproductLEU8.xvg and histo-chiprodLEU8.xvg 50: [ OK ] GmxChiTest.gmxchiWorksWithAll (608 ms) 50: [ RUN ] GmxChiTest.gmxchiWorksWithr0AndrN 50: Analyzing from residue 2 to residue 6 50: 5 residues with dihedrals found 50: 23 dihedrals found 50: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 50: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 50: j after resetting (nr. active dihedrals) = 23 50: Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi3ARG5.xvg Printing chi4ARG5.xvg 50: Now calculating transitions... 50: Total number of transitions: 0 50: Now printing out transitions and OPs... 50: Now printing out rotamer occupancies... 50: Now calculating Chi product trajectories... 50: Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg 50: [ OK ] GmxChiTest.gmxchiWorksWithr0AndrN (185 ms) 50: [----------] 2 tests from GmxChiTest (865 ms total) 50: 50: [----------] 10 tests from MindistTest 50: [ RUN ] MindistTest.mindistWorksWithSingleAtoms 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 0: 'atom1' 50: Selected 1: 'atom2' 50: [ OK ] MindistTest.mindistWorksWithSingleAtoms (8 ms) 50: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 2: 'atom3' 50: Selected 3: 'atoms12' 50: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (1 ms) 50: [ RUN ] MindistTest.mindistDoesNotPickUpContacts 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 0: 'atom1' 50: Selected 1: 'atom2' 50: [ OK ] MindistTest.mindistDoesNotPickUpContacts (0 ms) 50: [ RUN ] MindistTest.mindistPicksUpContacts 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 0: 'atom1' 50: Selected 1: 'atom2' 50: [ OK ] MindistTest.mindistPicksUpContacts (1 ms) 50: [ RUN ] MindistTest.ngWorks 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 0: 'atom1' 50: Selected 1: 'atom2' 50: Selected 2: 'atom3' 50: [ OK ] MindistTest.ngWorks (0 ms) 50: [ RUN ] MindistTest.groupWorks 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 3: 'atoms12' 50: Selected 2: 'atom3' 50: [ OK ] MindistTest.groupWorks (0 ms) 50: [ RUN ] MindistTest.maxDistWorks 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 2: 'atom3' 50: Selected 3: 'atoms12' 50: [ OK ] MindistTest.maxDistWorks (0 ms) 50: [ RUN ] MindistTest.noPbcWorks 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 0: 'atom1' 50: Selected 1: 'atom2' 50: [ OK ] MindistTest.noPbcWorks (0 ms) 50: [ RUN ] MindistTest.resPerTimeWorks 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 3: 'atoms12' 50: Selected 2: 'atom3' 50: [ OK ] MindistTest.resPerTimeWorks (2 ms) 50: [ RUN ] MindistTest.matrixWorks 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 5: 'atoms123' 50: Special case: making distance matrix between all atoms in group atoms123 50: [ OK ] MindistTest.matrixWorks (0 ms) 50: [----------] 10 tests from MindistTest (21 ms total) 50: 50: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: trr version: GMX_trn_file (single precision) 50: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (1 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (0 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 50: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (0 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (0 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (1 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (1 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 50: WARNING: If there are molecules in the input trajectory file 50: that are broken across periodic boundaries, they 50: cannot be made whole (or treated as whole) without 50: you providing a run input file. 50: 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: 50: WARNING: Masses and atomic (Van der Waals) radii will be guessed 50: based on residue and atom names, since they could not be 50: definitively assigned from the information in your input 50: files. These guessed numbers might deviate from the mass 50: and radius of the atom type. Please check the output 50: files if necessary. Note, that this functionality may 50: be removed in a future GROMACS version. Please, consider 50: using another file format for your input. 50: 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 (1 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 50: WARNING: If there are molecules in the input trajectory file 50: that are broken across periodic boundaries, they 50: cannot be made whole (or treated as whole) without 50: you providing a run input file. 50: 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: 50: WARNING: Masses and atomic (Van der Waals) radii will be guessed 50: based on residue and atom names, since they could not be 50: definitively assigned from the information in your input 50: files. These guessed numbers might deviate from the mass 50: and radius of the atom type. Please check the output 50: files if necessary. Note, that this functionality may 50: be removed in a future GROMACS version. Please, consider 50: using another file format for your input. 50: 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 (1 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 50: Reading frame 0 time 0.000 50: WARNING: If there are molecules in the input trajectory file 50: that are broken across periodic boundaries, they 50: cannot be made whole (or treated as whole) without 50: you providing a run input file. 50: 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: 50: WARNING: Masses and atomic (Van der Waals) radii will be guessed 50: based on residue and atom names, since they could not be 50: definitively assigned from the information in your input 50: files. These guessed numbers might deviate from the mass 50: and radius of the atom type. Please check the output 50: files if necessary. Note, that this functionality may 50: be removed in a future GROMACS version. Please, consider 50: using another file format for your input. 50: 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 (1 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 50: WARNING: If there are molecules in the input trajectory file 50: that are broken across periodic boundaries, they 50: cannot be made whole (or treated as whole) without 50: you providing a run input file. 50: 50: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: 50: WARNING: Masses and atomic (Van der Waals) radii will be guessed 50: based on residue and atom names, since they could not be 50: definitively assigned from the information in your input 50: files. These guessed numbers might deviate from the mass 50: and radius of the atom type. Please check the output 50: files if necessary. Note, that this functionality may 50: be removed in a future GROMACS version. Please, consider 50: using another file format for your input. 50: 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 (1 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 50: WARNING: If there are molecules in the input trajectory file 50: that are broken across periodic boundaries, they 50: cannot be made whole (or treated as whole) without 50: you providing a run input file. 50: 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: 50: WARNING: Masses and atomic (Van der Waals) radii will be guessed 50: based on residue and atom names, since they could not be 50: definitively assigned from the information in your input 50: files. These guessed numbers might deviate from the mass 50: and radius of the atom type. Please check the output 50: files if necessary. Note, that this functionality may 50: be removed in a future GROMACS version. Please, consider 50: using another file format for your input. 50: 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 (1 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 50: WARNING: If there are molecules in the input trajectory file 50: that are broken across periodic boundaries, they 50: cannot be made whole (or treated as whole) without 50: you providing a run input file. 50: 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: 50: WARNING: Masses and atomic (Van der Waals) radii will be guessed 50: based on residue and atom names, since they could not be 50: definitively assigned from the information in your input 50: files. These guessed numbers might deviate from the mass 50: and radius of the atom type. Please check the output 50: files if necessary. Note, that this functionality may 50: be removed in a future GROMACS version. Please, consider 50: using another file format for your input. 50: 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 (1 ms) 50: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj (19 ms total) 50: 50: [----------] Global test environment tear-down 50: [==========] 31 tests from 4 test suites ran. (907 ms total) 50: [ PASSED ] 31 tests. 50/91 Test #50: GmxAnaTest ................................... Passed 1.27 sec test 51 Start 51: GmxPreprocessTests 51: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/gmxpreprocess-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/GmxPreprocessTests.xml" 51: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests 51: Test timeout computed to be: 1920 51: [==========] Running 138 tests from 13 test suites. 51: [----------] Global test environment set-up. 51: [----------] 4 tests from GenconfTest 51: [ RUN ] GenconfTest.nbox_Works 51: [ OK ] GenconfTest.nbox_Works (1 ms) 51: [ RUN ] GenconfTest.nbox_norenumber_Works 51: [ OK ] GenconfTest.nbox_norenumber_Works (0 ms) 51: [ RUN ] GenconfTest.nbox_dist_Works 51: [ OK ] GenconfTest.nbox_dist_Works (0 ms) 51: [ RUN ] GenconfTest.nbox_rot_Works 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: [ OK ] GenconfTest.nbox_rot_Works (0 ms) 51: [----------] 4 tests from GenconfTest (2 ms total) 51: 51: [----------] 2 tests from GenionTest 51: [ RUN ] GenionTest.HighConcentrationIonPlacement 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 51: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 51: buffer. The cluster pair list does have a buffering effect, but choosing 51: a larger rlist might be necessary for good energy conservation. 51: 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 51: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 51: < 0 51: 51: 51: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: Generating 1-4 interactions: fudge = 0.5 51: Number of degrees of freedom in T-Coupling group rest is 1308.00 51: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 51: 51: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 51: You are using a plain Coulomb cut-off, which might produce artifacts. 51: You might want to consider using PME electrostatics. 51: 51: 51: 51: There were 4 NOTEs 51: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 51: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 51: Group 0 ( System) has 653 elements 51: Group 1 ( Water) has 648 elements 51: Group 2 ( SOL) has 648 elements 51: Group 3 ( non-Water) has 5 elements 51: Group 4 ( Other) has 5 elements 51: Group 5 ( METH) has 5 elements 51: Select a group: Number of (3-atomic) solvent molecules: 216 51: Using random seed 1997. 51: Replacing solvent molecule 56 (atom 168) with NA 51: Replacing solvent molecule 120 (atom 360) with NA 51: Replacing solvent molecule 182 (atom 546) with NA 51: Replacing solvent molecule 71 (atom 213) with NA 51: Replacing solvent molecule 189 (atom 567) with CL 51: Replacing solvent molecule 54 (atom 162) with CL 51: Replacing solvent molecule 155 (atom 465) with CL 51: Replacing solvent molecule 99 (atom 297) with CL 51: 51: Setting the LD random seed to 1035730335 51: 51: Generated 331705 of the 331705 non-bonded parameter combinations 51: 51: Generated 331705 of the 331705 1-4 parameter combinations 51: 51: Excluding 2 bonded neighbours molecule type 'SOL' 51: 51: Excluding 3 bonded neighbours molecule type 'methane' 51: Analysing residue names: 51: There are: 216 Water residues 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: This run will generate roughly 0 Mb of data 51: Will try to add 4 NA ions and 4 CL ions. 51: Select a continuous group of solvent molecules 51: Selected 1: 'Water' 51: [ OK ] GenionTest.HighConcentrationIonPlacement (353 ms) 51: [ RUN ] GenionTest.NoIonPlacement 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 51: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 51: buffer. The cluster pair list does have a buffering effect, but choosing 51: a larger rlist might be necessary for good energy conservation. 51: 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 51: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 51: < 0 51: 51: 51: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: Generating 1-4 interactions: fudge = 0.5 51: Number of degrees of freedom in T-Coupling group rest is 1308.00 51: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 51: 51: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 51: You are using a plain Coulomb cut-off, which might produce artifacts. 51: You might want to consider using PME electrostatics. 51: 51: 51: 51: There were 4 NOTEs 51: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 51: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 51: No ions to add, will just copy input configuration. 51: Setting the LD random seed to -378143237 51: 51: Generated 331705 of the 331705 non-bonded parameter combinations 51: 51: Generated 331705 of the 331705 1-4 parameter combinations 51: 51: Excluding 2 bonded neighbours molecule type 'SOL' 51: 51: Excluding 3 bonded neighbours molecule type 'methane' 51: Analysing residue names: 51: There are: 216 Water residues 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: This run will generate roughly 0 Mb of data 51: [ OK ] GenionTest.NoIonPlacement (399 ms) 51: [----------] 2 tests from GenionTest (755 ms total) 51: 51: [----------] 1 test from GenRestrTest 51: [ RUN ] GenRestrTest.SimpleRestraintsGenerated 51: 51: Reading structure file 51: Group 0 ( System) has 156 elements 51: Group 1 ( Protein) has 156 elements 51: Group 2 ( Protein-H) has 75 elements 51: Group 3 ( C-alpha) has 10 elements 51: Group 4 ( Backbone) has 30 elements 51: Group 5 ( MainChain) has 40 elements 51: Group 6 ( MainChain+Cb) has 49 elements 51: Group 7 ( MainChain+H) has 52 elements 51: Group 8 ( SideChain) has 104 elements 51: Group 9 ( SideChain-H) has 35 elements 51: Select a group: Select group to position restrain 51: Selected 3: 'C-alpha' 51: [ OK ] GenRestrTest.SimpleRestraintsGenerated (1 ms) 51: [----------] 1 test from GenRestrTest (2 ms total) 51: 51: [----------] 9 tests from PreprocessingAtomTypesTest 51: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate 51: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid 51: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks 51: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks 51: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry 51: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound 51: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound 51: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber 51: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber 51: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms) 51: [----------] 9 tests from PreprocessingAtomTypesTest (1 ms total) 51: 51: [----------] 10 tests from PreprocessingBondAtomTypeTest 51: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate 51: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid 51: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks 51: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks 51: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry 51: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType 51: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound 51: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound 51: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber 51: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber 51: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms) 51: [----------] 10 tests from PreprocessingBondAtomTypeTest (1 ms total) 51: 51: [----------] 1 test from GromppDirectiveTest 51: [ RUN ] GromppDirectiveTest.edgeCaseAtomTypeNames 51: Ignoring obsolete mdp entry 'title' 51: Generating 1-4 interactions: fudge = 0.5 51: 51: NOTE 1 [file directives.top, line 44]: 51: In moleculetype 'A' 2 atoms are not bound by a potential or constraint to 51: any other atom in the same moleculetype. Although technically this might 51: not cause issues in a simulation, this often means that the user forgot 51: to add a bond/potential/constraint or put multiple molecules in the same 51: moleculetype definition by mistake. Run with -v to get information for 51: each atom. 51: 51: Number of degrees of freedom in T-Coupling group rest is 9.00 51: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.mdp]: 51: NVE simulation: will use the initial temperature of 300.000 K for 51: determining the Verlet buffer size 51: 51: 51: There were 2 NOTEs 51: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 51: Setting the LD random seed to 2068770495 51: 51: Generated 10 of the 10 non-bonded parameter combinations 51: 51: Generated 10 of the 10 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -134945863 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: Analysing residue names: 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 51: 51: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 51: 51: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 51: 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: 51: This run will generate roughly 0 Mb of data 51: [ OK ] GromppDirectiveTest.edgeCaseAtomTypeNames (3 ms) 51: [----------] 1 test from GromppDirectiveTest (4 ms total) 51: 51: [----------] 5 tests from InsertMoleculesTest 51: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration 51: Reading solute configuration 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. 68 (1964) pp. 441-451 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Using random seed 1997 51: Try 1 success (now 8 atoms)! 51: 51: Added 1 molecules (out of 1 requested) 51: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro 51: 51: Output configuration contains 8 atoms in 4 residues 51: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (1 ms) 51: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. 68 (1964) pp. 441-451 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Using random seed 1997 51: Try 1 success (now 2 atoms)! 51: Try 2 success (now 4 atoms)! 51: Try 3 success (now 6 atoms)! 51: Try 4 success (now 8 atoms)! 51: Try 5 success (now 10 atoms)! 51: 51: Added 5 molecules (out of 5 requested) 51: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro 51: 51: Output configuration contains 10 atoms in 10 residues 51: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (1 ms) 51: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox 51: Reading solute configuration 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. 68 (1964) pp. 441-451 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Using random seed 1997 51: Try 1 success (now 8 atoms)! 51: Try 2 success (now 10 atoms)! 51: 51: Added 2 molecules (out of 2 requested) 51: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro 51: 51: Output configuration contains 10 atoms in 4 residues 51: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (1 ms) 51: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement 51: Reading solute configuration 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. 68 (1964) pp. 441-451 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Using random seed 1997 51: Try 1 success (now 650 atoms)! 51: Try 2 success (now 652 atoms)! 51: Try 3 success (now 654 atoms)! 51: Try 4 success (now 656 atoms)! 51: 51: Added 4 molecules (out of 4 requested) 51: Replaced 8 residues (24 atoms) 51: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro 51: 51: Output configuration contains 632 atoms in 212 residues 51: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (5 ms) 51: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. 68 (1964) pp. 441-451 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Using random seed 1997 51: Read 4 positions from file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat 51: 51: Try 1 success (now 2 atoms)! 51: Try 2 success (now 4 atoms)! 51: Try 3 Try 4 Try 5 Try 6 Try 7 Try 8 Try 9 Try 10 Try 11 Try 12 skipped position (0.990, 2.010, 3.000) 51: Try 13 success (now 6 atoms)! 51: 51: Added 3 molecules (out of 4 requested) 51: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro 51: 51: Output configuration contains 6 atoms in 3 residues 51: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (3 ms) 51: [----------] 5 tests from InsertMoleculesTest (15 ms total) 51: 51: [----------] 3 tests from MassRepartitioning 51: [ RUN ] MassRepartitioning.ValidCaseWorks 51: The smallest mass in the system is 2, setting the minimum mass to 6 51: [ OK ] MassRepartitioning.ValidCaseWorks (0 ms) 51: [ RUN ] MassRepartitioning.UnboundGivesWarning 51: 51: WARNING 1 [file unknown]: 51: The are 1 atoms that have a mass below the mass repartitioning limit but 51: are not bound. These masses cannot be repartitioned. 51: 51: The smallest mass in the system is 2, setting the minimum mass to 6 51: [ OK ] MassRepartitioning.UnboundGivesWarning (0 ms) 51: [ RUN ] MassRepartitioning.LightPartnerGivesError 51: 51: ERROR 1 [file unknown]: 51: Light atoms are bound to at least one atom that has a too low mass for 51: repartioning 51: 51: The smallest mass in the system is 2, setting the minimum mass to 6 51: [ OK ] MassRepartitioning.LightPartnerGivesError (0 ms) 51: [----------] 3 tests from MassRepartitioning (1 ms total) 51: 51: [----------] 35 tests from GetIrTest 51: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines 51: Ignoring obsolete mdp entry 'title' 51: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps' 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (2 ms) 51: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals 51: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (0 ms) 51: [ RUN ] GetIrTest.AcceptsKeyWithoutValue 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsKeyWithoutValue (1 ms) 51: [ RUN ] GetIrTest.RejectsValueWithoutKey 51: [ OK ] GetIrTest.RejectsValueWithoutKey (0 ms) 51: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue 51: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (0 ms) 51: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (1 ms) 51: [ RUN ] GetIrTest.AcceptsEmptyLines 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsEmptyLines (2 ms) 51: [ RUN ] GetIrTest.MtsCheckNstcalcenergy 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 51: With MTS, nstcalcenergy = 5 should be a multiple of mts-factor = 2 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.MtsCheckNstcalcenergy (1 ms) 51: [ RUN ] GetIrTest.MtsCheckNstenergy 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 51: With MTS, nstenergy = 5 should be a multiple of mts-factor = 2 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 51: Setting nstcalcenergy (100) equal to nstenergy (5) 51: 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.MtsCheckNstenergy (2 ms) 51: [ RUN ] GetIrTest.MtsCheckNstpcouple 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 51: Pressure coupling incorrect number of values (I need exactly 1) 51: 51: 51: ERROR 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 51: Pressure coupling incorrect number of values (I need exactly 1) 51: 51: 51: ERROR 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 51: With multiple time stepping, nstpcouple should be a multiple of 51: mts-factor 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: 51: ERROR 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 51: The Berendsen barostat does not generate any strictly correct ensemble, 51: and should not be used for new production simulations (in our opinion). 51: We recommend using the C-rescale barostat instead. 51: 51: 51: ERROR 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 51: compressibility must be > 0 when using pressure coupling Berendsen 51: 51: 51: [ OK ] GetIrTest.MtsCheckNstpcouple (4 ms) 51: [ RUN ] GetIrTest.MtsCheckNstdhdl 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 51: With MTS, nstdhdl = 5 should be a multiple of mts-factor = 2 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 51: Setting nstcalcenergy (100) equal to nstdhdl (5) 51: 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: 51: ERROR 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 51: Lambda state must be set, either with init-lambda-state or with 51: init-lambda 51: 51: [ OK ] GetIrTest.MtsCheckNstdhdl (2 ms) 51: [ RUN ] GetIrTest.MtsCheckSDNotSupported 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 51: Multiple time stepping is only supported with integrator md 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.MtsCheckSDNotSupported (1 ms) 51: [ RUN ] GetIrTest.AcceptsElectricField 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsElectricField (2 ms) 51: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (1 ms) 51: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (1 ms) 51: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys 51: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (0 ms) 51: [ RUN ] GetIrTest.AcceptsImplicitSolventNo 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsImplicitSolventNo (1 ms) 51: [ RUN ] GetIrTest.RejectsImplicitSolventYes 51: [ OK ] GetIrTest.RejectsImplicitSolventYes (0 ms) 51: [ RUN ] GetIrTest.AcceptsMimic 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsMimic (1 ms) 51: [ RUN ] GetIrTest.AcceptsTransformationCoord 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp, line 11]: 51: pull-coord2 has a non-zero force constant and is also referenced in 51: pull-coord1-expression. Make sure that this is intended. In most use 51: cases, the pull coordinates referenced by a transformation coordinate 51: should have their force constant set to zero. 51: 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsTransformationCoord (2 ms) 51: [ RUN ] GetIrTest.InvalidTransformationCoordWithConstraint 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp, line 7]: 51: pull-coord1 cannot have type 'constraint' and geometry 'transformation' 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.InvalidTransformationCoordWithConstraint (1 ms) 51: [ RUN ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp, line 10]: 51: pull-coord2 can not use pull-coord1 in the transformation since this is a 51: constraint 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression (1 ms) 51: [ RUN ] GetIrTest.InvalidTransformationCoordDxValue 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp, line 7]: 51: pull-coord1-dx cannot be set to zero for pull coordinate of geometry 51: 'transformation' 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.InvalidTransformationCoordDxValue (3 ms) 51: [ RUN ] GetIrTest.MissingTransformationCoordExpression 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp, line 5]: 51: pull-coord1-expression not set for pull coordinate of geometry 51: 'transformation' 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.MissingTransformationCoordExpression (2 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep 51: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta 51: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep 51: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta 51: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_input.mdp]: 51: With init-lambda = 0 and delta_lambda = 1e-05 and no explicit input, 51: coul-lambdas and vdw-lambdas will be greater than 1 after step 100000 of 51: in total 100001 steps. This is not compatible with using soft-core 51: potentials. 51: 51: 51: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta_input.mdp]: 51: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 51: won't change anymore after step 100000 until the end of the simulation 51: after 100001 steps. 51: 51: 51: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta_input.mdp]: 51: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 51: won't change anymore after step 100000 until the end of the simulation 51: after 100001 steps. 51: 51: 51: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_input.mdp]: 51: With init-lambda-state = 0 and delta_lambda = 1e-05, the lambda 51: components won't change anymore after step 100000 until the end of the 51: simulation after 100001 steps. 51: 51: 51: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta_input.mdp]: 51: With init-lambda-state = 2 and delta_lambda = -1e-05, the lambda 51: components won't change anymore after step 100000 until the end of the 51: simulation after 100001 steps. 51: 51: 51: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep 51: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta 51: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta (1 ms) 51: [----------] 35 tests from GetIrTest (61 ms total) 51: 51: [----------] 6 tests from SolvateTest 51: [ RUN ] SolvateTest.cs_box_Works 51: Reading solvent configuration 51: 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. 68 (1964) pp. 441-451 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Generating solvent configuration 51: Will generate new solvent configuration of 1x1x1 boxes 51: Solvent box contains 270 atoms in 90 residues 51: Removed 129 solvent atoms due to solvent-solvent overlap 51: Sorting configuration 51: Found 1 molecule type: 51: SOL ( 3 atoms): 47 residues 51: Generated solvent containing 141 atoms in 47 residues 51: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro 51: 51: Output configuration contains 141 atoms in 47 residues 51: Volume : 1.331 (nm^3) 51: Density : 1056.36 (g/l) 51: Number of solvent molecules: 47 51: 51: [ OK ] SolvateTest.cs_box_Works (4 ms) 51: [ RUN ] SolvateTest.cs_cp_Works 51: Reading solute configuration 51: Reading solvent configuration 51: 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. 68 (1964) pp. 441-451 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Generating solvent configuration 51: Will generate new solvent configuration of 2x2x2 boxes 51: Solvent box contains 3660 atoms in 1220 residues 51: Removed 987 solvent atoms due to solvent-solvent overlap 51: Removed 15 solvent atoms due to solute-solvent overlap 51: Sorting configuration 51: Found 1 molecule type: 51: SOL ( 3 atoms): 886 residues 51: Generated solvent containing 2658 atoms in 886 residues 51: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro 51: 51: Output configuration contains 2664 atoms in 888 residues 51: Volume : 27.2709 (nm^3) 51: Density : 974.777 (g/l) 51: Number of solvent molecules: 886 51: 51: [ OK ] SolvateTest.cs_cp_Works (13 ms) 51: [ RUN ] SolvateTest.cs_cp_p_Works 51: Reading solute configuration 51: Reading solvent configuration 51: 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. 68 (1964) pp. 441-451 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Generating solvent configuration 51: Will generate new solvent configuration of 2x2x2 boxes 51: Solvent box contains 3660 atoms in 1220 residues 51: Removed 987 solvent atoms due to solvent-solvent overlap 51: Removed 15 solvent atoms due to solute-solvent overlap 51: Sorting configuration 51: Found 1 molecule type: 51: SOL ( 3 atoms): 886 residues 51: Generated solvent containing 2658 atoms in 886 residues 51: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro 51: 51: Output configuration contains 2664 atoms in 888 residues 51: Volume : 27.2709 (nm^3) 51: Density : 974.777 (g/l) 51: Number of solvent molecules: 886 51: 51: Processing topology 51: Adding line for 886 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top) 51: [ OK ] SolvateTest.cs_cp_p_Works (19 ms) 51: [ RUN ] SolvateTest.shell_Works 51: Reading solute configuration 51: Reading solvent configuration 51: 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. 68 (1964) pp. 441-451 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Generating solvent configuration 51: Will generate new solvent configuration of 2x2x2 boxes 51: Solvent box contains 3660 atoms in 1220 residues 51: Removed 987 solvent atoms due to solvent-solvent overlap 51: Removed 1902 solvent atoms more than 1.000000 nm from solute. 51: Removed 15 solvent atoms due to solute-solvent overlap 51: Sorting configuration 51: Found 1 molecule type: 51: SOL ( 3 atoms): 252 residues 51: Generated solvent containing 756 atoms in 252 residues 51: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro 51: 51: Output configuration contains 762 atoms in 254 residues 51: Volume : 27.2709 (nm^3) 51: Density : 279.3 (g/l) 51: Number of solvent molecules: 252 51: 51: [ OK ] SolvateTest.shell_Works (10 ms) 51: [ RUN ] SolvateTest.update_Topology_Works 51: Reading solute configuration 51: Reading solvent configuration 51: 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. 68 (1964) pp. 441-451 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Generating solvent configuration 51: Will generate new solvent configuration of 3x3x3 boxes 51: Solvent box contains 14952 atoms in 4984 residues 51: Removed 2787 solvent atoms due to solvent-solvent overlap 51: Removed 30 solvent atoms due to solute-solvent overlap 51: Sorting configuration 51: Found 2 different molecule types: 51: HOH ( 3 atoms): 1876 residues 51: SOL ( 3 atoms): 2169 residues 51: Generated solvent containing 0 atoms in 0 residues 51: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro 51: 51: Output configuration contains 12141 atoms in 4047 residues 51: Volume : 125 (nm^3) 51: Density : 968.963 (g/l) 51: Number of solvent molecules: 4045 51: 51: Processing topology 51: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 51: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 51: [ OK ] SolvateTest.update_Topology_Works (97 ms) 51: [ RUN ] SolvateTest.cs_pdb_big_box_Works 51: Reading solvent configuration 51: 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. 68 (1964) pp. 441-451 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Generating solvent configuration 51: Will generate new solvent configuration of 2x2x2 boxes 51: Solvent box contains 1218 atoms in 406 residues 51: Removed 555 solvent atoms due to solvent-solvent overlap 51: Sorting configuration 51: Found 1 molecule type: 51: SOL ( 3 atoms): 221 residues 51: Generated solvent containing 663 atoms in 221 residues 51: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_pdb_big_box_Works_out.gro 51: 51: Output configuration contains 663 atoms in 221 residues 51: Volume : 8 (nm^3) 51: Density : 826.409 (g/l) 51: Number of solvent molecules: 221 51: 51: [ OK ] SolvateTest.cs_pdb_big_box_Works (3 ms) 51: [----------] 6 tests from SolvateTest (149 ms total) 51: 51: [----------] 1 test from TopDirTests 51: [ RUN ] TopDirTests.NamesArrayHasCorrectSize 51: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms) 51: [----------] 1 test from TopDirTests (0 ms total) 51: 51: [----------] 45 tests from SinglePeptideFragments/EditconfTest 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 (11 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 (6 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 (3 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 (7 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 (4 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 51: 51: Select a group for output: 51: Group 0 ( two_residues) has 23 elements 51: There is one group in the index 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 (8 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 51: 51: Select a group for output: 51: Group 0 ( two_residues) has 23 elements 51: There is one group in the index 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 51: 51: Select a group for output: 51: Group 0 ( two_residues) has 23 elements 51: There is one group in the index 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 (5 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 51: 51: Select a group for output: 51: Group 0 ( two_residues) has 23 elements 51: There is one group in the index 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 51: 51: Select a group for output: 51: Group 0 ( two_residues) has 23 elements 51: There is one group in the index 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 51: 51: Select a group for output: 51: Group 0 ( two_residues) has 23 elements 51: There is one group in the index 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 51: 51: Select a group for output: 51: Group 0 ( two_residues) has 23 elements 51: There is one group in the index 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 51: 51: Select a group for output: 51: Group 0 ( two_residues) has 23 elements 51: There is one group in the index 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 51: 51: Select a group for output: 51: Group 0 ( two_residues) has 23 elements 51: There is one group in the index 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 (4 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/0 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : 0.212 1.187 3.527 (nm) 51: new center : 4.028 2.819 3.723 (nm) 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/0 (12 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/1 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : 0.212 1.187 3.527 (nm) 51: new center : 4.028 2.819 3.723 (nm) 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/1 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/2 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : 0.212 1.187 3.527 (nm) 51: new center : 4.028 2.819 3.723 (nm) 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/2 (6 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/3 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : 0.212 1.187 3.527 (nm) 51: new center : 4.028 2.819 3.723 (nm) 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/3 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/4 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : 0.212 1.187 3.527 (nm) 51: new center : 4.028 2.819 3.723 (nm) 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/4 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/5 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : 0.212 1.187 3.527 (nm) 51: new center : 4.028 2.819 3.723 (nm) 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/5 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/6 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : 0.212 1.187 3.527 (nm) 51: new center : 4.028 2.819 3.723 (nm) 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/6 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/7 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : 0.212 1.187 3.527 (nm) 51: new center : 4.028 2.819 3.723 (nm) 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/7 (7 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/8 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : 0.212 1.187 3.527 (nm) 51: new center : 4.028 2.819 3.723 (nm) 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/8 (12 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/0 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : -0.814 1.104 2.657 (nm) 51: new center : 3.002 2.736 2.852 (nm) 51: new box vectors : 6.004 5.472 5.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 187.42 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/0 (3 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/1 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : -0.814 1.104 2.657 (nm) 51: new center : 3.002 2.736 2.852 (nm) 51: new box vectors : 6.004 5.472 5.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 187.42 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/1 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/2 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : -0.814 1.104 2.657 (nm) 51: new center : 3.002 2.736 2.852 (nm) 51: new box vectors : 6.004 5.472 5.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 187.42 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/2 (6 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/3 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : -0.814 1.104 2.657 (nm) 51: new center : 3.002 2.736 2.852 (nm) 51: new box vectors : 6.004 5.472 5.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 187.40 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/3 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/4 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : -0.814 1.104 2.657 (nm) 51: new center : 3.002 2.736 2.852 (nm) 51: new box vectors : 6.004 5.472 5.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 187.40 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/4 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/5 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : -0.814 1.104 2.657 (nm) 51: new center : 3.002 2.736 2.852 (nm) 51: new box vectors : 6.004 5.472 5.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 187.40 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/5 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/6 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : -0.814 1.104 2.657 (nm) 51: new center : 3.002 2.736 2.852 (nm) 51: new box vectors : 6.004 5.472 5.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 187.40 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/6 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/7 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : -0.814 1.104 2.657 (nm) 51: new center : 3.002 2.736 2.852 (nm) 51: new box vectors : 6.004 5.472 5.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 187.40 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/7 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/8 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : -0.814 1.104 2.657 (nm) 51: new center : 3.002 2.736 2.852 (nm) 51: new box vectors : 6.004 5.472 5.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 187.40 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/8 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/0 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: new center : 3.816 1.632 0.195 (nm) 51: new box vectors : 5.004 4.472 4.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 105.28 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/0 (3 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/1 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: new center : 3.816 1.632 0.195 (nm) 51: new box vectors : 5.004 4.472 4.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 105.28 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/1 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/2 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: new center : 3.816 1.632 0.195 (nm) 51: new box vectors : 5.004 4.472 4.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 105.28 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/2 (3 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/3 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: new center : 3.816 1.632 0.195 (nm) 51: new box vectors : 5.004 4.472 4.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 105.27 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/3 (4 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/4 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: new center : 3.816 1.632 0.195 (nm) 51: new box vectors : 5.004 4.472 4.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 105.27 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/4 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/5 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: new center : 3.816 1.632 0.195 (nm) 51: new box vectors : 5.004 4.472 4.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 105.27 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/5 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/6 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: new center : 3.816 1.632 0.195 (nm) 51: new box vectors : 5.004 4.472 4.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 105.27 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/6 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/7 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: new center : 3.816 1.632 0.195 (nm) 51: new box vectors : 5.004 4.472 4.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 105.27 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/7 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/8 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: new center : 3.816 1.632 0.195 (nm) 51: new box vectors : 5.004 4.472 4.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 105.27 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/8 (2 ms) 51: [----------] 45 tests from SinglePeptideFragments/EditconfTest (244 ms total) 51: 51: [----------] 16 tests from CorrectVelocity/MaxwellTest 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/0 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/0 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/1 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/1 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/2 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/2 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/3 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/3 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/4 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/4 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/5 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/5 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/6 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/6 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/7 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/7 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/8 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/8 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/9 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/9 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/10 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/10 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/11 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/11 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/12 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/12 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/13 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/13 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/14 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/14 (4 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/15 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/15 (0 ms) 51: [----------] 16 tests from CorrectVelocity/MaxwellTest (16 ms total) 51: 51: [----------] Global test environment tear-down 51: [==========] 138 tests from 13 test suites ran. (1258 ms total) 51: [ PASSED ] 138 tests. 51/91 Test #51: GmxPreprocessTests ........................... Passed 1.60 sec test 52 Start 52: Pdb2gmx1Test 52: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/pdb2gmx1-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/Pdb2gmx1Test.xml" 52: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests 52: Test timeout computed to be: 1920 52: [==========] Running 30 tests from 1 test suite. 52: [----------] Global test environment set-up. 52: [----------] 30 tests from Oplsaa/Pdb2gmxTest 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 663 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 0 virtual sites 52: 52: Total mass 1846.112 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (36 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 778 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 0 virtual sites 52: 52: Total mass 2088.357 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (25 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 696 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 0 virtual sites 52: 52: Total mass 1861.128 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (26 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: PRO-COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 618 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 0 virtual sites 52: 52: Total mass 1662.883 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (23 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2524 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 0 virtual sites 52: 52: Total mass 6908.578 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (71 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Marked 124 virtual sites 52: Added 16 dummy masses 52: Added 26 new constraints 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 663 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 130 virtual sites 52: 52: Total mass 1846.112 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (26 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Marked 132 virtual sites 52: Added 10 dummy masses 52: Added 19 new constraints 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 778 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 133 virtual sites 52: 52: Total mass 2088.357 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (27 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Marked 123 virtual sites 52: Added 22 dummy masses 52: Added 35 new constraints 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 696 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 132 virtual sites 52: 52: Total mass 1861.128 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (22 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Marked 111 virtual sites 52: Added 18 dummy masses 52: Added 31 new constraints 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: PRO-COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 618 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 116 virtual sites 52: 52: Total mass 1662.883 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (26 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Marked 447 virtual sites 52: Added 58 dummy masses 52: Added 101 new constraints 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2524 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 462 virtual sites 52: 52: Total mass 6908.578 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (72 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 663 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 0 virtual sites 52: 52: Total mass 1846.112 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (23 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 778 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 0 virtual sites 52: 52: Total mass 2088.357 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (24 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 696 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 0 virtual sites 52: 52: Total mass 1861.128 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (23 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: PRO-COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 618 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 0 virtual sites 52: 52: Total mass 1662.883 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (24 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2524 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 0 virtual sites 52: 52: Total mass 6908.578 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (67 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Marked 124 virtual sites 52: Added 16 dummy masses 52: Added 26 new constraints 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 663 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 130 virtual sites 52: 52: Total mass 1846.112 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (28 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Marked 132 virtual sites 52: Added 10 dummy masses 52: Added 19 new constraints 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 778 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 133 virtual sites 52: 52: Total mass 2088.357 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (23 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Marked 123 virtual sites 52: Added 22 dummy masses 52: Added 35 new constraints 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 696 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 132 virtual sites 52: 52: Total mass 1861.128 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (24 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Marked 111 virtual sites 52: Added 18 dummy masses 52: Added 31 new constraints 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: PRO-COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 618 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 116 virtual sites 52: 52: Total mass 1662.883 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (20 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Marked 447 virtual sites 52: Added 58 dummy masses 52: Added 101 new constraints 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2524 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 462 virtual sites 52: 52: Total mass 6908.578 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (41 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 663 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 0 virtual sites 52: 52: Total mass 1846.112 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (14 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 778 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 0 virtual sites 52: 52: Total mass 2088.357 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (25 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 696 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 0 virtual sites 52: 52: Total mass 1861.128 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (21 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: PRO-COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 618 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 0 virtual sites 52: 52: Total mass 1662.883 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (18 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2524 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 0 virtual sites 52: 52: Total mass 6908.578 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (36 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Marked 124 virtual sites 52: Added 16 dummy masses 52: Added 26 new constraints 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 663 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 130 virtual sites 52: 52: Total mass 1846.112 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (15 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Marked 132 virtual sites 52: Added 10 dummy masses 52: Added 19 new constraints 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 778 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 133 virtual sites 52: 52: Total mass 2088.357 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (17 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Marked 123 virtual sites 52: Added 22 dummy masses 52: Added 35 new constraints 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 696 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 132 virtual sites 52: 52: Total mass 1861.128 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (15 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Marked 111 virtual sites 52: Added 18 dummy masses 52: Added 31 new constraints 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: PRO-COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 618 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 116 virtual sites 52: 52: Total mass 1662.883 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (14 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Marked 447 virtual sites 52: Added 58 dummy masses 52: Added 101 new constraints 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2524 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 462 virtual sites 52: 52: Total mass 6908.578 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (40 ms) 52: [----------] 30 tests from Oplsaa/Pdb2gmxTest (982 ms total) 52: 52: [----------] Global test environment tear-down 52: [==========] 30 tests from 1 test suite ran. (983 ms total) 52: [ PASSED ] 30 tests. 52/91 Test #52: Pdb2gmx1Test ................................. Passed 1.35 sec test 53 Start 53: Pdb2gmx2Test 53: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/pdb2gmx2-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/Pdb2gmx2Test.xml" 53: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests 53: Test timeout computed to be: 1920 53: [==========] Running 40 tests from 2 test suites. 53: [----------] Global test environment set-up. 53: [----------] 20 tests from G43a1/Pdb2gmxTest 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 305 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 165 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 172, now 167 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 77 impropers, 241 angles 53: 267 pairs, 167 bonds and 0 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (30 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 429 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 202 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 216, now 211 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 134 impropers, 316 angles 53: 273 pairs, 211 bonds and 0 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (36 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 349 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 168 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 179, now 174 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 102 impropers, 260 angles 53: 242 pairs, 174 bonds and 0 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (32 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 299 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 150 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 159, now 154 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 80 impropers, 227 angles 53: 232 pairs, 154 bonds and 0 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (38 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1256 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 635 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 655, now 650 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 350 impropers, 955 angles 53: 972 pairs, 650 bonds and 0 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (49 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 37 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 305 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 165 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 172, now 167 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 77 impropers, 241 angles 53: 267 pairs, 167 bonds and 37 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (27 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 53 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 429 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 202 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 216, now 211 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 134 impropers, 316 angles 53: 273 pairs, 211 bonds and 51 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (36 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 36 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 349 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 168 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 179, now 174 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 102 impropers, 260 angles 53: 242 pairs, 174 bonds and 36 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (26 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 33 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 299 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 150 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 159, now 154 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 80 impropers, 227 angles 53: 232 pairs, 154 bonds and 31 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (27 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 146 virtual sites 53: Added 10 dummy masses 53: Added 29 new constraints 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1256 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 635 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 655, now 650 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 350 impropers, 955 angles 53: 972 pairs, 650 bonds and 137 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (51 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 305 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 165 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 172, now 167 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 77 impropers, 241 angles 53: 267 pairs, 167 bonds and 0 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (45 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 429 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 202 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 216, now 211 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 134 impropers, 316 angles 53: 273 pairs, 211 bonds and 0 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (39 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 349 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 168 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 179, now 174 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 102 impropers, 260 angles 53: 242 pairs, 174 bonds and 0 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (32 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 299 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 150 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 159, now 154 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 80 impropers, 227 angles 53: 232 pairs, 154 bonds and 0 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (33 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1256 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 635 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 655, now 650 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 350 impropers, 955 angles 53: 972 pairs, 650 bonds and 0 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (37 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 37 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 305 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 165 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 172, now 167 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 77 impropers, 241 angles 53: 267 pairs, 167 bonds and 37 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (21 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 53 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 429 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 202 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 216, now 211 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 134 impropers, 316 angles 53: 273 pairs, 211 bonds and 51 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (25 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 36 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 349 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 168 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 179, now 174 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 102 impropers, 260 angles 53: 242 pairs, 174 bonds and 36 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (41 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 33 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 299 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 150 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 159, now 154 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 80 impropers, 227 angles 53: 232 pairs, 154 bonds and 31 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (40 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 146 virtual sites 53: Added 10 dummy masses 53: Added 29 new constraints 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1256 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 635 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 655, now 650 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 350 impropers, 955 angles 53: 972 pairs, 650 bonds and 137 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (42 ms) 53: [----------] 20 tests from G43a1/Pdb2gmxTest (764 ms total) 53: 53: [----------] 20 tests from G53a6/Pdb2gmxTest 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 312 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 167 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 174, now 169 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 79 impropers, 245 angles 53: 267 pairs, 169 bonds and 0 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge -0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (22 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 443 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 206 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 220, now 215 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 138 impropers, 324 angles 53: 273 pairs, 215 bonds and 0 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (21 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 356 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 170 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 181, now 176 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 104 impropers, 264 angles 53: 242 pairs, 176 bonds and 0 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (24 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 306 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 152 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 161, now 156 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 82 impropers, 231 angles 53: 232 pairs, 156 bonds and 0 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge -0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (20 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1270 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 639 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 659, now 654 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 354 impropers, 963 angles 53: 972 pairs, 654 bonds and 0 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (36 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 39 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 312 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 167 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 174, now 169 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 79 impropers, 245 angles 53: 267 pairs, 169 bonds and 39 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge -0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (24 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 57 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 443 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 206 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 220, now 215 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 138 impropers, 324 angles 53: 273 pairs, 215 bonds and 55 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (27 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 38 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 356 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 170 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 181, now 176 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 104 impropers, 264 angles 53: 242 pairs, 176 bonds and 38 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (24 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 35 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 306 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 152 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 161, now 156 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 82 impropers, 231 angles 53: 232 pairs, 156 bonds and 33 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge -0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (30 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 150 virtual sites 53: Added 10 dummy masses 53: Added 29 new constraints 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1270 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 639 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 659, now 654 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 354 impropers, 963 angles 53: 972 pairs, 654 bonds and 141 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (41 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 312 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 167 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 174, now 169 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 79 impropers, 245 angles 53: 267 pairs, 169 bonds and 0 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge -0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (26 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 443 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 206 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 220, now 215 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 138 impropers, 324 angles 53: 273 pairs, 215 bonds and 0 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (21 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 356 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 170 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 181, now 176 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 104 impropers, 264 angles 53: 242 pairs, 176 bonds and 0 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (19 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 306 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 152 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 161, now 156 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 82 impropers, 231 angles 53: 232 pairs, 156 bonds and 0 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge -0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (23 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1270 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 639 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 659, now 654 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 354 impropers, 963 angles 53: 972 pairs, 654 bonds and 0 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (47 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 39 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 312 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 167 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 174, now 169 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 79 impropers, 245 angles 53: 267 pairs, 169 bonds and 39 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge -0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (21 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 57 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 443 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 206 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 220, now 215 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 138 impropers, 324 angles 53: 273 pairs, 215 bonds and 55 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (26 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 38 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 356 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 170 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 181, now 176 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 104 impropers, 264 angles 53: 242 pairs, 176 bonds and 38 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (26 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 35 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 306 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 152 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 161, now 156 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 82 impropers, 231 angles 53: 232 pairs, 156 bonds and 33 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge -0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (25 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 150 virtual sites 53: Added 10 dummy masses 53: Added 29 new constraints 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1270 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 639 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 659, now 654 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 354 impropers, 963 angles 53: 972 pairs, 654 bonds and 141 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (40 ms) 53: [----------] 20 tests from G53a6/Pdb2gmxTest (576 ms total) 53: 53: [----------] Global test environment tear-down 53: [==========] 40 tests from 2 test suites ran. (1341 ms total) 53: [ PASSED ] 40 tests. 53/91 Test #53: Pdb2gmx2Test ................................. Passed 1.67 sec test 54 Start 54: Pdb2gmx3Test 54: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/pdb2gmx3-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/Pdb2gmx3Test.xml" 54: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests 54: Test timeout computed to be: 1920 54: [==========] Running 39 tests from 6 test suites. 54: [----------] Global test environment set-up. 54: [----------] 10 tests from Amber/Pdb2gmxTest 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 54: Before cleaning: 653 pairs 54: Before cleaning: 691 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 255, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 691 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 0 virtual sites 54: 54: Total mass 1846.132 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (45 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 54: Before cleaning: 748 pairs 54: Before cleaning: 788 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 291, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 788 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 0 virtual sites 54: 54: Total mass 2088.366 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (44 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 54: Before cleaning: 676 pairs 54: Before cleaning: 727 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 262, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 727 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 0 virtual sites 54: 54: Total mass 1861.124 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (63 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 54: Before cleaning: 603 pairs 54: Before cleaning: 634 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 233, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 634 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 0 virtual sites 54: 54: Total mass 1662.888 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (50 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 54: Before cleaning: 2499 pairs 54: Before cleaning: 2631 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 952, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2631 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 0 virtual sites 54: 54: Total mass 6908.576 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (87 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 54: Marked 124 virtual sites 54: Added 16 dummy masses 54: Added 26 new constraints 54: Before cleaning: 653 pairs 54: Before cleaning: 691 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 255, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 691 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 130 virtual sites 54: 54: Total mass 1846.132 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (38 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 54: Marked 132 virtual sites 54: Added 10 dummy masses 54: Added 19 new constraints 54: Before cleaning: 748 pairs 54: Before cleaning: 788 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 291, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 788 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 133 virtual sites 54: 54: Total mass 2088.366 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (41 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 54: Marked 123 virtual sites 54: Added 22 dummy masses 54: Added 35 new constraints 54: Before cleaning: 676 pairs 54: Before cleaning: 727 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 262, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 727 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 132 virtual sites 54: 54: Total mass 1861.124 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (27 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 54: Marked 111 virtual sites 54: Added 18 dummy masses 54: Added 31 new constraints 54: Before cleaning: 603 pairs 54: Before cleaning: 634 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 233, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 634 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 116 virtual sites 54: 54: Total mass 1662.888 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (26 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 54: Marked 447 virtual sites 54: Added 58 dummy masses 54: Added 101 new constraints 54: Before cleaning: 2499 pairs 54: Before cleaning: 2631 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 952, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2631 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 462 virtual sites 54: 54: Total mass 6908.576 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (77 ms) 54: [----------] 10 tests from Amber/Pdb2gmxTest (512 ms total) 54: 54: [----------] 1 test from AmberTip4p/Pdb2gmxTest 54: [ RUN ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/tip4p.pdb... 54: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 2 4 (only water) 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (4 atoms, 2 residues) 54: 54: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 2 residues with 8 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 4, now 4 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 0 dihedrals, 0 impropers, 2 angles 54: 0 pairs, 4 bonds and 0 virtual sites 54: 54: Total mass 36.032 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/tip4p.pdb. 54: 54: The Amber99sb-ildn force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (13 ms) 54: [----------] 1 test from AmberTip4p/Pdb2gmxTest (13 ms total) 54: 54: [----------] 12 tests from Charmm/Pdb2gmxTest 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 663 dihedrals, 48 impropers, 457 angles 54: 650 pairs, 254 bonds and 0 virtual sites 54: 54: Total mass 1846.115 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (25 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 778 dihedrals, 49 impropers, 516 angles 54: 736 pairs, 290 bonds and 0 virtual sites 54: 54: Total mass 2088.361 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (26 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 696 dihedrals, 39 impropers, 472 angles 54: 667 pairs, 261 bonds and 0 virtual sites 54: 54: Total mass 1861.130 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (24 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 618 dihedrals, 38 impropers, 419 angles 54: 597 pairs, 232 bonds and 0 virtual sites 54: 54: Total mass 1662.885 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (22 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 56 cmap torsion pairs 54: 54: There are 2524 dihedrals, 149 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 0 virtual sites 54: 54: Total mass 6908.566 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (48 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 39 pairs 54: Before cleaning: 39 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/monomer.pdb... 54: Read 'GLU', 9 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 54: 54: chain #res #atoms 54: 54: 1 'X' 1 9 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'X' (9 atoms, 1 residues) 54: 54: Identified residue GLU1 as a starting terminus. 54: 54: Identified residue GLU1 as a ending terminus. 54: Start terminus GLU-1: NH3+ 54: End terminus GLU-1: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 1 residues with 18 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 17, now 17 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 39 dihedrals, 2 impropers, 30 angles 54: 39 pairs, 17 bonds and 0 virtual sites 54: 54: Total mass 146.123 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/monomer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file (13 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Marked 124 virtual sites 54: Added 16 dummy masses 54: Added 26 new constraints 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 663 dihedrals, 48 impropers, 457 angles 54: 650 pairs, 254 bonds and 130 virtual sites 54: 54: Total mass 1846.115 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (23 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Marked 132 virtual sites 54: Added 10 dummy masses 54: Added 19 new constraints 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 778 dihedrals, 49 impropers, 516 angles 54: 736 pairs, 290 bonds and 133 virtual sites 54: 54: Total mass 2088.361 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (25 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Marked 123 virtual sites 54: Added 22 dummy masses 54: Added 35 new constraints 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 696 dihedrals, 39 impropers, 472 angles 54: 667 pairs, 261 bonds and 132 virtual sites 54: 54: Total mass 1861.130 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (22 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Marked 111 virtual sites 54: Added 18 dummy masses 54: Added 31 new constraints 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 618 dihedrals, 38 impropers, 419 angles 54: 597 pairs, 232 bonds and 116 virtual sites 54: 54: Total mass 1662.885 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (21 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Marked 447 virtual sites 54: Added 58 dummy masses 54: Added 101 new constraints 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 56 cmap torsion pairs 54: 54: There are 2524 dihedrals, 149 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 462 virtual sites 54: 54: Total mass 6908.566 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (47 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Marked 8 virtual sites 54: Added 2 dummy masses 54: Added 3 new constraints 54: Before cleaning: 39 pairs 54: Before cleaning: 39 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/monomer.pdb... 54: Read 'GLU', 9 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 54: 54: chain #res #atoms 54: 54: 1 'X' 1 9 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'X' (9 atoms, 1 residues) 54: 54: Identified residue GLU1 as a starting terminus. 54: 54: Identified residue GLU1 as a ending terminus. 54: Start terminus GLU-1: NH3+ 54: End terminus GLU-1: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 1 residues with 18 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 17, now 17 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 39 dihedrals, 2 impropers, 30 angles 54: 39 pairs, 17 bonds and 9 virtual sites 54: 54: Total mass 146.123 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/monomer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file (12 ms) 54: [----------] 12 tests from Charmm/Pdb2gmxTest (318 ms total) 54: 54: [----------] 8 tests from ChainSep/Pdb2gmxTest 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 651 pairs 54: Before cleaning: 661 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on changing chain id only (ignoring TER records). 54: 54: Merged chains into joint molecule definitions at 2 places. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 16 127 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (127 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue GLU5 as a ending terminus. 54: 54: Identified residue PHE6 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus GLU-5: COO- 54: Start terminus PHE-6: NH3+ 54: End terminus MET-12: COO- 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 258 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 258, now 258 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 10 cmap torsion pairs 54: 54: There are 661 dihedrals, 46 impropers, 463 angles 54: 648 pairs, 258 bonds and 0 virtual sites 54: 54: Total mass 1882.146 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file (19 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 123 pairs 54: Before cleaning: 123 dihedrals 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 10 donors and 7 acceptors were found. 54: There are 7 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS8 54: NE223 54: MET12 SD55 0.990 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 317 pairs 54: Before cleaning: 322 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 211 pairs 54: Before cleaning: 216 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on changing chain id only (ignoring TER records). 54: 54: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 4 28 54: 54: 2 'B' 7 58 54: 54: 3 'C' 5 41 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (28 atoms, 4 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue GLU5 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus GLU-5: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 4 residues with 51 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 50, now 50 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2 cmap torsion pairs 54: 54: There are 123 dihedrals, 9 impropers, 88 angles 54: 123 pairs, 50 bonds and 0 virtual sites 54: 54: Total mass 434.421 a.m.u. 54: 54: Total charge -2.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (58 atoms, 7 residues) 54: 54: Identified residue PHE6 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: Start terminus PHE-6: NH3+ 54: End terminus MET-12: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 7 residues with 124 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 125, now 125 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 5 cmap torsion pairs 54: 54: There are 322 dihedrals, 19 impropers, 227 angles 54: 314 pairs, 125 bonds and 0 virtual sites 54: 54: Total mass 846.083 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Processing chain 3 'C' (41 atoms, 5 residues) 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 5 residues with 83 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 83, now 83 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 3 cmap torsion pairs 54: 54: There are 216 dihedrals, 18 impropers, 148 angles 54: 211 pairs, 83 bonds and 0 virtual sites 54: 54: Total mass 601.643 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 51 atoms 4 residues 54: 54: Including chain 2 in system: 124 atoms 7 residues 54: 54: Including chain 3 in system: 83 atoms 5 residues 54: 54: Now there are 258 atoms and 16 residues 54: 54: Total mass in system 1882.146 a.m.u. 54: 54: Total charge in system 0.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file (22 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 651 pairs 54: Before cleaning: 661 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records only (ignoring chain id). 54: 54: Merged chains into joint molecule definitions at 2 places. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 16 127 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (127 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue ILE9 as a ending terminus. 54: 54: Identified residue LYS10 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus ILE-9: COO- 54: Start terminus LYS-10: NH3+ 54: End terminus MET-12: COO- 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 258 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 258, now 258 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 10 cmap torsion pairs 54: 54: There are 661 dihedrals, 46 impropers, 463 angles 54: 648 pairs, 258 bonds and 0 virtual sites 54: 54: Total mass 1882.146 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file (23 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 10 donors and 12 acceptors were found. 54: There are 13 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 54: SG9 54: HIS8 NE251 1.055 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 288 pairs 54: Before cleaning: 293 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 152 pairs 54: Before cleaning: 152 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 211 pairs 54: Before cleaning: 216 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records only (ignoring chain id). 54: 54: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 8 61 54: 54: 2 'B' 3 25 54: 54: 3 'C' 5 41 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (61 atoms, 8 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue ILE9 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus ILE-9: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 8 residues with 114 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 115, now 115 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 6 cmap torsion pairs 54: 54: There are 293 dihedrals, 23 impropers, 203 angles 54: 285 pairs, 115 bonds and 0 virtual sites 54: 54: Total mass 888.952 a.m.u. 54: 54: Total charge -2.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (25 atoms, 3 residues) 54: 54: Identified residue LYS10 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: Start terminus LYS-10: NH3+ 54: End terminus MET-12: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 61 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 60, now 60 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 152 dihedrals, 5 impropers, 112 angles 54: 152 pairs, 60 bonds and 0 virtual sites 54: 54: Total mass 391.552 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Processing chain 3 'C' (41 atoms, 5 residues) 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 5 residues with 83 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 83, now 83 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 3 cmap torsion pairs 54: 54: There are 216 dihedrals, 18 impropers, 148 angles 54: 211 pairs, 83 bonds and 0 virtual sites 54: 54: Total mass 601.643 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 114 atoms 8 residues 54: 54: Including chain 2 in system: 61 atoms 3 residues 54: 54: Including chain 3 in system: 83 atoms 5 residues 54: 54: Now there are 258 atoms and 16 residues 54: 54: Total mass in system 1882.146 a.m.u. 54: 54: Total charge in system 0.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file (40 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 650 pairs 54: Before cleaning: 660 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: Merged chains into joint molecule definitions at 3 places. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 16 127 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (127 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue GLU5 as a ending terminus. 54: 54: Identified residue PHE6 as a starting terminus. 54: 54: Identified residue ILE9 as a ending terminus. 54: 54: Identified residue LYS10 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus GLU-5: COO- 54: Start terminus PHE-6: NH3+ 54: End terminus ILE-9: COO- 54: Start terminus LYS-10: NH3+ 54: End terminus MET-12: COO- 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 261 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 260, now 260 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 8 cmap torsion pairs 54: 54: There are 660 dihedrals, 45 impropers, 466 angles 54: 647 pairs, 260 bonds and 0 virtual sites 54: 54: Total mass 1900.162 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file (26 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 54: 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 123 pairs 54: Before cleaning: 123 dihedrals 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 6 donors and 4 acceptors were found. 54: There are 3 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 164 pairs 54: Before cleaning: 169 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 152 pairs 54: Before cleaning: 152 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 211 pairs 54: Before cleaning: 216 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 54: 54: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 4 28 54: 54: 2 'B' 4 33 54: 54: 3 'B' 3 25 54: 54: 4 'C' 5 41 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (28 atoms, 4 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue GLU5 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus GLU-5: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 4 residues with 51 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 50, now 50 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2 cmap torsion pairs 54: 54: There are 123 dihedrals, 9 impropers, 88 angles 54: 123 pairs, 50 bonds and 0 virtual sites 54: 54: Total mass 434.421 a.m.u. 54: 54: Total charge -2.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (33 atoms, 4 residues) 54: 54: Identified residue PHE6 as a starting terminus. 54: 54: Identified residue ILE9 as a ending terminus. 54: Start terminus PHE-6: NH3+ 54: End terminus ILE-9: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 4 residues with 66 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 67, now 67 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2 cmap torsion pairs 54: 54: There are 169 dihedrals, 13 impropers, 118 angles 54: 161 pairs, 67 bonds and 0 virtual sites 54: 54: Total mass 472.547 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Processing chain 3 'B' (25 atoms, 3 residues) 54: 54: Identified residue LYS10 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: Start terminus LYS-10: NH3+ 54: End terminus MET-12: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 61 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 60, now 60 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 152 dihedrals, 5 impropers, 112 angles 54: 152 pairs, 60 bonds and 0 virtual sites 54: 54: Total mass 391.552 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Processing chain 4 'C' (41 atoms, 5 residues) 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 5 residues with 83 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 83, now 83 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 3 cmap torsion pairs 54: 54: There are 216 dihedrals, 18 impropers, 148 angles 54: 211 pairs, 83 bonds and 0 virtual sites 54: 54: Total mass 601.643 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 51 atoms 4 residues 54: 54: Including chain 2 in system: 66 atoms 4 residues 54: 54: Including chain 3 in system: 61 atoms 3 residues 54: 54: Including chain 4 in system: 83 atoms 5 residues 54: 54: Now there are 261 atoms and 16 residues 54: 54: Total mass in system 1900.162 a.m.u. 54: 54: Total charge in system 0.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file (29 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 652 pairs 54: Before cleaning: 662 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records and chain id changing. 54: 54: Merged chains into joint molecule definitions at 1 places. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 16 127 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (127 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus MET-12: COO- 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 256, now 256 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 12 cmap torsion pairs 54: 54: There are 662 dihedrals, 47 impropers, 460 angles 54: 649 pairs, 256 bonds and 0 virtual sites 54: 54: Total mass 1864.131 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file (27 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 14 donors and 15 acceptors were found. 54: There are 20 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 441 pairs 54: Before cleaning: 446 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 211 pairs 54: Before cleaning: 216 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records and chain id changing. 54: 54: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 11 86 54: 54: 2 'C' 5 41 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (86 atoms, 11 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus MET-12: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 11 residues with 172 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 173, now 173 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 9 cmap torsion pairs 54: 54: There are 446 dihedrals, 29 impropers, 312 angles 54: 438 pairs, 173 bonds and 0 virtual sites 54: 54: Total mass 1262.488 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'C' (41 atoms, 5 residues) 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 5 residues with 83 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 83, now 83 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 3 cmap torsion pairs 54: 54: There are 216 dihedrals, 18 impropers, 148 angles 54: 211 pairs, 83 bonds and 0 virtual sites 54: 54: Total mass 601.643 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 172 atoms 11 residues 54: 54: Including chain 2 in system: 83 atoms 5 residues 54: 54: Now there are 255 atoms and 16 residues 54: 54: Total mass in system 1864.131 a.m.u. 54: 54: Total charge in system 0.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file (24 ms) 54: [----------] 8 tests from ChainSep/Pdb2gmxTest (240 ms total) 54: 54: [----------] 4 tests from ChainChanges/Pdb2gmxTest 54: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 83 pairs 54: Before cleaning: 83 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 145 pairs 54: Before cleaning: 150 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb... 54: Read 'Fragments of peptides and ions', 47 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on changing chain id only (ignoring TER records). 54: 54: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 3 19 54: 54: 2 'B' 3 28 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (19 atoms, 3 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue ASP4 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus ASP-4: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 36 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 35, now 35 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 83 dihedrals, 6 impropers, 61 angles 54: 83 pairs, 35 bonds and 0 virtual sites 54: 54: Total mass 306.314 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (28 atoms, 3 residues) 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue TRP20 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus TRP-20: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 57 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 58, now 58 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 150 dihedrals, 5 impropers, 103 angles 54: 142 pairs, 58 bonds and 0 virtual sites 54: 54: Total mass 404.468 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 36 atoms 3 residues 54: 54: Including chain 2 in system: 57 atoms 3 residues 54: 54: Now there are 93 atoms and 6 residues 54: 54: Total mass in system 710.782 a.m.u. 54: 54: Total charge in system -1.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file (21 ms) 54: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 83 pairs 54: Before cleaning: 83 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 145 pairs 54: Before cleaning: 150 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb... 54: Read 'Fragments of peptides and ions', 47 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records only (ignoring chain id). 54: 54: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 3 19 54: 54: 2 'B' 3 28 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (19 atoms, 3 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue ASP4 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus ASP-4: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 36 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 35, now 35 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 83 dihedrals, 6 impropers, 61 angles 54: 83 pairs, 35 bonds and 0 virtual sites 54: 54: Total mass 306.314 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (28 atoms, 3 residues) 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue TRP20 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus TRP-20: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 57 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 58, now 58 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 150 dihedrals, 5 impropers, 103 angles 54: 142 pairs, 58 bonds and 0 virtual sites 54: 54: Total mass 404.468 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 36 atoms 3 residues 54: 54: Including chain 2 in system: 57 atoms 3 residues 54: 54: Now there are 93 atoms and 6 residues 54: 54: Total mass in system 710.782 a.m.u. 54: 54: Total charge in system -1.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file (19 ms) 54: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 83 pairs 54: Before cleaning: 83 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 145 pairs 54: Before cleaning: 150 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb... 54: Read 'Fragments of peptides and ions', 47 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 3 19 54: 54: 2 'B' 3 28 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (19 atoms, 3 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue ASP4 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus ASP-4: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 36 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 35, now 35 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 83 dihedrals, 6 impropers, 61 angles 54: 83 pairs, 35 bonds and 0 virtual sites 54: 54: Total mass 306.314 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (28 atoms, 3 residues) 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue TRP20 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus TRP-20: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 57 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 58, now 58 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 150 dihedrals, 5 impropers, 103 angles 54: 142 pairs, 58 bonds and 0 virtual sites 54: 54: Total mass 404.468 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 36 atoms 3 residues 54: 54: Including chain 2 in system: 57 atoms 3 residues 54: 54: Now there are 93 atoms and 6 residues 54: 54: Total mass in system 710.782 a.m.u. 54: 54: Total charge in system -1.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file (25 ms) 54: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 83 pairs 54: Before cleaning: 83 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 145 pairs 54: Before cleaning: 150 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb... 54: Read 'Fragments of peptides and ions', 47 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records and chain id changing. 54: 54: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 3 19 54: 54: 2 'B' 3 28 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (19 atoms, 3 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue ASP4 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus ASP-4: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 36 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 35, now 35 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 83 dihedrals, 6 impropers, 61 angles 54: 83 pairs, 35 bonds and 0 virtual sites 54: 54: Total mass 306.314 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (28 atoms, 3 residues) 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue TRP20 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus TRP-20: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 57 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 58, now 58 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 150 dihedrals, 5 impropers, 103 angles 54: 142 pairs, 58 bonds and 0 virtual sites 54: 54: Total mass 404.468 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 36 atoms 3 residues 54: 54: Including chain 2 in system: 57 atoms 3 residues 54: 54: Now there are 93 atoms and 6 residues 54: 54: Total mass in system 710.782 a.m.u. 54: 54: Total charge in system -1.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file (19 ms) 54: [----------] 4 tests from ChainChanges/Pdb2gmxTest (106 ms total) 54: 54: [----------] 4 tests from Cyclic/Pdb2gmxTest 54: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: WARNING: all CONECT records are ignored 54: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 54: 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 6040 pairs 54: Before cleaning: 6605 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 6040 pairs 54: Before cleaning: 6605 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 54: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 54: 54: Moved all the water blocks to the end 54: 54: There are 3 chains and 2 blocks of water and 175 residues with 3087 atoms 54: 54: chain #res #atoms 54: 54: 1 'P' 71 1527 54: 54: 2 'Q' 71 1527 54: 54: 3 'Q' 7 7 54: 54: 4 ' ' 10 10 (only water) 54: 54: 5 ' ' 16 16 (only water) 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'P' (1527 atoms, 71 residues) 54: 54: Identified residue G1 as a starting terminus. 54: 54: Identified residue U71 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 71 residues with 2297 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 2481, now 2481 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 6605 dihedrals, 183 impropers, 4434 angles 54: 5827 pairs, 2481 bonds and 0 virtual sites 54: 54: Total mass 22984.514 a.m.u. 54: 54: Total charge -71.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'Q' (1527 atoms, 71 residues) 54: 54: Identified residue G1 as a starting terminus. 54: 54: Identified residue U71 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 71 residues with 2297 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 2481, now 2481 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 6605 dihedrals, 183 impropers, 4434 angles 54: 5827 pairs, 2481 bonds and 0 virtual sites 54: 54: Total mass 22984.514 a.m.u. 54: 54: Total charge -71.000 e 54: 54: Writing topology 54: 54: Processing chain 3 'Q' (7 atoms, 7 residues) 54: 54: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 54: 54: Disabling further notes about ions. 54: 54: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 7 residues with 7 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: No bonds 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 0 dihedrals, 0 impropers, 0 angles 54: 0 pairs, 0 bonds and 0 virtual sites 54: 54: Total mass 170.135 a.m.u. 54: 54: Total charge 14.000 e 54: 54: Writing topology 54: 54: Processing chain 4 (10 atoms, 10 residues) 54: 54: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 10 residues with 30 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 30, now 30 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 0 dihedrals, 0 impropers, 30 angles 54: 0 pairs, 30 bonds and 0 virtual sites 54: 54: Total mass 180.154 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Processing chain 5 (16 atoms, 16 residues) 54: 54: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 48 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 48, now 48 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 0 dihedrals, 0 impropers, 48 angles 54: 0 pairs, 48 bonds and 0 virtual sites 54: 54: Total mass 288.246 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Including chain 1 in system: 2297 atoms 71 residues 54: 54: Including chain 2 in system: 2297 atoms 71 residues 54: 54: Including chain 3 in system: 7 atoms 7 residues 54: 54: Including chain 4 in system: 30 atoms 10 residues 54: 54: Including chain 5 in system: 48 atoms 16 residues 54: 54: Now there are 4679 atoms and 175 residues 54: 54: Total mass in system 46607.562 a.m.u. 54: 54: Total charge in system -128.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file (191 ms) 54: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 2325 pairs 54: Before cleaning: 2325 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 54: Read 'CARNOCYCLIN-A', 413 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 60 413 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (413 atoms, 60 residues) 54: 54: Identified residue LEU1 as a starting terminus. 54: 54: Identified residue LEU60 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 60 residues with 878 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 880, now 880 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 60 cmap torsion pairs 54: 54: There are 2325 dihedrals, 137 impropers, 1614 angles 54: 2319 pairs, 880 bonds and 0 virtual sites 54: 54: Total mass 5866.087 a.m.u. 54: 54: Total charge 4.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file (47 ms) 54: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: WARNING: all CONECT records are ignored 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 12080 pairs 54: Before cleaning: 13210 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 54: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: Moved all the water blocks to the end 54: 54: Merged chains into joint molecule definitions at 2 places. 54: 54: There are 1 chains and 2 blocks of water and 175 residues with 3087 atoms 54: 54: chain #res #atoms 54: 54: 1 'P' 149 3061 54: 54: 2 ' ' 10 10 (only water) 54: 54: 3 ' ' 16 16 (only water) 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'P' (3061 atoms, 149 residues) 54: 54: Identified residue G1 as a starting terminus. 54: 54: Identified residue U71 as a ending terminus. 54: 54: Identified residue G1 as a starting terminus. 54: 54: Identified residue U71 as a ending terminus. 54: 54: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 54: 54: Disabling further notes about ions. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 149 residues with 4601 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 4962, now 4962 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 13210 dihedrals, 366 impropers, 8868 angles 54: 11654 pairs, 4962 bonds and 0 virtual sites 54: 54: Total mass 46139.162 a.m.u. 54: 54: Total charge -128.000 e 54: 54: Writing topology 54: 54: Processing chain 2 (10 atoms, 10 residues) 54: 54: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 10 residues with 30 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 30, now 30 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 0 dihedrals, 0 impropers, 30 angles 54: 0 pairs, 30 bonds and 0 virtual sites 54: 54: Total mass 180.154 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Processing chain 3 (16 atoms, 16 residues) 54: 54: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 48 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 48, now 48 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 0 dihedrals, 0 impropers, 48 angles 54: 0 pairs, 48 bonds and 0 virtual sites 54: 54: Total mass 288.246 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Including chain 1 in system: 4601 atoms 149 residues 54: 54: Including chain 2 in system: 30 atoms 10 residues 54: 54: Including chain 3 in system: 48 atoms 16 residues 54: 54: Now there are 4679 atoms and 175 residues 54: 54: Total mass in system 46607.562 a.m.u. 54: 54: Total charge in system -128.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file (305 ms) 54: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 2325 pairs 54: Before cleaning: 2325 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 54: Read 'CARNOCYCLIN-A', 413 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 60 413 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (413 atoms, 60 residues) 54: 54: Identified residue LEU1 as a starting terminus. 54: 54: Identified residue LEU60 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 60 residues with 878 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 880, now 880 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 60 cmap torsion pairs 54: 54: There are 2325 dihedrals, 137 impropers, 1614 angles 54: 2319 pairs, 880 bonds and 0 virtual sites 54: 54: Total mass 5866.087 a.m.u. 54: 54: Total charge 4.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file (48 ms) 54: [----------] 4 tests from Cyclic/Pdb2gmxTest (612 ms total) 54: 54: [----------] Global test environment tear-down 54: [==========] 39 tests from 6 test suites ran. (1806 ms total) 54: [ PASSED ] 39 tests. 54/91 Test #54: Pdb2gmx3Test ................................. Passed 2.20 sec test 55 Start 55: CorrelationsTest 55: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/correlations-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/CorrelationsTest.xml" 55: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/correlationfunctions/tests 55: Test timeout computed to be: 30 55: [==========] Running 21 tests from 3 test suites. 55: [----------] Global test environment set-up. 55: [----------] 10 tests from AutocorrTest 55: [ RUN ] AutocorrTest.EacNormal 55: [ OK ] AutocorrTest.EacNormal (59 ms) 55: [ RUN ] AutocorrTest.EacNoNormalize 55: [ OK ] AutocorrTest.EacNoNormalize (20 ms) 55: [ RUN ] AutocorrTest.EacCos 55: [ OK ] AutocorrTest.EacCos (83 ms) 55: [ RUN ] AutocorrTest.EacVector 55: [ OK ] AutocorrTest.EacVector (88 ms) 55: [ RUN ] AutocorrTest.EacRcross 55: [ OK ] AutocorrTest.EacRcross (0 ms) 55: [ RUN ] AutocorrTest.EacP0 55: [ OK ] AutocorrTest.EacP0 (123 ms) 55: [ RUN ] AutocorrTest.EacP1 55: [ OK ] AutocorrTest.EacP1 (99 ms) 55: [ RUN ] AutocorrTest.EacP2 55: [ OK ] AutocorrTest.EacP2 (224 ms) 55: [ RUN ] AutocorrTest.EacP3 55: [ OK ] AutocorrTest.EacP3 (1 ms) 55: [ RUN ] AutocorrTest.EacP4 55: [ OK ] AutocorrTest.EacP4 (125 ms) 55: [----------] 10 tests from AutocorrTest (828 ms total) 55: 55: [----------] 10 tests from ExpfitTest 55: [ RUN ] ExpfitTest.EffnEXP1 55: [ OK ] ExpfitTest.EffnEXP1 (0 ms) 55: [ RUN ] ExpfitTest.EffnEXP2 55: [ OK ] ExpfitTest.EffnEXP2 (0 ms) 55: [ RUN ] ExpfitTest.EffnEXPEXP 55: [ OK ] ExpfitTest.EffnEXPEXP (0 ms) 55: [ RUN ] ExpfitTest.EffnEXP5 55: [ OK ] ExpfitTest.EffnEXP5 (5 ms) 55: [ RUN ] ExpfitTest.EffnEXP7 55: [ OK ] ExpfitTest.EffnEXP7 (1 ms) 55: [ RUN ] ExpfitTest.EffnEXP9 55: [ OK ] ExpfitTest.EffnEXP9 (10 ms) 55: [ RUN ] ExpfitTest.EffnERF 55: [ OK ] ExpfitTest.EffnERF (0 ms) 55: [ RUN ] ExpfitTest.EffnERREST 55: [ OK ] ExpfitTest.EffnERREST (0 ms) 55: [ RUN ] ExpfitTest.EffnVAC 55: [ OK ] ExpfitTest.EffnVAC (2 ms) 55: [ RUN ] ExpfitTest.EffnPRES 55: [ OK ] ExpfitTest.EffnPRES (5 ms) 55: [----------] 10 tests from ExpfitTest (38 ms total) 55: 55: [----------] 1 test from ManyAutocorrelationTest 55: [ RUN ] ManyAutocorrelationTest.Empty 55: [ OK ] ManyAutocorrelationTest.Empty (0 ms) 55: [----------] 1 test from ManyAutocorrelationTest (0 ms total) 55: 55: [----------] Global test environment tear-down 55: [==========] 21 tests from 3 test suites ran. (869 ms total) 55: [ PASSED ] 21 tests. 55/91 Test #55: CorrelationsTest ............................. Passed 1.22 sec test 56 Start 56: AnalysisDataUnitTests 56: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/analysisdata-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/AnalysisDataUnitTests.xml" 56: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/analysisdata/tests 56: Test timeout computed to be: 30 56: [==========] Running 69 tests from 14 test suites. 56: [----------] Global test environment set-up. 56: [----------] 3 tests from AnalysisDataInitializationTest 56: [ RUN ] AnalysisDataInitializationTest.BasicInitialization 56: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms) 56: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules 56: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms) 56: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules 56: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms) 56: [----------] 3 tests from AnalysisDataInitializationTest (0 ms total) 56: 56: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = (anonymous namespace)::SimpleInputData 56: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly 56: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames 56: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 56: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks 56: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (0 ms) 56: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData 56: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (0 ms) 56: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks 56: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (0 ms) 56: [----------] 8 tests from AnalysisDataCommonTest/0 (1 ms total) 56: 56: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = (anonymous namespace)::DataSetsInputData 56: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly 56: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames 56: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks 56: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData 56: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks 56: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (0 ms) 56: [----------] 8 tests from AnalysisDataCommonTest/1 (0 ms total) 56: 56: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = (anonymous namespace)::MultipointInputData 56: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly 56: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames 56: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks 56: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData 56: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks 56: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (0 ms) 56: [----------] 8 tests from AnalysisDataCommonTest/2 (1 ms total) 56: 56: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = (anonymous namespace)::MultipointDataSetsInputData 56: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly 56: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames 56: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks 56: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData 56: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks 56: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (0 ms) 56: [----------] 8 tests from AnalysisDataCommonTest/3 (1 ms total) 56: 56: [----------] 4 tests from AnalysisArrayDataTest 56: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly 56: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (0 ms) 56: [ RUN ] AnalysisArrayDataTest.StorageWorks 56: [ OK ] AnalysisArrayDataTest.StorageWorks (0 ms) 56: [ RUN ] AnalysisArrayDataTest.CanSetXAxis 56: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms) 56: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount 56: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms) 56: [----------] 4 tests from AnalysisArrayDataTest (0 ms total) 56: 56: [----------] 6 tests from AverageModuleTest 56: [ RUN ] AverageModuleTest.BasicTest 56: [ OK ] AverageModuleTest.BasicTest (0 ms) 56: [ RUN ] AverageModuleTest.HandlesMultipointData 56: [ OK ] AverageModuleTest.HandlesMultipointData (4 ms) 56: [ RUN ] AverageModuleTest.HandlesMultipleDataSets 56: [ OK ] AverageModuleTest.HandlesMultipleDataSets (0 ms) 56: [ RUN ] AverageModuleTest.HandlesDataSetAveraging 56: [ OK ] AverageModuleTest.HandlesDataSetAveraging (0 ms) 56: [ RUN ] AverageModuleTest.CanCustomizeXAxis 56: [ OK ] AverageModuleTest.CanCustomizeXAxis (0 ms) 56: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis 56: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (0 ms) 56: [----------] 6 tests from AverageModuleTest (5 ms total) 56: 56: [----------] 2 tests from FrameAverageModuleTest 56: [ RUN ] FrameAverageModuleTest.BasicTest 56: [ OK ] FrameAverageModuleTest.BasicTest (0 ms) 56: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets 56: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (0 ms) 56: [----------] 2 tests from FrameAverageModuleTest (0 ms total) 56: 56: [----------] 7 tests from AnalysisHistogramSettingsTest 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms) 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms) 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms) 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms) 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms) 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms) 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms) 56: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total) 56: 56: [----------] 2 tests from SimpleHistogramModuleTest 56: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly 56: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (0 ms) 56: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll 56: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) 56: [----------] 2 tests from SimpleHistogramModuleTest (0 ms total) 56: 56: [----------] 3 tests from WeightedHistogramModuleTest 56: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly 56: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (0 ms) 56: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll 56: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) 56: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets 56: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (0 ms) 56: [----------] 3 tests from WeightedHistogramModuleTest (1 ms total) 56: 56: [----------] 3 tests from BinAverageModuleTest 56: [ RUN ] BinAverageModuleTest.ComputesCorrectly 56: [ OK ] BinAverageModuleTest.ComputesCorrectly (0 ms) 56: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll 56: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (4 ms) 56: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets 56: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (0 ms) 56: [----------] 3 tests from BinAverageModuleTest (4 ms total) 56: 56: [----------] 4 tests from AbstractAverageHistogramTest 56: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly 56: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (0 ms) 56: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram 56: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (0 ms) 56: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth 56: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (0 ms) 56: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins 56: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (0 ms) 56: [----------] 4 tests from AbstractAverageHistogramTest (1 ms total) 56: 56: [----------] 3 tests from LifetimeModuleTest 56: [ RUN ] LifetimeModuleTest.BasicTest 56: [ OK ] LifetimeModuleTest.BasicTest (0 ms) 56: [ RUN ] LifetimeModuleTest.CumulativeTest 56: [ OK ] LifetimeModuleTest.CumulativeTest (0 ms) 56: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets 56: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (0 ms) 56: [----------] 3 tests from LifetimeModuleTest (0 ms total) 56: 56: [----------] Global test environment tear-down 56: [==========] 69 tests from 14 test suites ran. (19 ms total) 56: [ PASSED ] 69 tests. 56/91 Test #56: AnalysisDataUnitTests ........................ Passed 0.39 sec test 57 Start 57: CoordinateIOTests 57: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/coordinateio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/CoordinateIOTests.xml" 57: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/coordinateio/tests 57: Test timeout computed to be: 30 57: [==========] Running 67 tests from 20 test suites. 57: [----------] Global test environment set-up. 57: [----------] 1 test from OutputSelectorDeathTest 57: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (1 ms) 57: [----------] 1 test from OutputSelectorDeathTest (1 ms total) 57: 57: [----------] 5 tests from TrajectoryFrameWriterTest 57: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (1 ms) 57: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (0 ms) 57: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (1 ms) 57: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (3 ms) 57: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks 57: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms) 57: [----------] 5 tests from TrajectoryFrameWriterTest (19 ms total) 57: 57: [----------] 5 tests from OutputAdapterContainer 57: [ RUN ] OutputAdapterContainer.MakeEmpty 57: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms) 57: [ RUN ] OutputAdapterContainer.AddAdapter 57: [ OK ] OutputAdapterContainer.AddAdapter (0 ms) 57: [ RUN ] OutputAdapterContainer.RejectBadAdapter 57: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms) 57: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter 57: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms) 57: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters 57: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms) 57: [----------] 5 tests from OutputAdapterContainer (0 ms total) 57: 57: [----------] 3 tests from RegisterFrameConverterTest 57: [ RUN ] RegisterFrameConverterTest.NoConverterWorks 57: [ OK ] RegisterFrameConverterTest.NoConverterWorks (0 ms) 57: [ RUN ] RegisterFrameConverterTest.RegistrationWorks 57: [ OK ] RegisterFrameConverterTest.RegistrationWorks (0 ms) 57: [ RUN ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees 57: [ OK ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees (0 ms) 57: [----------] 3 tests from RegisterFrameConverterTest (0 ms total) 57: 57: [----------] 5 tests from FlagTest 57: [ RUN ] FlagTest.CanSetSimpleFlag 57: [ OK ] FlagTest.CanSetSimpleFlag (0 ms) 57: [ RUN ] FlagTest.CanAddNewBox 57: [ OK ] FlagTest.CanAddNewBox (0 ms) 57: [ RUN ] FlagTest.SetsImplicitPrecisionChange 57: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms) 57: [ RUN ] FlagTest.SetsImplicitStartTimeChange 57: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms) 57: [ RUN ] FlagTest.SetsImplicitTimeStepChange 57: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms) 57: [----------] 5 tests from FlagTest (0 ms total) 57: 57: [----------] 5 tests from SetAtomsTest 57: [ RUN ] SetAtomsTest.RemovesExistingAtoms 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] SetAtomsTest.RemovesExistingAtoms (1 ms) 57: [ RUN ] SetAtomsTest.AddsNewAtoms 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] SetAtomsTest.AddsNewAtoms (3 ms) 57: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (1 ms) 57: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (1 ms) 57: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (1 ms) 57: [----------] 5 tests from SetAtomsTest (12 ms total) 57: 57: [----------] 2 tests from SetBothTimeTest 57: [ RUN ] SetBothTimeTest.StartTimeZeroWorks 57: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms) 57: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks 57: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms) 57: [----------] 2 tests from SetBothTimeTest (0 ms total) 57: 57: [----------] 2 tests from SetStartTimeTest 57: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart 57: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms) 57: [ RUN ] SetStartTimeTest.WorksWithZeroStart 57: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms) 57: [----------] 2 tests from SetStartTimeTest (0 ms total) 57: 57: [----------] 1 test from SetTimeStepTest 57: [ RUN ] SetTimeStepTest.SetTimeStepWorks 57: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms) 57: [----------] 1 test from SetTimeStepTest (0 ms total) 57: 57: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest 57: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (1 ms) 57: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (1 ms) 57: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (1 ms) 57: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (1 ms) 57: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (1 ms) 57: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (1 ms) 57: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (19 ms total) 57: 57: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles 57: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (1 ms) 57: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (2 ms) 57: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (1 ms) 57: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (11 ms total) 57: 57: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles 57: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 57: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms) 57: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 57: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms) 57: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 57: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms) 57: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (0 ms total) 57: 57: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles 57: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (3 ms) 57: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (2 ms) 57: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (2 ms) 57: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (2 ms) 57: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (17 ms total) 57: 57: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles 57: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (0 ms) 57: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (1 ms) 57: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (1 ms) 57: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (4 ms total) 57: 57: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles 57: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 57: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms) 57: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 57: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms) 57: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 57: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms) 57: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (0 ms total) 57: 57: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles 57: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (1 ms) 57: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (1 ms) 57: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (2 ms total) 57: 57: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles 57: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 57: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms) 57: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 57: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms) 57: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 57: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms) 57: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 57: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms) 57: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (0 ms total) 57: 57: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles 57: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (1 ms) 57: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (1 ms) 57: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (2 ms total) 57: 57: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles 57: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 57: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms) 57: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 57: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms) 57: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 57: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms) 57: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 57: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms) 57: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (0 ms total) 57: 57: [----------] 4 tests from ModuleSupported/NoOptionalOutput 57: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (1 ms) 57: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (1 ms) 57: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (1 ms) 57: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (1 ms) 57: [----------] 4 tests from ModuleSupported/NoOptionalOutput (5 ms total) 57: 57: [----------] Global test environment tear-down 57: [==========] 67 tests from 20 test suites ran. (102 ms total) 57: [ PASSED ] 67 tests. 57/91 Test #57: CoordinateIOTests ............................ Passed 0.46 sec test 58 Start 58: TrajectoryAnalysisUnitTests 58: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/trajectoryanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/TrajectoryAnalysisUnitTests.xml" 58: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests 58: Test timeout computed to be: 1920 58: [==========] Running 385 tests from 24 test suites. 58: [----------] Global test environment set-up. 58: [----------] 11 tests from AngleModuleTest 58: [ RUN ] AngleModuleTest.ComputesSimpleAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesSimpleAngles (1 ms) 58: [ RUN ] AngleModuleTest.ComputesDihedrals 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesDihedrals (1 ms) 58: [ RUN ] AngleModuleTest.ComputesVectorPairAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesVectorPairAngles (1 ms) 58: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (5 ms) 58: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (6 ms) 58: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (1 ms) 58: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles 58: Reading frames from gro file 'Test system for different angles', 33 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (1 ms) 58: [ RUN ] AngleModuleTest.ComputesMultipleAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesMultipleAngles (1 ms) 58: [ RUN ] AngleModuleTest.HandlesDynamicSelections 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.HandlesDynamicSelections (1 ms) 58: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (1 ms) 58: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (5 ms) 58: [----------] 11 tests from AngleModuleTest (28 ms total) 58: 58: [----------] 5 tests from ClustsizeTest 58: [ RUN ] ClustsizeTest.NoMolDefaultCutoff 58: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 58: There is one group in the index 58: '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Total number of atoms in clusters = 24 58: cmid: 2, cmax: 4, max_size: 6 58: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 58: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (2 ms) 58: [ RUN ] ClustsizeTest.NoMolShortCutoff 58: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 58: There is one group in the index 58: '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Total number of atoms in clusters = 24 58: cmid: 1, cmax: 6, max_size: 6 58: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 58: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (1 ms) 58: [ RUN ] ClustsizeTest.MolDefaultCutoff 58: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Total number of atoms in clusters = 8 58: cmid: 2, cmax: 4, max_size: 2 58: 50%100%cmid: 2, cmax: 6, max_size: 2 58: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (1 ms) 58: [ RUN ] ClustsizeTest.MolShortCutoff 58: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Total number of atoms in clusters = 8 58: cmid: 1, cmax: 6, max_size: 2 58: 50%100%cmid: 2, cmax: 6, max_size: 2 58: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (1 ms) 58: [ RUN ] ClustsizeTest.MolCSize 58: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Total number of atoms in clusters = 8 58: cmid: 2, cmax: 4, max_size: 2 58: 50%100%cmid: 2, cmax: 6, max_size: 2 58: 50%100%[ OK ] ClustsizeTest.MolCSize (2 ms) 58: [----------] 5 tests from ClustsizeTest (9 ms total) 58: 58: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest 58: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp 58: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (0 ms) 58: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory 58: Reading frames from gro file 'Test system', 8 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (0 ms) 58: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset 58: Reading frames from gro file 'Test system', 8 atoms. 58: Reading frame 0 time 0.000 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (1 ms) 58: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory 58: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (0 ms) 58: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (2 ms total) 58: 58: [----------] 4 tests from ConvertTrjModuleTest 58: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: Reading frame 0 time 0.000 Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (25 ms) 58: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: Reading frame 0 time 0.000 Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (5 ms) 58: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (1 ms) 58: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (1 ms) 58: [----------] 4 tests from ConvertTrjModuleTest (35 ms total) 58: 58: [----------] 6 tests from DistanceModuleTest 58: [ RUN ] DistanceModuleTest.ComputesDistances 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: atomname S1 S2: 58: Number of samples: 5 58: Average distance: 1.43246 nm 58: Standard deviation: 0.96700 nm 58: [ OK ] DistanceModuleTest.ComputesDistances (1 ms) 58: [ RUN ] DistanceModuleTest.ComputesMultipleDistances 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: atomname S1 S2: 58: Number of samples: 5 58: Average distance: 1.43246 nm 58: Standard deviation: 0.96700 nm 58: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB: 58: Number of samples: 4 58: Average distance: 1.81066 nm 58: Standard deviation: 0.79289 nm 58: [ OK ] DistanceModuleTest.ComputesMultipleDistances (1 ms) 58: [ RUN ] DistanceModuleTest.HandlesDynamicSelections 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: atomname S1 S2 and res_cog x < 2.8: 58: Number of samples: 3 58: Average distance: 1.72076 nm 58: Standard deviation: 1.24839 nm 58: [ OK ] DistanceModuleTest.HandlesDynamicSelections (1 ms) 58: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroup 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: Contacts: 58: Number of samples: 2 58: Average distance: 1.00000 nm 58: Standard deviation: 0.00000 nm 58: [ OK ] DistanceModuleTest.HandlesSelectionFromGroup (5 ms) 58: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: SuccessiveContacts: 58: Number of samples: 2 58: Average distance: 1.00000 nm 58: Standard deviation: 0.00000 nm 58: [ OK ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices (3 ms) 58: [ RUN ] DistanceModuleTest.HandlesSelectionFromLargeGroup 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: ManyContacts: 58: Number of samples: 10 58: Average distance: 1.82913 nm 58: Standard deviation: 0.78478 nm 58: [ OK ] DistanceModuleTest.HandlesSelectionFromLargeGroup (3 ms) 58: [----------] 6 tests from DistanceModuleTest (18 ms total) 58: 58: [----------] 2 tests from ExtractClusterModuleTest 58: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms 58: trr version: GMX_trn_file (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 58: Analyzed 26 frames, last time 0.050 58: There are 8 clusters containing 26 structures, highest framenr is 25 58: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (4 ms) 58: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset 58: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 58: Analyzed 26 frames, last time 0.050 58: There are 8 clusters containing 26 structures, highest framenr is 25 58: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (1 ms) 58: [----------] 2 tests from ExtractClusterModuleTest (6 ms total) 58: 58: [----------] 2 tests from FreeVolumeModuleTest 58: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. 68 (1964) pp. 441-451 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for 40 particles. These were set to zero. 58: Reading frame 0 time 0.000 Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: cutoff = 0.18 nm 58: probe_radius = 0 nm 58: seed = 13 58: ninsert = 1000 probes per nm^3 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. 68 (1964) pp. 441-451 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David 58: van der Spoel and Luciano T. Costa 58: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 58: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 58: Environ. Sci. Technol. 47 (2013) pp. 7421-7429 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Free volume 38.02 +/- 0.00 % 58: Total volume 68.92 +/- 0.00 nm^3 58: Number of molecules 340 total mass 63491.38 Dalton 58: Average molar mass: 186.74 Dalton 58: Density rho: 1529.71 +/- 0.00 nm^3 58: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 58: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3 58: Fractional free volume 0.194 +/- 0.000 58: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (65 ms) 58: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. 68 (1964) pp. 441-451 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Reading frame 0 time 0.000 Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: cutoff = 0.18 nm 58: probe_radius = 0 nm 58: seed = 17 58: ninsert = 1000 probes per nm^3 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. 68 (1964) pp. 441-451 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David 58: van der Spoel and Luciano T. Costa 58: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 58: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 58: Environ. Sci. Technol. 47 (2013) pp. 7421-7429 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Free volume 38.48 +/- 0.00 % 58: Total volume 68.92 +/- 0.00 nm^3 58: Number of molecules 340 total mass 63491.38 Dalton 58: Average molar mass: 186.74 Dalton 58: Density rho: 1529.71 +/- 0.00 nm^3 58: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 58: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3 58: Fractional free volume 0.200 +/- 0.000 58: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (66 ms) 58: [----------] 2 tests from FreeVolumeModuleTest (132 ms total) 58: 58: [----------] 11 tests from MsdModuleTest 58: [ RUN ] MsdModuleTest.threeDimensionalDiffusion 58: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 58: Analyzed 10 frames, last time 9.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] MsdModuleTest.threeDimensionalDiffusion (2 ms) 58: [ RUN ] MsdModuleTest.twoDimensionalDiffusion 58: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 58: Analyzed 10 frames, last time 9.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] MsdModuleTest.twoDimensionalDiffusion (1 ms) 58: [ RUN ] MsdModuleTest.oneDimensionalDiffusion 58: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 58: Analyzed 10 frames, last time 9.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] MsdModuleTest.oneDimensionalDiffusion (1 ms) 58: [ RUN ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau 58: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 58: Analyzed 10 frames, last time 9.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau (4 ms) 58: [ RUN ] MsdModuleTest.roundingFail 58: Reading frame 0 time 0.000 Reading frame 1 time 0.001 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] MsdModuleTest.roundingFail (0 ms) 58: [ RUN ] MsdModuleTest.multipleGroupsWork 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 58: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 58: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 58: Analyzed 21 frames, last time 40.000 58: Setting the LD random seed to -578814241 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.multipleGroupsWork (19 ms) 58: [ DISABLED ] MsdModuleTest.DISABLED_trestartLessThanDt 58: [ RUN ] MsdModuleTest.trestartGreaterThanDt 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 58: Analyzed 21 frames, last time 40.000 58: Setting the LD random seed to 2046520825 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.trestartGreaterThanDt (18 ms) 58: [ RUN ] MsdModuleTest.molTest 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 58: Analyzed 21 frames, last time 40.000 58: Setting the LD random seed to -33568489 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.molTest (17 ms) 58: [ RUN ] MsdModuleTest.beginFit 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 58: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 58: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 58: Analyzed 21 frames, last time 40.000 58: Setting the LD random seed to 1743770541 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.beginFit (16 ms) 58: [ RUN ] MsdModuleTest.endFit 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 58: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 58: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 58: Analyzed 21 frames, last time 40.000 58: Setting the LD random seed to 2145381375 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.endFit (18 ms) 58: [ RUN ] MsdModuleTest.notEnoughPointsForFitErrorEstimate 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: NOTE: You provided an index file 58: /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/alanine_vsite_solvated.ndx 58: (with -n), but it was not used by any selection. 58: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 58: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 58: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 58: Analyzed 21 frames, last time 40.000 58: Setting the LD random seed to -1612189729 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.notEnoughPointsForFitErrorEstimate (17 ms) 58: [----------] 11 tests from MsdModuleTest (127 ms total) 58: 58: [----------] 9 tests from PairDistanceModuleTest 58: [ RUN ] PairDistanceModuleTest.ComputesAllDistances 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesAllDistances (1 ms) 58: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (1 ms) 58: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (1 ms) 58: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (1 ms) 58: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (1 ms) 58: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (1 ms) 58: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (1 ms) 58: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (1 ms) 58: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (1 ms) 58: [----------] 9 tests from PairDistanceModuleTest (10 ms total) 58: 58: [----------] 5 tests from RdfModuleTest 58: [ RUN ] RdfModuleTest.BasicTest 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] RdfModuleTest.BasicTest (12 ms) 58: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork 58: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms. 58: Reading frame 0 time 0.000 Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (11 ms) 58: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (12 ms) 58: [ RUN ] RdfModuleTest.CalculatesSurf 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] RdfModuleTest.CalculatesSurf (5 ms) 58: [ RUN ] RdfModuleTest.CalculatesXY 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] RdfModuleTest.CalculatesXY (13 ms) 58: [----------] 5 tests from RdfModuleTest (55 ms total) 58: 58: [----------] 5 tests from SasaModuleTest 58: [ RUN ] SasaModuleTest.BasicTest 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 58: Michael Scharf 58: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 58: of Surface Area and Volume and to Dot Surface Contouring of Molecular 58: Assemblies 58: J. Comp. Chem. 16 (1995) pp. 273-284 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. 68 (1964) pp. 441-451 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Analyzed topology coordinates 58: [ OK ] SasaModuleTest.BasicTest (6 ms) 58: [ RUN ] SasaModuleTest.HandlesSelectedResidues 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 58: Michael Scharf 58: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 58: of Surface Area and Volume and to Dot Surface Contouring of Molecular 58: Assemblies 58: J. Comp. Chem. 16 (1995) pp. 273-284 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. 68 (1964) pp. 441-451 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Analyzed topology coordinates 58: [ OK ] SasaModuleTest.HandlesSelectedResidues (3 ms) 58: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 58: Michael Scharf 58: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 58: of Surface Area and Volume and to Dot Surface Contouring of Molecular 58: Assemblies 58: J. Comp. Chem. 16 (1995) pp. 273-284 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. 68 (1964) pp. 441-451 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Analyzed topology coordinates 58: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (7 ms) 58: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 58: Michael Scharf 58: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 58: of Surface Area and Volume and to Dot Surface Contouring of Molecular 58: Assemblies 58: J. Comp. Chem. 16 (1995) pp. 273-284 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. 68 (1964) pp. 441-451 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Analyzed topology coordinates 58: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (6 ms) 58: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 58: Michael Scharf 58: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 58: of Surface Area and Volume and to Dot Surface Contouring of Molecular 58: Assemblies 58: J. Comp. Chem. 16 (1995) pp. 273-284 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. 68 (1964) pp. 441-451 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Analyzed topology coordinates 58: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (7 ms) 58: [----------] 5 tests from SasaModuleTest (33 ms total) 58: 58: [----------] 8 tests from SelectModuleTest 58: [ RUN ] SelectModuleTest.BasicTest 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.BasicTest (3 ms) 58: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (2 ms) 58: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (1 ms) 58: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (1 ms) 58: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (2 ms) 58: [ RUN ] SelectModuleTest.NormalizesSizes 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.NormalizesSizes (1 ms) 58: [ RUN ] SelectModuleTest.WritesResidueNumbers 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.WritesResidueNumbers (1 ms) 58: [ RUN ] SelectModuleTest.WritesResidueIndices 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.WritesResidueIndices (1 ms) 58: [----------] 8 tests from SelectModuleTest (22 ms total) 58: 58: [----------] 10 tests from SurfaceAreaTest 58: [ RUN ] SurfaceAreaTest.ComputesSinglePoint 58: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms) 58: [ RUN ] SurfaceAreaTest.ComputesTwoPoints 58: [ OK ] SurfaceAreaTest.ComputesTwoPoints (0 ms) 58: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius 58: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (0 ms) 58: [ RUN ] SurfaceAreaTest.SurfacePoints12 58: [ OK ] SurfaceAreaTest.SurfacePoints12 (0 ms) 58: [ RUN ] SurfaceAreaTest.SurfacePoints32 58: [ OK ] SurfaceAreaTest.SurfacePoints32 (0 ms) 58: [ RUN ] SurfaceAreaTest.SurfacePoints42 58: [ OK ] SurfaceAreaTest.SurfacePoints42 (0 ms) 58: [ RUN ] SurfaceAreaTest.SurfacePoints122 58: [ OK ] SurfaceAreaTest.SurfacePoints122 (0 ms) 58: [ RUN ] SurfaceAreaTest.Computes100Points 58: [ OK ] SurfaceAreaTest.Computes100Points (0 ms) 58: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC 58: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (1 ms) 58: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC 58: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (1 ms) 58: [----------] 10 tests from SurfaceAreaTest (8 ms total) 58: 58: [----------] 4 tests from TopologyInformation 58: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile 58: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms) 58: [ RUN ] TopologyInformation.WorksWithGroFile 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TopologyInformation.WorksWithGroFile (1 ms) 58: [ RUN ] TopologyInformation.WorksWithPdbFile 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TopologyInformation.WorksWithPdbFile (1 ms) 58: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file lysozyme.top, line 1465]: 58: System has non-zero total charge: 2.000000 58: Total charge should normally be an integer. See 58: https://manual.gromacs.org/current/user-guide/floating-point.html 58: for discussion on how close it should be to an integer. 58: 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 465.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 58: NVE simulation with an initial temperature of zero: will use a Verlet 58: buffer of 10%. Check your energy drift! 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 4 NOTEs 58: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Setting the LD random seed to -197149971 58: 58: Generated 330891 of the 330891 non-bonded parameter combinations 58: 58: Generated 330891 of the 330891 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 58: Analysing residue names: 58: There are: 10 Protein residues 58: Analysing Protein... 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (443 ms) 58: [----------] 4 tests from TopologyInformation (448 ms total) 58: 58: [----------] 4 tests from TrajectoryModuleTest 58: [ RUN ] TrajectoryModuleTest.BasicTest 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TrajectoryModuleTest.BasicTest (2 ms) 58: [ RUN ] TrajectoryModuleTest.PlotsXOnly 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TrajectoryModuleTest.PlotsXOnly (1 ms) 58: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (1 ms) 58: [ RUN ] TrajectoryModuleTest.HandlesNoForces 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TrajectoryModuleTest.HandlesNoForces (1 ms) 58: [----------] 4 tests from TrajectoryModuleTest (10 ms total) 58: 58: [----------] 5 tests from UnionFinderTest 58: [ RUN ] UnionFinderTest.WorksEmpty 58: [ OK ] UnionFinderTest.WorksEmpty (0 ms) 58: [ RUN ] UnionFinderTest.BasicMerges 58: [ OK ] UnionFinderTest.BasicMerges (0 ms) 58: [ RUN ] UnionFinderTest.LargerMerges 58: [ OK ] UnionFinderTest.LargerMerges (0 ms) 58: [ RUN ] UnionFinderTest.LongRightMerge 58: [ OK ] UnionFinderTest.LongRightMerge (0 ms) 58: [ RUN ] UnionFinderTest.LongLeftMerge 58: [ OK ] UnionFinderTest.LongLeftMerge (0 ms) 58: [----------] 5 tests from UnionFinderTest (0 ms total) 58: 58: [----------] 1 test from MappedUnionFinderTest 58: [ RUN ] MappedUnionFinderTest.BasicMerges 58: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms) 58: [----------] 1 test from MappedUnionFinderTest (0 ms total) 58: 58: [----------] 160 tests from MoleculeTests/DsspModuleTestDsspNB 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/0 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 708 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/0 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/1 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 708 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/1 (13 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/2 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 708 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/2 (14 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/3 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 708 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/3 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/4 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 708 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/4 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/5 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 708 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/5 (7 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/6 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 708 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/6 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/7 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 708 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/7 (7 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/8 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2066 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/8 (16 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/9 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2066 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/9 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/10 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2066 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/10 (29 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/11 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2066 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/11 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/12 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2066 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/12 (33 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/13 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2066 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/13 (32 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/14 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2066 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/14 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/15 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2066 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/15 (30 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/16 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2564 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/16 (34 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/17 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2564 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/17 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/18 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2564 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/18 (24 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/19 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2564 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/19 (24 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/20 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2564 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/20 (25 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/21 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2564 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/21 (24 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/22 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2564 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/22 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/23 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2564 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/23 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/24 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/24 (45 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/25 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/25 (30 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/26 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/26 (32 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/27 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/27 (24 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/28 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/28 (44 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/29 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/29 (42 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/30 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/30 (47 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/31 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/31 (44 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/32 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 798 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/32 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/33 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 798 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/33 (13 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/34 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 798 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/34 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/35 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 798 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/35 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/36 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 798 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/36 (13 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/37 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 798 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/37 (13 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/38 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 798 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/38 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/39 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 798 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/39 (7 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/40 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/40 (7 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/41 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/41 (7 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/42 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/42 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/43 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/43 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/44 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/44 (7 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/45 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/45 (14 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/46 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/46 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/47 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/47 (14 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/48 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/48 (7 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/49 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/49 (7 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/50 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/50 (7 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/51 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/51 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/52 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/52 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/53 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/53 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/54 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/54 (6 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/55 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/55 (6 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/56 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 3419 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/56 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/57 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 3419 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/57 (32 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/58 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 3419 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/58 (31 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/59 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 3419 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/59 (30 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/60 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 3419 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/60 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/61 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 3419 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/61 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/62 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 3419 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/62 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/63 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 3419 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/63 (20 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/64 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2923 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/64 (17 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/65 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2923 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/65 (20 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/66 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2923 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/66 (16 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/67 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2923 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/67 (14 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/68 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2923 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/68 (32 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/69 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2923 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/69 (32 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/70 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2923 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/70 (67 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/71 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2923 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/71 (24 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/72 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/72 (20 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/73 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/73 (16 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/74 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/74 (16 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/75 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/75 (17 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/76 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/76 (20 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/77 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/77 (20 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/78 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/78 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/79 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/79 (14 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/80 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2745 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/80 (45 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/81 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2745 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/81 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/82 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2745 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/82 (26 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/83 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2745 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/83 (14 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/84 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2745 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/84 (15 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/85 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2745 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/85 (24 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/86 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2745 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/86 (27 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/87 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2745 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/87 (27 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/88 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1742 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/88 (24 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/89 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1742 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/89 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/90 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1742 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/90 (14 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/91 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1742 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/91 (17 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/92 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1742 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/92 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/93 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1742 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/93 (14 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/94 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1742 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/94 (31 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/95 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1742 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/95 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/96 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1643 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/96 (16 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/97 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1643 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/97 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/98 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1643 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/98 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/99 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1643 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/99 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/100 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1643 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/100 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/101 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1643 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/101 (17 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/102 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1643 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/102 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/103 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1643 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/103 (33 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/104 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1380 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/104 (25 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/105 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1380 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/105 (13 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/106 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1380 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/106 (17 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/107 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1380 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/107 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/108 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1380 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/108 (9 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/109 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1380 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/109 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/110 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1380 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/110 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/111 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1380 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/111 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/112 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1060 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/112 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/113 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1060 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/113 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/114 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1060 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/114 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/115 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1060 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/115 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/116 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1060 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/116 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/117 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1060 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/117 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/118 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1060 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/118 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/119 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1060 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/119 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/120 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 5347 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/120 (70 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/121 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 5347 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/121 (106 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/122 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 5347 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/122 (71 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/123 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 5347 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/123 (66 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/124 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 5347 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/124 (73 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/125 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 5347 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/125 (71 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/126 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 5347 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/126 (67 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/127 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 5347 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/127 (69 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/128 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1264 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/128 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/129 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1264 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/129 (15 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/130 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1264 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/130 (20 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/131 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1264 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/131 (15 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/132 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1264 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/132 (20 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/133 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1264 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/133 (14 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/134 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1264 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/134 (9 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/135 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1264 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/135 (9 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/136 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1429 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/136 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/137 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1429 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/137 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/138 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1429 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/138 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/139 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1429 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/139 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/140 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1429 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/140 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/141 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1429 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/141 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/142 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1429 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/142 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/143 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1429 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/143 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/144 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1285 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/144 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/145 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1285 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/145 (9 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/146 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1285 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/146 (9 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/147 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1285 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/147 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/148 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1285 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/148 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/149 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1285 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/149 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/150 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1285 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/150 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/151 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1285 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/151 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/152 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2595 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/152 (15 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/153 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2595 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/153 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/154 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2595 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/154 (27 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/155 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2595 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/155 (20 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/156 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2595 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/156 (16 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/157 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2595 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/157 (17 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/158 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2595 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/158 (15 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/159 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2595 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/159 (16 ms) 58: [----------] 160 tests from MoleculeTests/DsspModuleTestDsspNB (3535 ms total) 58: 58: [----------] 24 tests from MoleculeTests/DsspModuleTestGromacsNB 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/0 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/0 (29 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/1 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/1 (28 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/2 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/2 (28 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/3 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/3 (33 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/4 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/4 (30 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/5 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/5 (29 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/6 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/6 (27 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/7 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/7 (27 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/8 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/8 (9 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/9 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/9 (9 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/10 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/10 (9 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/11 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/11 (9 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/12 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/12 (9 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/13 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/13 (9 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/14 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/14 (9 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/15 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/15 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/16 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/16 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/17 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/17 (7 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/18 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/18 (7 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/19 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/19 (7 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/20 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/20 (7 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/21 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/21 (7 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/22 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/22 (7 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/23 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/23 (7 ms) 58: [----------] 24 tests from MoleculeTests/DsspModuleTestGromacsNB (373 ms total) 58: 58: [----------] 80 tests from MoleculeTests/DsspModuleTestDsspNoNB 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/0 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 708 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/0 (4 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/1 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 708 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/1 (4 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/2 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 708 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/2 (4 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/3 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 708 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/3 (4 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/4 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2066 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/4 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/5 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2066 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/5 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/6 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2066 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/6 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/7 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2066 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/7 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/8 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2564 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/8 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/9 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2564 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/9 (14 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/10 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2564 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/10 (14 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/11 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2564 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/11 (14 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/12 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/12 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/13 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/13 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/14 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/14 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/15 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/15 (17 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/16 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 798 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/16 (4 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/17 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 798 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/17 (4 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/18 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 798 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/18 (4 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/19 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 798 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/19 (4 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/20 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/20 (7 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/21 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/21 (7 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/22 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/22 (7 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/23 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/23 (7 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/24 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/24 (5 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/25 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/25 (6 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/26 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/26 (6 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/27 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/27 (6 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/28 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 3419 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/28 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/29 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 3419 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/29 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/30 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 3419 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/30 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/31 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 3419 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/31 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/32 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2923 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/32 (16 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/33 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2923 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/33 (17 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/34 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2923 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/34 (16 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/35 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2923 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/35 (16 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/36 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/36 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/37 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/37 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/38 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/38 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/39 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/39 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/40 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2745 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/40 (16 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/41 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2745 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/41 (16 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/42 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2745 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/42 (15 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/43 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2745 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/43 (16 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/44 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1742 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/44 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/45 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1742 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/45 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/46 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1742 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/46 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/47 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1742 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/47 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/48 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1643 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/48 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/49 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1643 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/49 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/50 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1643 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/50 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/51 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1643 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/51 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/52 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1380 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/52 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/53 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1380 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/53 (14 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/54 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1380 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/54 (16 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/55 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1380 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/55 (16 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/56 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1060 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/56 (7 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/57 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1060 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/57 (7 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/58 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1060 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/58 (6 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/59 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1060 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/59 (7 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/60 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 5347 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/60 (35 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/61 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 5347 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/61 (35 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/62 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 5347 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/62 (34 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/63 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 5347 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/63 (35 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/64 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1264 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/64 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/65 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1264 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/65 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/66 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1264 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/66 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/67 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1264 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/67 (9 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/68 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1429 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/68 (9 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/69 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1429 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/69 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/70 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1429 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/70 (9 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/71 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1429 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/71 (9 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/72 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1285 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/72 (9 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/73 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1285 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/73 (9 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/74 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1285 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/74 (9 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/75 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1285 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/75 (9 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/76 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2595 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/76 (13 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/77 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2595 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/77 (14 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/78 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2595 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/78 (14 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/79 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2595 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/79 (15 ms) 58: [----------] 80 tests from MoleculeTests/DsspModuleTestDsspNoNB (1041 ms total) 58: 58: [----------] 12 tests from MoleculeTests/DsspModuleTestGromacsNoNB 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/0 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/0 (29 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/1 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/1 (29 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/2 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/2 (28 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/3 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/3 (30 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/4 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/4 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/5 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/5 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/6 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/6 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/7 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/7 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/8 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/8 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/9 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/9 (9 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/10 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/10 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/11 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/11 (8 ms) 58: [----------] 12 tests from MoleculeTests/DsspModuleTestGromacsNoNB (198 ms total) 58: 58: [----------] 3 tests from GyrateTests/GyrateModuleTest 58: [ RUN ] GyrateTests/GyrateModuleTest.Works/0 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: [ OK ] GyrateTests/GyrateModuleTest.Works/0 (3 ms) 58: [ RUN ] GyrateTests/GyrateModuleTest.Works/1 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: [ OK ] GyrateTests/GyrateModuleTest.Works/1 (3 ms) 58: [ RUN ] GyrateTests/GyrateModuleTest.Works/2 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: [ OK ] GyrateTests/GyrateModuleTest.Works/2 (2 ms) 58: [----------] 3 tests from GyrateTests/GyrateModuleTest (9 ms total) 58: 58: [----------] 6 tests from HBondTests/HbondModuleTest 58: [ RUN ] HBondTests/HbondModuleTest.Works/0 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: [ OK ] HBondTests/HbondModuleTest.Works/0 (6 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/1 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: [ OK ] HBondTests/HbondModuleTest.Works/1 (6 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/2 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: [ OK ] HBondTests/HbondModuleTest.Works/2 (28 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/3 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/3 (28 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/4 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: [ OK ] HBondTests/HbondModuleTest.Works/4 (27 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/5 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: [ OK ] HBondTests/HbondModuleTest.Works/5 (27 ms) 58: [----------] 6 tests from HBondTests/HbondModuleTest (141 ms total) 58: 58: [----------] 4 tests from MoleculeTests/ScatteringModule 58: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/0 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev & V. V. Isaev-Ivanov 58: Method for calculating small-angle neutron scattering spectra using all-atom 58: molecular dynamics trajectories 58: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques 7 (2013) pp. 1124–1127 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/ScatteringModule.DirectMode/0 (5 ms) 58: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/1 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev & V. V. Isaev-Ivanov 58: Method for calculating small-angle neutron scattering spectra using all-atom 58: molecular dynamics trajectories 58: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques 7 (2013) pp. 1124–1127 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: D. T. Cromer & J. B. Mann 58: X-ray scattering factors computed from numerical Hartree-Fock wave functions 58: Acta Cryst. A 24 (1968) pp. 321 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/ScatteringModule.DirectMode/1 (101 ms) 58: [ RUN ] MoleculeTests/ScatteringModule.MCMode/0 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev & V. V. Isaev-Ivanov 58: Method for calculating small-angle neutron scattering spectra using all-atom 58: molecular dynamics trajectories 58: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques 7 (2013) pp. 1124–1127 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/ScatteringModule.MCMode/0 (5 ms) 58: [ RUN ] MoleculeTests/ScatteringModule.MCMode/1 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev & V. V. Isaev-Ivanov 58: Method for calculating small-angle neutron scattering spectra using all-atom 58: molecular dynamics trajectories 58: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques 7 (2013) pp. 1124–1127 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: D. T. Cromer & J. B. Mann 58: X-ray scattering factors computed from numerical Hartree-Fock wave functions 58: Acta Cryst. A 24 (1968) pp. 321 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/ScatteringModule.MCMode/1 (26 ms) 58: [----------] 4 tests from MoleculeTests/ScatteringModule (140 ms total) 58: 58: [----------] Global test environment tear-down 58: [==========] 385 tests from 24 test suites ran. (6397 ms total) 58: [ PASSED ] 385 tests. 58: 58: YOU HAVE 1 DISABLED TEST 58: 58/91 Test #58: TrajectoryAnalysisUnitTests .................. Passed 6.78 sec test 59 Start 59: EnergyAnalysisUnitTests 59: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/energyanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/EnergyAnalysisUnitTests.xml" 59: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/energyanalysis/tests 59: Test timeout computed to be: 30 59: [==========] Running 11 tests from 5 test suites. 59: [----------] Global test environment set-up. 59: [----------] 2 tests from EnergyTermTest 59: [ RUN ] EnergyTermTest.ConstructWorks 59: [ OK ] EnergyTermTest.ConstructWorks (0 ms) 59: [ RUN ] EnergyTermTest.AddFrameWorks 59: [ OK ] EnergyTermTest.AddFrameWorks (0 ms) 59: [----------] 2 tests from EnergyTermTest (0 ms total) 59: 59: [----------] 1 test from DhdlTest 59: [ RUN ] DhdlTest.ExtractDhdl 59: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file 59: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision) 59: Note: file tpx version 110, software tpx version 134 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Reading energy frame 6 time 0.060 Reading energy frame 7 time 0.070 Reading energy frame 8 time 0.080 Reading energy frame 9 time 0.090 Reading energy frame 10 time 0.100 Reading energy frame 11 time 0.110 Reading energy frame 12 time 0.120 Reading energy frame 13 time 0.130 Reading energy frame 14 time 0.140 Reading energy frame 15 time 0.150 Reading energy frame 16 time 0.160 Reading energy frame 17 time 0.170 Reading energy frame 18 time 0.180 Reading energy frame 19 time 0.190 Reading energy frame 20 time 0.200 Reading energy frame 30 time 0.300 Reading energy frame 40 time 0.400 Reading energy frame 50 time 0.500 Reading energy frame 60 time 0.600 Reading energy frame 70 time 0.700 Reading energy frame 80 time 0.800 Reading energy frame 90 time 0.900 Reading energy frame 100 time 1.000 Last energy frame read 100 time 1.000 59: 59: 59: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg 59: [ OK ] DhdlTest.ExtractDhdl (6 ms) 59: [----------] 1 test from DhdlTest (6 ms total) 59: 59: [----------] 1 test from OriresTest 59: [ RUN ] OriresTest.ExtractOrires 59: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file 59: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision) 59: Note: file tpx version 111, software tpx version 134 59: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all) 59: End your selection with 0 59: Selecting all 7 orientation restraints 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Reading energy frame 3 time 0.006 Reading energy frame 4 time 0.008 Reading energy frame 5 time 0.010 Reading energy frame 6 time 0.012 Reading energy frame 7 time 0.014 Reading energy frame 8 time 0.016 Reading energy frame 9 time 0.018 Reading energy frame 10 time 0.020 Last energy frame read 10 time 0.020 59: [ OK ] OriresTest.ExtractOrires (12 ms) 59: [----------] 1 test from OriresTest (12 ms total) 59: 59: [----------] 5 tests from EnergyTest 59: [ RUN ] EnergyTest.ExtractEnergy 59: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 59: 59: Select the terms you want from the following list by 59: selecting either (part of) the name or the number or a combination. 59: End your selection with an empty line or a zero. 59: ------------------------------------------------------------------- 59: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 59: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 59: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 59: 13 Box-Z 14 Volume 15 Density 16 pV 59: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 59: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 59: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 59: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 59: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 59: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 59: 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 59: 59: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 59: All statistics are over 5001 points 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: Potential -34142.2 39 228.993 -62.8906 (kJ/mol) 59: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 59: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 59: [ OK ] EnergyTest.ExtractEnergy (1 ms) 59: [ RUN ] EnergyTest.ExtractEnergyByNumber 59: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 59: 59: Select the terms you want from the following list by 59: selecting either (part of) the name or the number or a combination. 59: End your selection with an empty line or a zero. 59: ------------------------------------------------------------------- 59: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 59: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 59: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 59: 13 Box-Z 14 Volume 15 Density 16 pV 59: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 59: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 59: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 59: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 59: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 59: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 59: 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 59: 59: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 59: All statistics are over 5001 points 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol) 59: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 59: Pres. DC -268.49 3 8.52175 13.2804 (bar) 59: [ OK ] EnergyTest.ExtractEnergyByNumber (1 ms) 59: [ RUN ] EnergyTest.ExtractEnergyMixed 59: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 59: 59: Select the terms you want from the following list by 59: selecting either (part of) the name or the number or a combination. 59: End your selection with an empty line or a zero. 59: ------------------------------------------------------------------- 59: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 59: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 59: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 59: 13 Box-Z 14 Volume 15 Density 16 pV 59: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 59: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 59: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 59: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 59: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 59: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 59: 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 59: 59: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets 59: All statistics are over 5001 points 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 59: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 59: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm) 59: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 59: [ OK ] EnergyTest.ExtractEnergyMixed (12 ms) 59: [ RUN ] EnergyTest.ExtractEnergyWithNumberInName 59: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 59: 59: Select the terms you want from the following list by 59: selecting either (part of) the name or the number or a combination. 59: End your selection with an empty line or a zero. 59: ------------------------------------------------------------------- 59: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 59: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 59: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 59: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 59: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 59: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 59: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 59: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 59: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 59: 37 1/Viscosity 38 T-System 39 Lamb-System 59: 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 59: 59: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 1 data sets 59: All statistics are over 3 points (frames) 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 59: [ OK ] EnergyTest.ExtractEnergyWithNumberInName (0 ms) 59: [ RUN ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber 59: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 59: 59: Select the terms you want from the following list by 59: selecting either (part of) the name or the number or a combination. 59: End your selection with an empty line or a zero. 59: ------------------------------------------------------------------- 59: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 59: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 59: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 59: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 59: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 59: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 59: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 59: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 59: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 59: 37 1/Viscosity 38 T-System 39 Lamb-System 59: 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 59: 59: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 2 data sets 59: All statistics are over 3 points (frames) 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: LJ (SR) -14.1095 -- 0.384124 0.932214 (kJ/mol) 59: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 59: [ OK ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber (0 ms) 59: [----------] 5 tests from EnergyTest (15 ms total) 59: 59: [----------] 2 tests from ViscosityTest 59: [ RUN ] ViscosityTest.EinsteinViscosity 59: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 59: 59: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 59: All statistics are over 5001 points 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: Pres-XX 20.2092 65 717.193 185.978 (bar) 59: Pres-XY -47.7351 39 372.522 207.456 (bar) 59: Pres-XZ 11.477 31 379.79 6.80818 (bar) 59: Pres-YX -47.7106 39 372.525 207.5 (bar) 59: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 59: Pres-YZ -41.3534 45 401.216 114.663 (bar) 59: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 59: Pres-ZY -41.3119 45 401.196 114.743 (bar) 59: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 59: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 59: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 59: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 59: 59: Computing shear viscosity using the Einstein relation with 14 start points separated by 0.2 ps 59: [ OK ] ViscosityTest.EinsteinViscosity (150 ms) 59: [ RUN ] ViscosityTest.EinsteinViscosityIntegral 59: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 59: 59: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 59: All statistics are over 5001 points 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: Pres-XX 20.2092 65 717.193 185.978 (bar) 59: Pres-XY -47.7351 39 372.522 207.456 (bar) 59: Pres-XZ 11.477 31 379.79 6.80818 (bar) 59: Pres-YX -47.7106 39 372.525 207.5 (bar) 59: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 59: Pres-YZ -41.3534 45 401.216 114.663 (bar) 59: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 59: Pres-ZY -41.3119 45 401.196 114.743 (bar) 59: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 59: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 59: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 59: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 59: 59: Computing shear viscosity using the Einstein relation with 14 start points separated by 0.2 ps 59: [ OK ] ViscosityTest.EinsteinViscosityIntegral (147 ms) 59: [----------] 2 tests from ViscosityTest (298 ms total) 59: 59: [----------] Global test environment tear-down 59: [==========] 11 tests from 5 test suites ran. (333 ms total) 59: [ PASSED ] 11 tests. 59/91 Test #59: EnergyAnalysisUnitTests ...................... Passed 0.68 sec test 60 Start 60: ToolUnitTests 60: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/tool-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/ToolUnitTests.xml" 60: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests 60: Test timeout computed to be: 1920 60: [==========] Running 62 tests from 7 test suites. 60: [----------] Global test environment set-up. 60: [----------] 2 tests from DumpTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Setting the LD random seed to 804183991 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: [ RUN ] DumpTest.WorksWithTpr 60: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 60: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr: 60: inputrec: 60: integrator = md 60: tinit = 0 60: dt = 0.001 60: nsteps = 0 60: init-step = 0 60: simulation-part = 1 60: mts = false 60: mass-repartition-factor = 1 60: comm-mode = Linear 60: nstcomm = 100 60: bd-fric = 0 60: ld-seed = 804183991 60: emtol = 10 60: emstep = 0.01 60: niter = 20 60: fcstep = 0 60: nstcgsteep = 1000 60: nbfgscorr = 10 60: rtpi = 0.05 60: nstxout = 0 60: nstvout = 0 60: nstfout = 0 60: nstlog = 1000 60: nstcalcenergy = 100 60: nstenergy = 1000 60: nstxout-compressed = 0 60: compressed-x-precision = 1000 60: cutoff-scheme = Verlet 60: nstlist = 10 60: pbc = xyz 60: periodic-molecules = false 60: verlet-buffer-tolerance = -1 60: verlet-buffer-pressure-tolerance = 0.5 60: rlist = 1.1 60: coulombtype = Cut-off 60: coulomb-modifier = Potential-shift 60: rcoulomb-switch = 0 60: rcoulomb = 1 60: epsilon-r = 1 60: epsilon-rf = inf 60: vdw-type = Cut-off 60: vdw-modifier = Potential-shift 60: rvdw-switch = 0 60: rvdw = 1 60: DispCorr = No 60: table-extension = 1 60: fourierspacing = 0.12 60: fourier-nx = 0 60: fourier-ny = 0 60: fourier-nz = 0 60: pme-order = 4 60: ewald-rtol = 1e-05 60: ewald-rtol-lj = 0.001 60: lj-pme-comb-rule = Geometric 60: ewald-geometry = 3d 60: epsilon-surface = 0 60: ensemble-temperature-setting = not available 60: tcoupl = No 60: nsttcouple = -1 60: nh-chain-length = 0 60: print-nose-hoover-chain-variables = false 60: pcoupl = No 60: refcoord-scaling = No 60: posres-com (3): 60: posres-com[0]= 0.00000e+00 60: posres-com[1]= 0.00000e+00 60: posres-com[2]= 0.00000e+00 60: posres-comB (3): 60: posres-comB[0]= 0.00000e+00 60: posres-comB[1]= 0.00000e+00 60: posres-comB[2]= 0.00000e+00 60: QMMM = false 60: qm-opts: 60: ngQM = 0 60: constraint-algorithm = Lincs 60: continuation = false 60: Shake-SOR = false 60: shake-tol = 0.0001 60: lincs-order = 4 60: lincs-iter = 1 60: lincs-warnangle = 30 60: nwall = 0 60: wall-type = 9-3 60: wall-r-linpot = -1 60: wall-atomtype[0] = -1 60: wall-atomtype[1] = -1 60: wall-density[0] = 0 60: wall-density[1] = 0 60: wall-ewald-zfac = 3 60: pull = false 60: awh = false 60: rotation = false 60: interactiveMD = false 60: disre = No 60: disre-weighting = Conservative 60: disre-mixed = false 60: dr-fc = 1000 60: dr-tau = 0 60: nstdisreout = 100 60: orire-fc = 0 60: orire-tau = 0 60: nstorireout = 100 60: free-energy = no 60: cos-acceleration = 0 60: deform (3x3): 60: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: simulated-tempering = false 60: swapcoords = no 60: userint1 = 0 60: userint2 = 0 60: userint3 = 0 60: userint4 = 0 60: userreal1 = 0 60: userreal2 = 0 60: userreal3 = 0 60: userreal4 = 0 60: applied-forces: 60: electric-field: 60: x: 60: E0 = 0 60: omega = 0 60: t0 = 0 60: sigma = 0 60: y: 60: E0 = 0 60: omega = 0 60: t0 = 0 60: sigma = 0 60: z: 60: E0 = 0 60: omega = 0 60: t0 = 0 60: sigma = 0 60: density-guided-simulation: 60: active = false 60: group = protein 60: similarity-measure = inner-product 60: atom-spreading-weight = unity 60: force-constant = 1e+09 60: gaussian-transform-spreading-width = 0.2 60: gaussian-transform-spreading-range-in-multiples-of-width = 4 60: reference-density-filename = reference.mrc 60: nst = 1 60: normalize-densities = true 60: adaptive-force-scaling = false 60: adaptive-force-scaling-time-constant = 4 60: shift-vector = 60: transformation-matrix = 60: qmmm-cp2k: 60: active = false 60: qmgroup = System 60: qmmethod = PBE 60: qmfilenames = 60: qmcharge = 0 60: qmmultiplicity = 1 60: colvars: 60: active = false 60: configfile = 60: seed = -1 60: grpopts: 60: nrdf: 465 60: ref-t: 0 60: tau-t: 0 60: annealing: No 60: annealing-npoints: 0 60: acc: 0 0 0 60: nfreeze: N N N 60: energygrp-flags[ 0]: 0 60: header: 60: bIr = present 60: bBox = present 60: bTop = present 60: bX = present 60: bV = present 60: bF = not present 60: natoms = 156 60: lambda = 0.000000e+00 60: buffer size = 46180 60: topology: 60: name="First 10 residues from 1AKI" 60: #atoms = 156 60: #molblock = 1 60: molblock (0): 60: moltype = 0 "Protein_chain_B" 60: #molecules = 1 60: #posres_xA = 0 60: #posres_xB = 0 60: bIntermolecularInteractions = false 60: ffparams: 60: atnr=10 60: ntypes=212 60: functype[0]=LJ_SR, c6= 3.35274590e-03, c12= 3.95094276e-06 60: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[2]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06 60: functype[3]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07 60: functype[4]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06 60: functype[5]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06 60: functype[6]=LJ_SR, c6= 2.80388421e-03, c12= 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functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02 60: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02 60: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02 60: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02 60: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02 60: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02 60: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02 60: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02 60: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02 60: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39319992e+01, phiB= 1.80000000e+02, cpB= 4.39319992e+01, mult=2 60: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400002e+00, phiB= 1.80000000e+02, cpB= 4.18400002e+00, mult=2 60: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60239983e+00, phiB= 1.80000000e+02, cpB= 4.60239983e+00, mult=2 60: functype[143]=RBDIHS, rbcA[0]= 5.46010017e-01, rbcA[1]= 1.63803005e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405008e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 5.46010017e-01, rbcB[1]= 1.63803005e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405008e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[144]=RBDIHS, rbcA[0]= 7.25920022e-01, rbcA[1]= 2.17776990e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 7.25920022e-01, rbcB[1]= 2.17776990e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[145]=RBDIHS, rbcA[0]= 1.27611995e+00, rbcA[1]= 1.16734004e+00, rbcA[2]= 8.95380020e-01, rbcA[3]=-3.33884001e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 1.27611995e+00, rbcB[1]= 1.16734004e+00, rbcB[2]= 8.95380020e-01, rbcB[3]=-3.33884001e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[146]=RBDIHS, rbcA[0]=-6.91824007e+00, rbcA[1]= 4.67562008e+00, rbcA[2]= 2.24261999e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-6.91824007e+00, rbcB[1]= 4.67562008e+00, rbcB[2]= 2.24261999e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[147]=RBDIHS, rbcA[0]= 9.70690012e-01, rbcA[1]= 2.91206002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275003e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 9.70690012e-01, rbcB[1]= 2.91206002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275003e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[148]=RBDIHS, rbcA[0]= 6.27600014e-01, rbcA[1]= 1.88279998e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040006e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 6.27600014e-01, rbcB[1]= 1.88279998e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040006e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[149]=RBDIHS, rbcA[0]=-1.58989996e-01, rbcA[1]=-4.76980001e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35959983e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-1.58989996e-01, rbcB[1]=-4.76980001e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35959983e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654020e+00, rbcA[2]=-1.04934702e+01, rbcA[3]= 6.73623991e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654020e+00, rbcB[2]=-1.04934702e+01, rbcB[3]= 6.73623991e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[151]=RBDIHS, rbcA[0]= 5.00825024e+00, rbcA[1]=-1.69869995e+00, rbcA[2]=-3.72379988e-01, rbcA[3]=-2.93716002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 5.00825024e+00, rbcB[1]=-1.69869995e+00, rbcB[2]=-3.72379988e-01, rbcB[3]=-2.93716002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[152]=RBDIHS, rbcA[0]= 2.92880011e+00, rbcA[1]=-1.46440005e+00, rbcA[2]= 2.09199995e-01, rbcA[3]=-1.67359996e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 2.92880011e+00, rbcB[1]=-1.46440005e+00, rbcB[2]= 2.09199995e-01, rbcB[3]=-1.67359996e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[153]=RBDIHS, rbcA[0]= 5.77183008e+00, rbcA[1]=-2.67147994e+00, rbcA[2]= 9.58140016e-01, rbcA[3]=-4.05847979e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 5.77183008e+00, rbcB[1]=-2.67147994e+00, rbcB[2]= 9.58140016e-01, rbcB[3]=-4.05847979e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[154]=RBDIHS, rbcA[0]= 8.03330004e-01, rbcA[1]= 2.40999007e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 8.03330004e-01, rbcB[1]= 2.40999007e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[155]=RBDIHS, rbcA[0]= 2.05016003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 2.05016003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[156]=RBDIHS, rbcA[0]= 3.02879791e+01, rbcA[1]=-4.81160021e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.02879791e+01, rbcB[1]=-4.81160021e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[157]=RBDIHS, rbcA[0]= 2.54763794e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 2.54763794e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[158]=RBDIHS, rbcA[0]= 1.57025499e+01, rbcA[1]= 3.17565594e+01, rbcA[2]=-3.66935992e+00, rbcA[3]=-4.37897491e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 1.57025499e+01, rbcB[1]= 3.17565594e+01, rbcB[2]=-3.66935992e+00, rbcB[3]=-4.37897491e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[159]=RBDIHS, rbcA[0]=-1.03574896e+01, rbcA[1]=-2.95871601e+01, rbcA[2]=-1.16734004e+00, rbcA[3]= 4.11119919e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-1.03574896e+01, rbcB[1]=-2.95871601e+01, rbcB[2]=-1.16734004e+00, rbcB[3]= 4.11119919e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[160]=RBDIHS, rbcA[0]= 4.50198984e+00, rbcA[1]= 7.82410026e-01, rbcA[2]=-1.60247004e+00, rbcA[3]=-3.68192005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 4.50198984e+00, rbcB[1]= 7.82410026e-01, rbcB[2]=-1.60247004e+00, rbcB[3]=-3.68192005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[161]=RBDIHS, rbcA[0]= 4.22589988e-01, rbcA[1]= 2.70705009e+00, rbcA[2]=-3.12964010e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 4.22589988e-01, rbcB[1]= 2.70705009e+00, rbcB[2]=-3.12964010e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[162]=RBDIHS, rbcA[0]=-7.65670002e-01, rbcA[1]= 2.70705009e+00, rbcA[2]= 4.02501011e+00, rbcA[3]=-5.96639013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-7.65670002e-01, rbcB[1]= 2.70705009e+00, rbcB[2]= 4.02501011e+00, rbcB[3]=-5.96639013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[163]=RBDIHS, rbcA[0]= 9.66499984e-01, rbcA[1]= 2.89950991e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86600995e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 9.66499984e-01, rbcB[1]= 2.89950991e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86600995e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[164]=RBDIHS, rbcA[0]=-4.23421001e+00, rbcA[1]= 7.22159004e+00, rbcA[2]= 1.90789998e+00, rbcA[3]=-4.89527988e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-4.23421001e+00, rbcB[1]= 7.22159004e+00, rbcB[2]= 1.90789998e+00, rbcB[3]=-4.89527988e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[165]=RBDIHS, rbcA[0]= 3.03339996e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03339996e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.03339996e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03339996e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[166]=RBDIHS, rbcA[0]= 1.02319698e+01, rbcA[1]= 3.52082992e+00, rbcA[2]=-3.97899008e+00, rbcA[3]=-9.77381992e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 1.02319698e+01, rbcB[1]= 3.52082992e+00, rbcB[2]=-3.97899008e+00, rbcB[3]=-9.77381992e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[167]=RBDIHS, rbcA[0]= 5.49777985e+00, rbcA[1]= 1.41838002e+00, rbcA[2]=-6.91615009e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 5.49777985e+00, rbcB[1]= 1.41838002e+00, rbcB[2]=-6.91615009e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[168]=RBDIHS, rbcA[0]=-1.21755004e+00, rbcA[1]=-3.65264010e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-1.21755004e+00, rbcB[1]=-3.65264010e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[169]=RBDIHS, rbcA[0]=-1.26775002e+00, rbcA[1]= 3.02084994e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49781990e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-1.26775002e+00, rbcB[1]= 3.02084994e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49781990e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[170]=RBDIHS, rbcA[0]= 3.80117011e+00, rbcA[1]=-6.95172024e+00, rbcA[2]=-1.01671004e+00, rbcA[3]= 4.16726017e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.80117011e+00, rbcB[1]=-6.95172024e+00, rbcB[2]=-1.01671004e+00, rbcB[3]= 4.16726017e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[171]=RBDIHS, rbcA[0]= 3.70279998e-01, rbcA[1]= 1.11085999e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.70279998e-01, rbcB[1]= 1.11085999e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[172]=RBDIHS, rbcA[0]= 3.32042198e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042198e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.32042198e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042198e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[173]=RBDIHS, rbcA[0]= 1.63176003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 1.63176003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[174]=RBDIHS, rbcA[0]= 3.40787005e+00, rbcA[1]=-2.80537009e+00, rbcA[2]=-3.59820008e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.40787005e+00, rbcB[1]=-2.80537009e+00, rbcB[2]=-3.59820008e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[175]=RBDIHS, rbcA[0]=-1.62590199e+01, rbcA[1]= 9.08765030e+00, rbcA[2]= 7.17138004e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-1.62590199e+01, rbcB[1]= 9.08765030e+00, rbcB[2]= 7.17138004e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[176]=RBDIHS, rbcA[0]= 9.45590019e-01, rbcA[1]= 2.83675003e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 9.45590019e-01, rbcB[1]= 2.83675003e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[177]=RBDIHS, rbcA[0]=-1.50624001e+00, rbcA[1]= 5.37225008e+00, rbcA[2]= 1.17989004e+00, rbcA[3]=-5.04589987e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-1.50624001e+00, rbcB[1]= 5.37225008e+00, rbcB[2]= 1.17989004e+00, rbcB[3]=-5.04589987e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[178]=RBDIHS, rbcA[0]= 1.00416005e+00, rbcA[1]= 3.01248002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664019e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 1.00416005e+00, rbcB[1]= 3.01248002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664019e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[179]=RBDIHS, rbcA[0]= 8.79267979e+00, rbcA[1]=-1.18344402e+01, rbcA[2]= 1.07528996e+00, rbcA[3]= 1.96648002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 8.79267979e+00, rbcB[1]=-1.18344402e+01, rbcB[2]= 1.07528996e+00, rbcB[3]= 1.96648002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[180]=RBDIHS, rbcA[0]=-5.77392006e+00, rbcA[1]= 3.38485003e+00, rbcA[2]= 2.38906002e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-5.77392006e+00, rbcB[1]= 3.38485003e+00, rbcB[2]= 2.38906002e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[181]=RBDIHS, rbcA[0]=-9.08345985e+00, rbcA[1]= 9.75708961e+00, rbcA[2]= 3.45180011e+00, rbcA[3]=-4.12542009e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-9.08345985e+00, rbcB[1]= 9.75708961e+00, rbcB[2]= 3.45180011e+00, rbcB[3]=-4.12542009e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[182]=RBDIHS, rbcA[0]=-4.70699996e-01, rbcA[1]=-1.41209996e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88279998e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-4.70699996e-01, rbcB[1]=-1.41209996e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88279998e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[183]=RBDIHS, rbcA[0]= 3.43088007e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088007e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.43088007e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088007e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[184]=RBDIHS, rbcA[0]= 2.57315993e+00, rbcA[1]= 3.49781990e+00, rbcA[2]=-1.10038996e+00, rbcA[3]=-4.97059011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 2.57315993e+00, rbcB[1]= 3.49781990e+00, rbcB[2]=-1.10038996e+00, rbcB[3]=-4.97059011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[185]=RBDIHS, rbcA[0]=-8.22160006e-01, rbcA[1]= 1.12758994e+00, rbcA[2]=-3.05440009e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-8.22160006e-01, rbcB[1]= 1.12758994e+00, rbcB[2]=-3.05440009e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[186]=LJ14, c6A= 3.20536114e-04, c12A= 1.71928207e-07, c6B= 3.20536114e-04, c12B= 1.71928207e-07 60: functype[187]=LJ14, c6A= 1.30458479e-03, c12A= 1.92011203e-06, c6B= 1.30458479e-03, c12B= 1.92011203e-06 60: functype[188]=LJ14, c6A= 1.40760513e-03, c12A= 1.25315830e-06, c6B= 1.40760513e-03, c12B= 1.25315830e-06 60: functype[189]=LJ14, c6A= 1.67637295e-03, c12A= 1.97547138e-06, c6B= 1.67637295e-03, c12B= 1.97547138e-06 60: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00 60: functype[191]=LJ14, c6A= 2.49447097e-04, c12A= 1.67110088e-07, c6B= 2.49447097e-04, c12B= 1.67110088e-07 60: functype[192]=LJ14, c6A= 1.01525197e-03, c12A= 1.86630257e-06, c6B= 1.01525197e-03, c12B= 1.86630257e-06 60: functype[193]=LJ14, c6A= 6.12890653e-05, c12A= 1.49631507e-08, c6B= 6.12890653e-05, c12B= 1.49631507e-08 60: functype[194]=LJ14, c6A= 2.69145414e-04, c12A= 1.09064160e-07, c6B= 2.69145414e-04, c12B= 1.09064160e-07 60: functype[195]=LJ14, c6A= 1.09542510e-03, c12A= 1.21804135e-06, c6B= 1.09542510e-03, c12B= 1.21804135e-06 60: functype[196]=LJ14, c6A= 3.86982108e-04, c12A= 3.18863499e-07, c6B= 3.86982108e-04, c12B= 3.18863499e-07 60: functype[197]=LJ14, c6A= 1.57502061e-03, c12A= 3.56110013e-06, c6B= 1.57502061e-03, c12B= 3.56110013e-06 60: functype[198]=LJ14, c6A= 2.44342256e-03, c12A= 6.79494860e-06, c6B= 2.44342256e-03, c12B= 6.79494860e-06 60: functype[199]=LJ14, c6A= 1.40194211e-03, c12A= 2.15310411e-06, c6B= 1.40194211e-03, c12B= 2.15310411e-06 60: functype[200]=LJ14, c6A= 1.09101785e-03, c12A= 2.09276800e-06, c6B= 1.09101785e-03, c12B= 2.09276800e-06 60: functype[201]=LJ14, c6A= 2.68062693e-04, c12A= 1.87387855e-07, c6B= 2.68062693e-04, c12B= 1.87387855e-07 60: functype[202]=LJ14, c6A= 2.26258271e-04, c12A= 1.37484790e-07, c6B= 2.26258271e-04, c12B= 1.37484790e-07 60: functype[203]=LJ14, c6A= 2.43143426e-04, c12A= 1.54167822e-07, c6B= 2.43143426e-04, c12B= 1.54167822e-07 60: functype[204]=LJ14, c6A= 1.17243768e-03, c12A= 2.34671188e-06, c6B= 1.17243768e-03, c12B= 2.34671188e-06 60: functype[205]=LJ14, c6A= 1.69256027e-03, c12A= 3.99321743e-06, c6B= 1.69256027e-03, c12B= 3.99321743e-06 60: functype[206]=LJ14, c6A= 5.04237469e-05, c12A= 1.01280841e-08, c6B= 5.04237469e-05, c12B= 1.01280841e-08 60: functype[207]=LJ14, c6A= 2.34763342e-04, c12A= 1.14652082e-07, c6B= 2.34763342e-04, c12B= 1.14652082e-07 60: functype[208]=LJ14, c6A= 5.76812672e-05, c12A= 1.02660236e-08, c6B= 5.76812672e-05, c12B= 1.02660236e-08 60: functype[209]=LJ14, c6A= 3.60245234e-03, c12A= 5.76973571e-06, c6B= 3.60245234e-03, c12B= 5.76973571e-06 60: functype[210]=LJ14, c6A= 6.88817876e-04, c12A= 5.02148339e-07, c6B= 6.88817876e-04, c12B= 5.02148339e-07 60: functype[211]=LJ14, c6A= 4.34922846e-03, c12A= 1.07007354e-05, c6B= 4.34922846e-03, c12B= 1.07007354e-05 60: reppow = 12 60: fudgeQQ = 0.5 60: cmap 60: moltype (0): 60: name="Protein_chain_B" 60: atoms: 60: atom (156): 60: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 60: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 60: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 60: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 60: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6} 60: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 60: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 60: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 60: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6} 60: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 60: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 60: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 60: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 60: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6} 60: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8} 60: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7} 60: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1} 60: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6} 60: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6} 60: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 60: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 60: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6} 60: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8} 60: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7} 60: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1} 60: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6} 60: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 60: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6} 60: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 60: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 60: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 60: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 60: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 60: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 60: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 60: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 60: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 60: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 60: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 60: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 60: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 60: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6} 60: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8} 60: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7} 60: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1} 60: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6} 60: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 60: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 60: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6} 60: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8} 60: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7} 60: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1} 60: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6} 60: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6} 60: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6} 60: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6} 60: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7} 60: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1} 60: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6} 60: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 60: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 60: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 60: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 60: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 60: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 60: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6} 60: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8} 60: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7} 60: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1} 60: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6} 60: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 60: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6} 60: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 60: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 60: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16} 60: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1} 60: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6} 60: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8} 60: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7} 60: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1} 60: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6} 60: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 60: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6} 60: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 60: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 60: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6} 60: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 60: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 60: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6} 60: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 60: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 60: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6} 60: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8} 60: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7} 60: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1} 60: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6} 60: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6} 60: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6} 60: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 60: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 60: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6} 60: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8} 60: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7} 60: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1} 60: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6} 60: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 60: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6} 60: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 60: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 60: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 60: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6} 60: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8} 60: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7} 60: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1} 60: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6} 60: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 60: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6} 60: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 60: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 60: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 60: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6} 60: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8} 60: atom (156): 60: atom[0]={name="N"} 60: atom[1]={name="H1"} 60: atom[2]={name="H2"} 60: atom[3]={name="H3"} 60: atom[4]={name="CA"} 60: atom[5]={name="HA"} 60: atom[6]={name="CB"} 60: atom[7]={name="HB1"} 60: atom[8]={name="HB2"} 60: atom[9]={name="CG"} 60: atom[10]={name="HG1"} 60: atom[11]={name="HG2"} 60: atom[12]={name="CD"} 60: atom[13]={name="HD1"} 60: atom[14]={name="HD2"} 60: atom[15]={name="CE"} 60: atom[16]={name="HE1"} 60: atom[17]={name="HE2"} 60: atom[18]={name="NZ"} 60: atom[19]={name="HZ1"} 60: atom[20]={name="HZ2"} 60: atom[21]={name="HZ3"} 60: atom[22]={name="C"} 60: atom[23]={name="O"} 60: atom[24]={name="N"} 60: atom[25]={name="H"} 60: atom[26]={name="CA"} 60: atom[27]={name="HA"} 60: atom[28]={name="CB"} 60: atom[29]={name="HB"} 60: atom[30]={name="CG1"} 60: atom[31]={name="HG11"} 60: atom[32]={name="HG12"} 60: atom[33]={name="HG13"} 60: atom[34]={name="CG2"} 60: atom[35]={name="HG21"} 60: atom[36]={name="HG22"} 60: atom[37]={name="HG23"} 60: atom[38]={name="C"} 60: atom[39]={name="O"} 60: atom[40]={name="N"} 60: atom[41]={name="H"} 60: atom[42]={name="CA"} 60: atom[43]={name="HA"} 60: atom[44]={name="CB"} 60: atom[45]={name="HB1"} 60: atom[46]={name="HB2"} 60: atom[47]={name="CG"} 60: atom[48]={name="CD1"} 60: atom[49]={name="HD1"} 60: atom[50]={name="CD2"} 60: atom[51]={name="HD2"} 60: atom[52]={name="CE1"} 60: atom[53]={name="HE1"} 60: atom[54]={name="CE2"} 60: atom[55]={name="HE2"} 60: atom[56]={name="CZ"} 60: atom[57]={name="HZ"} 60: atom[58]={name="C"} 60: atom[59]={name="O"} 60: atom[60]={name="N"} 60: atom[61]={name="H"} 60: atom[62]={name="CA"} 60: atom[63]={name="HA1"} 60: atom[64]={name="HA2"} 60: atom[65]={name="C"} 60: atom[66]={name="O"} 60: atom[67]={name="N"} 60: atom[68]={name="H"} 60: atom[69]={name="CA"} 60: atom[70]={name="HA"} 60: atom[71]={name="CB"} 60: atom[72]={name="HB1"} 60: atom[73]={name="HB2"} 60: atom[74]={name="CG"} 60: atom[75]={name="HG1"} 60: atom[76]={name="HG2"} 60: atom[77]={name="CD"} 60: atom[78]={name="HD1"} 60: atom[79]={name="HD2"} 60: atom[80]={name="NE"} 60: atom[81]={name="HE"} 60: atom[82]={name="CZ"} 60: atom[83]={name="NH1"} 60: atom[84]={name="HH11"} 60: atom[85]={name="HH12"} 60: atom[86]={name="NH2"} 60: atom[87]={name="HH21"} 60: atom[88]={name="HH22"} 60: atom[89]={name="C"} 60: atom[90]={name="O"} 60: atom[91]={name="N"} 60: atom[92]={name="H"} 60: atom[93]={name="CA"} 60: atom[94]={name="HA"} 60: atom[95]={name="CB"} 60: atom[96]={name="HB1"} 60: atom[97]={name="HB2"} 60: atom[98]={name="SG"} 60: atom[99]={name="HG"} 60: atom[100]={name="C"} 60: atom[101]={name="O"} 60: atom[102]={name="N"} 60: atom[103]={name="H"} 60: atom[104]={name="CA"} 60: atom[105]={name="HA"} 60: atom[106]={name="CB"} 60: atom[107]={name="HB1"} 60: atom[108]={name="HB2"} 60: atom[109]={name="CG"} 60: atom[110]={name="HG1"} 60: atom[111]={name="HG2"} 60: atom[112]={name="CD"} 60: atom[113]={name="OE1"} 60: atom[114]={name="OE2"} 60: atom[115]={name="C"} 60: atom[116]={name="O"} 60: atom[117]={name="N"} 60: atom[118]={name="H"} 60: atom[119]={name="CA"} 60: atom[120]={name="HA"} 60: atom[121]={name="CB"} 60: atom[122]={name="HB1"} 60: atom[123]={name="HB2"} 60: atom[124]={name="CG"} 60: atom[125]={name="HG"} 60: atom[126]={name="CD1"} 60: atom[127]={name="HD11"} 60: atom[128]={name="HD12"} 60: atom[129]={name="HD13"} 60: atom[130]={name="CD2"} 60: atom[131]={name="HD21"} 60: atom[132]={name="HD22"} 60: atom[133]={name="HD23"} 60: atom[134]={name="C"} 60: atom[135]={name="O"} 60: atom[136]={name="N"} 60: atom[137]={name="H"} 60: atom[138]={name="CA"} 60: atom[139]={name="HA"} 60: atom[140]={name="CB"} 60: atom[141]={name="HB1"} 60: atom[142]={name="HB2"} 60: atom[143]={name="HB3"} 60: atom[144]={name="C"} 60: atom[145]={name="O"} 60: atom[146]={name="N"} 60: atom[147]={name="H"} 60: atom[148]={name="CA"} 60: atom[149]={name="HA"} 60: atom[150]={name="CB"} 60: atom[151]={name="HB1"} 60: atom[152]={name="HB2"} 60: atom[153]={name="HB3"} 60: atom[154]={name="C"} 60: atom[155]={name="O"} 60: type (156): 60: type[0]={name="opls_287",nameB="opls_287"} 60: type[1]={name="opls_290",nameB="opls_290"} 60: type[2]={name="opls_290",nameB="opls_290"} 60: type[3]={name="opls_290",nameB="opls_290"} 60: type[4]={name="opls_293B",nameB="opls_293B"} 60: type[5]={name="opls_140",nameB="opls_140"} 60: type[6]={name="opls_136",nameB="opls_136"} 60: type[7]={name="opls_140",nameB="opls_140"} 60: type[8]={name="opls_140",nameB="opls_140"} 60: type[9]={name="opls_136",nameB="opls_136"} 60: type[10]={name="opls_140",nameB="opls_140"} 60: type[11]={name="opls_140",nameB="opls_140"} 60: type[12]={name="opls_136",nameB="opls_136"} 60: type[13]={name="opls_140",nameB="opls_140"} 60: type[14]={name="opls_140",nameB="opls_140"} 60: type[15]={name="opls_292",nameB="opls_292"} 60: type[16]={name="opls_140",nameB="opls_140"} 60: type[17]={name="opls_140",nameB="opls_140"} 60: type[18]={name="opls_287",nameB="opls_287"} 60: type[19]={name="opls_290",nameB="opls_290"} 60: type[20]={name="opls_290",nameB="opls_290"} 60: type[21]={name="opls_290",nameB="opls_290"} 60: type[22]={name="opls_235",nameB="opls_235"} 60: type[23]={name="opls_236",nameB="opls_236"} 60: type[24]={name="opls_238",nameB="opls_238"} 60: type[25]={name="opls_241",nameB="opls_241"} 60: type[26]={name="opls_224B",nameB="opls_224B"} 60: type[27]={name="opls_140",nameB="opls_140"} 60: type[28]={name="opls_137",nameB="opls_137"} 60: type[29]={name="opls_140",nameB="opls_140"} 60: type[30]={name="opls_135",nameB="opls_135"} 60: type[31]={name="opls_140",nameB="opls_140"} 60: type[32]={name="opls_140",nameB="opls_140"} 60: type[33]={name="opls_140",nameB="opls_140"} 60: type[34]={name="opls_135",nameB="opls_135"} 60: type[35]={name="opls_140",nameB="opls_140"} 60: type[36]={name="opls_140",nameB="opls_140"} 60: type[37]={name="opls_140",nameB="opls_140"} 60: type[38]={name="opls_235",nameB="opls_235"} 60: type[39]={name="opls_236",nameB="opls_236"} 60: type[40]={name="opls_238",nameB="opls_238"} 60: type[41]={name="opls_241",nameB="opls_241"} 60: type[42]={name="opls_224B",nameB="opls_224B"} 60: type[43]={name="opls_140",nameB="opls_140"} 60: type[44]={name="opls_149",nameB="opls_149"} 60: type[45]={name="opls_140",nameB="opls_140"} 60: type[46]={name="opls_140",nameB="opls_140"} 60: type[47]={name="opls_145",nameB="opls_145"} 60: type[48]={name="opls_145",nameB="opls_145"} 60: type[49]={name="opls_146",nameB="opls_146"} 60: type[50]={name="opls_145",nameB="opls_145"} 60: type[51]={name="opls_146",nameB="opls_146"} 60: type[52]={name="opls_145",nameB="opls_145"} 60: type[53]={name="opls_146",nameB="opls_146"} 60: type[54]={name="opls_145",nameB="opls_145"} 60: type[55]={name="opls_146",nameB="opls_146"} 60: type[56]={name="opls_145",nameB="opls_145"} 60: type[57]={name="opls_146",nameB="opls_146"} 60: type[58]={name="opls_235",nameB="opls_235"} 60: type[59]={name="opls_236",nameB="opls_236"} 60: type[60]={name="opls_238",nameB="opls_238"} 60: type[61]={name="opls_241",nameB="opls_241"} 60: type[62]={name="opls_223B",nameB="opls_223B"} 60: type[63]={name="opls_140",nameB="opls_140"} 60: type[64]={name="opls_140",nameB="opls_140"} 60: type[65]={name="opls_235",nameB="opls_235"} 60: type[66]={name="opls_236",nameB="opls_236"} 60: type[67]={name="opls_238",nameB="opls_238"} 60: type[68]={name="opls_241",nameB="opls_241"} 60: type[69]={name="opls_224B",nameB="opls_224B"} 60: type[70]={name="opls_140",nameB="opls_140"} 60: type[71]={name="opls_136",nameB="opls_136"} 60: type[72]={name="opls_140",nameB="opls_140"} 60: type[73]={name="opls_140",nameB="opls_140"} 60: type[74]={name="opls_308",nameB="opls_308"} 60: type[75]={name="opls_140",nameB="opls_140"} 60: type[76]={name="opls_140",nameB="opls_140"} 60: type[77]={name="opls_307",nameB="opls_307"} 60: type[78]={name="opls_140",nameB="opls_140"} 60: type[79]={name="opls_140",nameB="opls_140"} 60: type[80]={name="opls_303",nameB="opls_303"} 60: type[81]={name="opls_304",nameB="opls_304"} 60: type[82]={name="opls_302",nameB="opls_302"} 60: type[83]={name="opls_300",nameB="opls_300"} 60: type[84]={name="opls_301",nameB="opls_301"} 60: type[85]={name="opls_301",nameB="opls_301"} 60: type[86]={name="opls_300",nameB="opls_300"} 60: type[87]={name="opls_301",nameB="opls_301"} 60: type[88]={name="opls_301",nameB="opls_301"} 60: type[89]={name="opls_235",nameB="opls_235"} 60: type[90]={name="opls_236",nameB="opls_236"} 60: type[91]={name="opls_238",nameB="opls_238"} 60: type[92]={name="opls_241",nameB="opls_241"} 60: type[93]={name="opls_224B",nameB="opls_224B"} 60: type[94]={name="opls_140",nameB="opls_140"} 60: type[95]={name="opls_206",nameB="opls_206"} 60: type[96]={name="opls_140",nameB="opls_140"} 60: type[97]={name="opls_140",nameB="opls_140"} 60: type[98]={name="opls_200",nameB="opls_200"} 60: type[99]={name="opls_204",nameB="opls_204"} 60: type[100]={name="opls_235",nameB="opls_235"} 60: type[101]={name="opls_236",nameB="opls_236"} 60: type[102]={name="opls_238",nameB="opls_238"} 60: type[103]={name="opls_241",nameB="opls_241"} 60: type[104]={name="opls_224B",nameB="opls_224B"} 60: type[105]={name="opls_140",nameB="opls_140"} 60: type[106]={name="opls_136",nameB="opls_136"} 60: type[107]={name="opls_140",nameB="opls_140"} 60: type[108]={name="opls_140",nameB="opls_140"} 60: type[109]={name="opls_274",nameB="opls_274"} 60: type[110]={name="opls_140",nameB="opls_140"} 60: type[111]={name="opls_140",nameB="opls_140"} 60: type[112]={name="opls_271",nameB="opls_271"} 60: type[113]={name="opls_272",nameB="opls_272"} 60: type[114]={name="opls_272",nameB="opls_272"} 60: type[115]={name="opls_235",nameB="opls_235"} 60: type[116]={name="opls_236",nameB="opls_236"} 60: type[117]={name="opls_238",nameB="opls_238"} 60: type[118]={name="opls_241",nameB="opls_241"} 60: type[119]={name="opls_224B",nameB="opls_224B"} 60: type[120]={name="opls_140",nameB="opls_140"} 60: type[121]={name="opls_136",nameB="opls_136"} 60: type[122]={name="opls_140",nameB="opls_140"} 60: type[123]={name="opls_140",nameB="opls_140"} 60: type[124]={name="opls_137",nameB="opls_137"} 60: type[125]={name="opls_140",nameB="opls_140"} 60: type[126]={name="opls_135",nameB="opls_135"} 60: type[127]={name="opls_140",nameB="opls_140"} 60: type[128]={name="opls_140",nameB="opls_140"} 60: type[129]={name="opls_140",nameB="opls_140"} 60: type[130]={name="opls_135",nameB="opls_135"} 60: type[131]={name="opls_140",nameB="opls_140"} 60: type[132]={name="opls_140",nameB="opls_140"} 60: type[133]={name="opls_140",nameB="opls_140"} 60: type[134]={name="opls_235",nameB="opls_235"} 60: type[135]={name="opls_236",nameB="opls_236"} 60: type[136]={name="opls_238",nameB="opls_238"} 60: type[137]={name="opls_241",nameB="opls_241"} 60: type[138]={name="opls_224B",nameB="opls_224B"} 60: type[139]={name="opls_140",nameB="opls_140"} 60: type[140]={name="opls_135",nameB="opls_135"} 60: type[141]={name="opls_140",nameB="opls_140"} 60: type[142]={name="opls_140",nameB="opls_140"} 60: type[143]={name="opls_140",nameB="opls_140"} 60: type[144]={name="opls_235",nameB="opls_235"} 60: type[145]={name="opls_236",nameB="opls_236"} 60: type[146]={name="opls_238",nameB="opls_238"} 60: type[147]={name="opls_241",nameB="opls_241"} 60: type[148]={name="opls_224B",nameB="opls_224B"} 60: type[149]={name="opls_140",nameB="opls_140"} 60: type[150]={name="opls_135",nameB="opls_135"} 60: type[151]={name="opls_140",nameB="opls_140"} 60: type[152]={name="opls_140",nameB="opls_140"} 60: type[153]={name="opls_140",nameB="opls_140"} 60: type[154]={name="opls_235",nameB="opls_235"} 60: type[155]={name="opls_236",nameB="opls_236"} 60: residue (10): 60: residue[0]={name="LYS", nr=1, ic=' '} 60: residue[1]={name="VAL", nr=2, ic=' '} 60: residue[2]={name="PHE", nr=3, ic=' '} 60: residue[3]={name="GLY", nr=4, ic=' '} 60: residue[4]={name="ARG", nr=5, ic=' '} 60: residue[5]={name="CYS", nr=6, ic=' '} 60: residue[6]={name="GLU", nr=7, ic=' '} 60: residue[7]={name="LEU", nr=8, ic=' '} 60: residue[8]={name="ALA", nr=9, ic=' '} 60: residue[9]={name="ALA", nr=10, ic=' '} 60: excls: 60: numLists=156 60: numElements=1828 60: excls[0][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 60: excls[1][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 60: excls[2][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 60: excls[3][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 60: excls[4][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 60: 23, 24, 25, 26} 60: excls[5][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 60: excls[6][num=19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 60: 14, 15, 22, 23, 24} 60: excls[7][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 60: excls[8][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 60: excls[9][num=17]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 60: 16, 17, 18, 22} 60: excls[10][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 60: excls[11][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 60: excls[12][num=17]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 60: 17, 18, 19, 20, 21} 60: excls[13][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 60: excls[14][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 60: excls[15][num=14]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 60: 20, 21} 60: excls[16][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 60: excls[17][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 60: excls[18][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 60: excls[19][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 60: excls[20][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 60: excls[21][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 60: excls[22][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 60: 26, 27, 28, 38} 60: excls[23][num=9]={0, 4, 5, 6, 22, 23, 24, 25, 26} 60: excls[24][num=17]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 60: 30, 34, 38, 39, 40} 60: excls[25][num=9]={4, 22, 23, 24, 25, 26, 27, 28, 38} 60: excls[26][num=22]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 60: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42} 60: excls[27][num=12]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 60: 40} 60: excls[28][num=18]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 60: 34, 35, 36, 37, 38, 39, 40} 60: excls[29][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 60: 36, 37, 38} 60: excls[30][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 60: 36, 37, 38} 60: excls[31][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 60: excls[32][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 60: excls[33][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 60: excls[34][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 60: 36, 37, 38} 60: excls[35][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 60: excls[36][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 60: excls[37][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 60: excls[38][num=17]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 60: 40, 41, 42, 43, 44, 58} 60: excls[39][num=9]={24, 26, 27, 28, 38, 39, 40, 41, 42} 60: excls[40][num=17]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 60: 45, 46, 47, 58, 59, 60} 60: excls[41][num=9]={26, 38, 39, 40, 41, 42, 43, 44, 58} 60: excls[42][num=18]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 60: 48, 50, 58, 59, 60, 61, 62} 60: excls[43][num=12]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 60: 60} 60: excls[44][num=18]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 60: 50, 51, 52, 54, 58, 59, 60} 60: excls[45][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 60: excls[46][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 60: excls[47][num=17]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 60: 52, 53, 54, 55, 56, 58} 60: excls[48][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 60: 54, 56, 57} 60: excls[49][num=8]={44, 47, 48, 49, 50, 52, 53, 56} 60: excls[50][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 60: 55, 56, 57} 60: excls[51][num=8]={44, 47, 48, 50, 51, 54, 55, 56} 60: excls[52][num=11]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57} 60: excls[53][num=8]={47, 48, 49, 52, 53, 54, 56, 57} 60: excls[54][num=11]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57} 60: excls[55][num=8]={47, 50, 51, 52, 54, 55, 56, 57} 60: excls[56][num=11]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57} 60: excls[57][num=8]={48, 50, 52, 53, 54, 55, 56, 57} 60: excls[58][num=17]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 60: 60, 61, 62, 63, 64, 65} 60: excls[59][num=9]={40, 42, 43, 44, 58, 59, 60, 61, 62} 60: excls[60][num=14]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64, 60: 65, 66, 67} 60: excls[61][num=9]={42, 58, 59, 60, 61, 62, 63, 64, 65} 60: excls[62][num=13]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 60: 68, 69} 60: excls[63][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 60: excls[64][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 60: excls[65][num=14]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 60: 70, 71, 89} 60: excls[66][num=9]={60, 62, 63, 64, 65, 66, 67, 68, 69} 60: excls[67][num=17]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 60: 72, 73, 74, 89, 90, 91} 60: excls[68][num=9]={62, 65, 66, 67, 68, 69, 70, 71, 89} 60: excls[69][num=19]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 60: 75, 76, 77, 89, 90, 91, 92, 93} 60: excls[70][num=12]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 60: 91} 60: excls[71][num=18]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 60: 77, 78, 79, 80, 89, 90, 91} 60: excls[72][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 60: excls[73][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 60: excls[74][num=16]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 60: 79, 80, 81, 82, 89} 60: excls[75][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 60: excls[76][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 60: excls[77][num=15]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 60: 81, 82, 83, 86} 60: excls[78][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 60: excls[79][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 60: excls[80][num=16]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 60: 84, 85, 86, 87, 88} 60: excls[81][num=9]={74, 77, 78, 79, 80, 81, 82, 83, 86} 60: excls[82][num=13]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 60: 87, 88} 60: excls[83][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 60: excls[84][num=6]={80, 82, 83, 84, 85, 86} 60: excls[85][num=6]={80, 82, 83, 84, 85, 86} 60: excls[86][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 60: excls[87][num=6]={80, 82, 83, 86, 87, 88} 60: excls[88][num=6]={80, 82, 83, 86, 87, 88} 60: excls[89][num=17]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 60: 91, 92, 93, 94, 95, 100} 60: excls[90][num=9]={67, 69, 70, 71, 89, 90, 91, 92, 93} 60: excls[91][num=17]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94, 95, 60: 96, 97, 98, 100, 101, 102} 60: excls[92][num=9]={69, 89, 90, 91, 92, 93, 94, 95, 100} 60: excls[93][num=17]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 60: 99, 100, 101, 102, 103, 104} 60: excls[94][num=12]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 60: 102} 60: excls[95][num=13]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 60: 101, 102} 60: excls[96][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 60: excls[97][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 60: excls[98][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 60: excls[99][num=6]={93, 95, 96, 97, 98, 99} 60: excls[100][num=17]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 60: 102, 103, 104, 105, 106, 115} 60: excls[101][num=9]={91, 93, 94, 95, 100, 101, 102, 103, 104} 60: excls[102][num=17]={91, 93, 94, 95, 100, 101, 102, 103, 104, 105, 60: 106, 107, 108, 109, 115, 116, 117} 60: excls[103][num=9]={93, 100, 101, 102, 103, 104, 105, 106, 115} 60: excls[104][num=19]={93, 100, 101, 102, 103, 104, 105, 106, 107, 60: 108, 109, 110, 111, 112, 115, 116, 117, 118, 119} 60: excls[105][num=12]={100, 102, 103, 104, 105, 106, 107, 108, 109, 60: 115, 116, 117} 60: excls[106][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 60: 110, 111, 112, 113, 114, 115, 116, 117} 60: excls[107][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 60: 112, 115} 60: excls[108][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 60: 112, 115} 60: excls[109][num=13]={102, 104, 105, 106, 107, 108, 109, 110, 111, 60: 112, 113, 114, 115} 60: excls[110][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 60: 114} 60: excls[111][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 60: 114} 60: excls[112][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 60: 114} 60: excls[113][num=7]={106, 109, 110, 111, 112, 113, 114} 60: excls[114][num=7]={106, 109, 110, 111, 112, 113, 114} 60: excls[115][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 60: 115, 116, 117, 118, 119, 120, 121, 134} 60: excls[116][num=9]={102, 104, 105, 106, 115, 116, 117, 118, 119} 60: excls[117][num=17]={102, 104, 105, 106, 115, 116, 117, 118, 119, 60: 120, 121, 122, 123, 124, 134, 135, 136} 60: excls[118][num=9]={104, 115, 116, 117, 118, 119, 120, 121, 134} 60: excls[119][num=19]={104, 115, 116, 117, 118, 119, 120, 121, 122, 60: 123, 124, 125, 126, 130, 134, 135, 136, 137, 138} 60: excls[120][num=12]={115, 117, 118, 119, 120, 121, 122, 123, 124, 60: 134, 135, 136} 60: excls[121][num=21]={115, 117, 118, 119, 120, 121, 122, 123, 124, 60: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136} 60: excls[122][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 60: 130, 134} 60: excls[123][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 60: 130, 134} 60: excls[124][num=17]={117, 119, 120, 121, 122, 123, 124, 125, 126, 60: 127, 128, 129, 130, 131, 132, 133, 134} 60: excls[125][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 60: 129, 130, 131, 132, 133} 60: excls[126][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 60: 129, 130, 131, 132, 133} 60: excls[127][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 60: excls[128][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 60: excls[129][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 60: excls[130][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 60: 129, 130, 131, 132, 133} 60: excls[131][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 60: excls[132][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 60: excls[133][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 60: excls[134][num=17]={115, 117, 118, 119, 120, 121, 122, 123, 124, 60: 134, 135, 136, 137, 138, 139, 140, 144} 60: excls[135][num=9]={117, 119, 120, 121, 134, 135, 136, 137, 138} 60: excls[136][num=17]={117, 119, 120, 121, 134, 135, 136, 137, 138, 60: 139, 140, 141, 142, 143, 144, 145, 146} 60: excls[137][num=9]={119, 134, 135, 136, 137, 138, 139, 140, 144} 60: excls[138][num=16]={119, 134, 135, 136, 137, 138, 139, 140, 141, 60: 142, 143, 144, 145, 146, 147, 148} 60: excls[139][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 60: 144, 145, 146} 60: excls[140][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 60: 144, 145, 146} 60: excls[141][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 60: excls[142][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 60: excls[143][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 60: excls[144][num=17]={134, 136, 137, 138, 139, 140, 141, 142, 143, 60: 144, 145, 146, 147, 148, 149, 150, 154} 60: excls[145][num=9]={136, 138, 139, 140, 144, 145, 146, 147, 148} 60: excls[146][num=16]={136, 138, 139, 140, 144, 145, 146, 147, 148, 60: 149, 150, 151, 152, 153, 154, 155} 60: excls[147][num=9]={138, 144, 145, 146, 147, 148, 149, 150, 154} 60: excls[148][num=13]={138, 144, 145, 146, 147, 148, 149, 150, 151, 60: 152, 153, 154, 155} 60: excls[149][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 60: 154, 155} 60: excls[150][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 60: 154, 155} 60: excls[151][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 60: excls[152][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 60: excls[153][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 60: excls[154][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 60: 154, 155} 60: excls[155][num=6]={146, 148, 149, 150, 154, 155} 60: Bond: 60: nr: 468 60: iatoms: 60: 0 type=100 (BONDS) 0 1 60: 1 type=100 (BONDS) 0 2 60: 2 type=100 (BONDS) 0 3 60: 3 type=101 (BONDS) 0 4 60: 4 type=102 (BONDS) 4 5 60: 5 type=103 (BONDS) 4 6 60: 6 type=104 (BONDS) 4 22 60: 7 type=102 (BONDS) 6 7 60: 8 type=102 (BONDS) 6 8 60: 9 type=103 (BONDS) 6 9 60: 10 type=102 (BONDS) 9 10 60: 11 type=102 (BONDS) 9 11 60: 12 type=103 (BONDS) 9 12 60: 13 type=102 (BONDS) 12 13 60: 14 type=102 (BONDS) 12 14 60: 15 type=103 (BONDS) 12 15 60: 16 type=102 (BONDS) 15 16 60: 17 type=102 (BONDS) 15 17 60: 18 type=101 (BONDS) 15 18 60: 19 type=100 (BONDS) 18 19 60: 20 type=100 (BONDS) 18 20 60: 21 type=100 (BONDS) 18 21 60: 22 type=105 (BONDS) 22 23 60: 23 type=106 (BONDS) 22 24 60: 24 type=100 (BONDS) 24 25 60: 25 type=107 (BONDS) 24 26 60: 26 type=102 (BONDS) 26 27 60: 27 type=103 (BONDS) 26 28 60: 28 type=104 (BONDS) 26 38 60: 29 type=102 (BONDS) 28 29 60: 30 type=103 (BONDS) 28 30 60: 31 type=103 (BONDS) 28 34 60: 32 type=102 (BONDS) 30 31 60: 33 type=102 (BONDS) 30 32 60: 34 type=102 (BONDS) 30 33 60: 35 type=102 (BONDS) 34 35 60: 36 type=102 (BONDS) 34 36 60: 37 type=102 (BONDS) 34 37 60: 38 type=105 (BONDS) 38 39 60: 39 type=106 (BONDS) 38 40 60: 40 type=100 (BONDS) 40 41 60: 41 type=107 (BONDS) 40 42 60: 42 type=102 (BONDS) 42 43 60: 43 type=103 (BONDS) 42 44 60: 44 type=104 (BONDS) 42 58 60: 45 type=102 (BONDS) 44 45 60: 46 type=102 (BONDS) 44 46 60: 47 type=108 (BONDS) 44 47 60: 48 type=109 (BONDS) 47 48 60: 49 type=109 (BONDS) 47 50 60: 50 type=110 (BONDS) 48 49 60: 51 type=109 (BONDS) 48 52 60: 52 type=110 (BONDS) 50 51 60: 53 type=109 (BONDS) 50 54 60: 54 type=110 (BONDS) 52 53 60: 55 type=109 (BONDS) 52 56 60: 56 type=110 (BONDS) 54 55 60: 57 type=109 (BONDS) 54 56 60: 58 type=110 (BONDS) 56 57 60: 59 type=105 (BONDS) 58 59 60: 60 type=106 (BONDS) 58 60 60: 61 type=100 (BONDS) 60 61 60: 62 type=107 (BONDS) 60 62 60: 63 type=102 (BONDS) 62 63 60: 64 type=102 (BONDS) 62 64 60: 65 type=104 (BONDS) 62 65 60: 66 type=105 (BONDS) 65 66 60: 67 type=106 (BONDS) 65 67 60: 68 type=100 (BONDS) 67 68 60: 69 type=107 (BONDS) 67 69 60: 70 type=102 (BONDS) 69 70 60: 71 type=103 (BONDS) 69 71 60: 72 type=104 (BONDS) 69 89 60: 73 type=102 (BONDS) 71 72 60: 74 type=102 (BONDS) 71 73 60: 75 type=103 (BONDS) 71 74 60: 76 type=102 (BONDS) 74 75 60: 77 type=102 (BONDS) 74 76 60: 78 type=103 (BONDS) 74 77 60: 79 type=102 (BONDS) 77 78 60: 80 type=102 (BONDS) 77 79 60: 81 type=111 (BONDS) 77 80 60: 82 type=100 (BONDS) 80 81 60: 83 type=112 (BONDS) 80 82 60: 84 type=112 (BONDS) 82 83 60: 85 type=112 (BONDS) 82 86 60: 86 type=100 (BONDS) 83 84 60: 87 type=100 (BONDS) 83 85 60: 88 type=100 (BONDS) 86 87 60: 89 type=100 (BONDS) 86 88 60: 90 type=105 (BONDS) 89 90 60: 91 type=106 (BONDS) 89 91 60: 92 type=100 (BONDS) 91 92 60: 93 type=107 (BONDS) 91 93 60: 94 type=102 (BONDS) 93 94 60: 95 type=103 (BONDS) 93 95 60: 96 type=104 (BONDS) 93 100 60: 97 type=102 (BONDS) 95 96 60: 98 type=102 (BONDS) 95 97 60: 99 type=113 (BONDS) 95 98 60: 100 type=114 (BONDS) 98 99 60: 101 type=105 (BONDS) 100 101 60: 102 type=106 (BONDS) 100 102 60: 103 type=100 (BONDS) 102 103 60: 104 type=107 (BONDS) 102 104 60: 105 type=102 (BONDS) 104 105 60: 106 type=103 (BONDS) 104 106 60: 107 type=104 (BONDS) 104 115 60: 108 type=102 (BONDS) 106 107 60: 109 type=102 (BONDS) 106 108 60: 110 type=103 (BONDS) 106 109 60: 111 type=102 (BONDS) 109 110 60: 112 type=102 (BONDS) 109 111 60: 113 type=104 (BONDS) 109 112 60: 114 type=115 (BONDS) 112 113 60: 115 type=115 (BONDS) 112 114 60: 116 type=105 (BONDS) 115 116 60: 117 type=106 (BONDS) 115 117 60: 118 type=100 (BONDS) 117 118 60: 119 type=107 (BONDS) 117 119 60: 120 type=102 (BONDS) 119 120 60: 121 type=103 (BONDS) 119 121 60: 122 type=104 (BONDS) 119 134 60: 123 type=102 (BONDS) 121 122 60: 124 type=102 (BONDS) 121 123 60: 125 type=103 (BONDS) 121 124 60: 126 type=102 (BONDS) 124 125 60: 127 type=103 (BONDS) 124 126 60: 128 type=103 (BONDS) 124 130 60: 129 type=102 (BONDS) 126 127 60: 130 type=102 (BONDS) 126 128 60: 131 type=102 (BONDS) 126 129 60: 132 type=102 (BONDS) 130 131 60: 133 type=102 (BONDS) 130 132 60: 134 type=102 (BONDS) 130 133 60: 135 type=105 (BONDS) 134 135 60: 136 type=106 (BONDS) 134 136 60: 137 type=100 (BONDS) 136 137 60: 138 type=107 (BONDS) 136 138 60: 139 type=102 (BONDS) 138 139 60: 140 type=103 (BONDS) 138 140 60: 141 type=104 (BONDS) 138 144 60: 142 type=102 (BONDS) 140 141 60: 143 type=102 (BONDS) 140 142 60: 144 type=102 (BONDS) 140 143 60: 145 type=105 (BONDS) 144 145 60: 146 type=106 (BONDS) 144 146 60: 147 type=100 (BONDS) 146 147 60: 148 type=107 (BONDS) 146 148 60: 149 type=102 (BONDS) 148 149 60: 150 type=103 (BONDS) 148 150 60: 151 type=104 (BONDS) 148 154 60: 152 type=102 (BONDS) 150 151 60: 153 type=102 (BONDS) 150 152 60: 154 type=102 (BONDS) 150 153 60: 155 type=105 (BONDS) 154 155 60: G96Bond: 60: nr: 0 60: Morse: 60: nr: 0 60: Cubic Bonds: 60: nr: 0 60: Connect Bonds: 60: nr: 0 60: Harmonic Pot.: 60: nr: 0 60: FENE Bonds: 60: nr: 0 60: Tab. Bonds: 60: nr: 0 60: Tab. Bonds NC: 60: nr: 0 60: Restraint Pot.: 60: nr: 0 60: Angle: 60: nr: 1124 60: iatoms: 60: 0 type=116 (ANGLES) 1 0 2 60: 1 type=116 (ANGLES) 1 0 3 60: 2 type=116 (ANGLES) 1 0 4 60: 3 type=116 (ANGLES) 2 0 3 60: 4 type=116 (ANGLES) 2 0 4 60: 5 type=116 (ANGLES) 3 0 4 60: 6 type=116 (ANGLES) 0 4 5 60: 7 type=117 (ANGLES) 0 4 6 60: 8 type=117 (ANGLES) 0 4 22 60: 9 type=118 (ANGLES) 5 4 6 60: 10 type=116 (ANGLES) 5 4 22 60: 11 type=119 (ANGLES) 6 4 22 60: 12 type=118 (ANGLES) 4 6 7 60: 13 type=118 (ANGLES) 4 6 8 60: 14 type=120 (ANGLES) 4 6 9 60: 15 type=121 (ANGLES) 7 6 8 60: 16 type=118 (ANGLES) 7 6 9 60: 17 type=118 (ANGLES) 8 6 9 60: 18 type=118 (ANGLES) 6 9 10 60: 19 type=118 (ANGLES) 6 9 11 60: 20 type=120 (ANGLES) 6 9 12 60: 21 type=121 (ANGLES) 10 9 11 60: 22 type=118 (ANGLES) 10 9 12 60: 23 type=118 (ANGLES) 11 9 12 60: 24 type=118 (ANGLES) 9 12 13 60: 25 type=118 (ANGLES) 9 12 14 60: 26 type=120 (ANGLES) 9 12 15 60: 27 type=121 (ANGLES) 13 12 14 60: 28 type=118 (ANGLES) 13 12 15 60: 29 type=118 (ANGLES) 14 12 15 60: 30 type=118 (ANGLES) 12 15 16 60: 31 type=118 (ANGLES) 12 15 17 60: 32 type=117 (ANGLES) 12 15 18 60: 33 type=121 (ANGLES) 16 15 17 60: 34 type=116 (ANGLES) 16 15 18 60: 35 type=116 (ANGLES) 17 15 18 60: 36 type=116 (ANGLES) 15 18 19 60: 37 type=116 (ANGLES) 15 18 20 60: 38 type=116 (ANGLES) 15 18 21 60: 39 type=116 (ANGLES) 19 18 20 60: 40 type=116 (ANGLES) 19 18 21 60: 41 type=116 (ANGLES) 20 18 21 60: 42 type=122 (ANGLES) 4 22 23 60: 43 type=123 (ANGLES) 4 22 24 60: 44 type=124 (ANGLES) 23 22 24 60: 45 type=125 (ANGLES) 22 24 25 60: 46 type=126 (ANGLES) 22 24 26 60: 47 type=127 (ANGLES) 25 24 26 60: 48 type=116 (ANGLES) 24 26 27 60: 49 type=128 (ANGLES) 24 26 28 60: 50 type=129 (ANGLES) 24 26 38 60: 51 type=118 (ANGLES) 27 26 28 60: 52 type=116 (ANGLES) 27 26 38 60: 53 type=119 (ANGLES) 28 26 38 60: 54 type=118 (ANGLES) 26 28 29 60: 55 type=120 (ANGLES) 26 28 30 60: 56 type=120 (ANGLES) 26 28 34 60: 57 type=118 (ANGLES) 29 28 30 60: 58 type=118 (ANGLES) 29 28 34 60: 59 type=120 (ANGLES) 30 28 34 60: 60 type=118 (ANGLES) 28 30 31 60: 61 type=118 (ANGLES) 28 30 32 60: 62 type=118 (ANGLES) 28 30 33 60: 63 type=121 (ANGLES) 31 30 32 60: 64 type=121 (ANGLES) 31 30 33 60: 65 type=121 (ANGLES) 32 30 33 60: 66 type=118 (ANGLES) 28 34 35 60: 67 type=118 (ANGLES) 28 34 36 60: 68 type=118 (ANGLES) 28 34 37 60: 69 type=121 (ANGLES) 35 34 36 60: 70 type=121 (ANGLES) 35 34 37 60: 71 type=121 (ANGLES) 36 34 37 60: 72 type=122 (ANGLES) 26 38 39 60: 73 type=123 (ANGLES) 26 38 40 60: 74 type=124 (ANGLES) 39 38 40 60: 75 type=125 (ANGLES) 38 40 41 60: 76 type=126 (ANGLES) 38 40 42 60: 77 type=127 (ANGLES) 41 40 42 60: 78 type=116 (ANGLES) 40 42 43 60: 79 type=128 (ANGLES) 40 42 44 60: 80 type=129 (ANGLES) 40 42 58 60: 81 type=118 (ANGLES) 43 42 44 60: 82 type=116 (ANGLES) 43 42 58 60: 83 type=119 (ANGLES) 44 42 58 60: 84 type=118 (ANGLES) 42 44 45 60: 85 type=118 (ANGLES) 42 44 46 60: 86 type=130 (ANGLES) 42 44 47 60: 87 type=121 (ANGLES) 45 44 46 60: 88 type=116 (ANGLES) 45 44 47 60: 89 type=116 (ANGLES) 46 44 47 60: 90 type=131 (ANGLES) 44 47 48 60: 91 type=131 (ANGLES) 44 47 50 60: 92 type=132 (ANGLES) 48 47 50 60: 93 type=133 (ANGLES) 47 48 49 60: 94 type=132 (ANGLES) 47 48 52 60: 95 type=133 (ANGLES) 49 48 52 60: 96 type=133 (ANGLES) 47 50 51 60: 97 type=132 (ANGLES) 47 50 54 60: 98 type=133 (ANGLES) 51 50 54 60: 99 type=133 (ANGLES) 48 52 53 60: 100 type=132 (ANGLES) 48 52 56 60: 101 type=133 (ANGLES) 53 52 56 60: 102 type=133 (ANGLES) 50 54 55 60: 103 type=132 (ANGLES) 50 54 56 60: 104 type=133 (ANGLES) 55 54 56 60: 105 type=132 (ANGLES) 52 56 54 60: 106 type=133 (ANGLES) 52 56 57 60: 107 type=133 (ANGLES) 54 56 57 60: 108 type=122 (ANGLES) 42 58 59 60: 109 type=123 (ANGLES) 42 58 60 60: 110 type=124 (ANGLES) 59 58 60 60: 111 type=125 (ANGLES) 58 60 61 60: 112 type=126 (ANGLES) 58 60 62 60: 113 type=127 (ANGLES) 61 60 62 60: 114 type=116 (ANGLES) 60 62 63 60: 115 type=116 (ANGLES) 60 62 64 60: 116 type=129 (ANGLES) 60 62 65 60: 117 type=121 (ANGLES) 63 62 64 60: 118 type=116 (ANGLES) 63 62 65 60: 119 type=116 (ANGLES) 64 62 65 60: 120 type=122 (ANGLES) 62 65 66 60: 121 type=123 (ANGLES) 62 65 67 60: 122 type=124 (ANGLES) 66 65 67 60: 123 type=125 (ANGLES) 65 67 68 60: 124 type=126 (ANGLES) 65 67 69 60: 125 type=127 (ANGLES) 68 67 69 60: 126 type=116 (ANGLES) 67 69 70 60: 127 type=128 (ANGLES) 67 69 71 60: 128 type=129 (ANGLES) 67 69 89 60: 129 type=118 (ANGLES) 70 69 71 60: 130 type=116 (ANGLES) 70 69 89 60: 131 type=119 (ANGLES) 71 69 89 60: 132 type=118 (ANGLES) 69 71 72 60: 133 type=118 (ANGLES) 69 71 73 60: 134 type=120 (ANGLES) 69 71 74 60: 135 type=121 (ANGLES) 72 71 73 60: 136 type=118 (ANGLES) 72 71 74 60: 137 type=118 (ANGLES) 73 71 74 60: 138 type=118 (ANGLES) 71 74 75 60: 139 type=118 (ANGLES) 71 74 76 60: 140 type=120 (ANGLES) 71 74 77 60: 141 type=121 (ANGLES) 75 74 76 60: 142 type=118 (ANGLES) 75 74 77 60: 143 type=118 (ANGLES) 76 74 77 60: 144 type=118 (ANGLES) 74 77 78 60: 145 type=118 (ANGLES) 74 77 79 60: 146 type=117 (ANGLES) 74 77 80 60: 147 type=121 (ANGLES) 78 77 79 60: 148 type=116 (ANGLES) 78 77 80 60: 149 type=116 (ANGLES) 79 77 80 60: 150 type=134 (ANGLES) 77 80 81 60: 151 type=135 (ANGLES) 77 80 82 60: 152 type=133 (ANGLES) 81 80 82 60: 153 type=131 (ANGLES) 80 82 83 60: 154 type=131 (ANGLES) 80 82 86 60: 155 type=131 (ANGLES) 83 82 86 60: 156 type=133 (ANGLES) 82 83 84 60: 157 type=133 (ANGLES) 82 83 85 60: 158 type=133 (ANGLES) 84 83 85 60: 159 type=133 (ANGLES) 82 86 87 60: 160 type=133 (ANGLES) 82 86 88 60: 161 type=133 (ANGLES) 87 86 88 60: 162 type=122 (ANGLES) 69 89 90 60: 163 type=123 (ANGLES) 69 89 91 60: 164 type=124 (ANGLES) 90 89 91 60: 165 type=125 (ANGLES) 89 91 92 60: 166 type=126 (ANGLES) 89 91 93 60: 167 type=127 (ANGLES) 92 91 93 60: 168 type=116 (ANGLES) 91 93 94 60: 169 type=128 (ANGLES) 91 93 95 60: 170 type=129 (ANGLES) 91 93 100 60: 171 type=118 (ANGLES) 94 93 95 60: 172 type=116 (ANGLES) 94 93 100 60: 173 type=119 (ANGLES) 95 93 100 60: 174 type=118 (ANGLES) 93 95 96 60: 175 type=118 (ANGLES) 93 95 97 60: 176 type=136 (ANGLES) 93 95 98 60: 177 type=121 (ANGLES) 96 95 97 60: 178 type=116 (ANGLES) 96 95 98 60: 179 type=116 (ANGLES) 97 95 98 60: 180 type=137 (ANGLES) 95 98 99 60: 181 type=122 (ANGLES) 93 100 101 60: 182 type=123 (ANGLES) 93 100 102 60: 183 type=124 (ANGLES) 101 100 102 60: 184 type=125 (ANGLES) 100 102 103 60: 185 type=126 (ANGLES) 100 102 104 60: 186 type=127 (ANGLES) 103 102 104 60: 187 type=116 (ANGLES) 102 104 105 60: 188 type=128 (ANGLES) 102 104 106 60: 189 type=129 (ANGLES) 102 104 115 60: 190 type=118 (ANGLES) 105 104 106 60: 191 type=116 (ANGLES) 105 104 115 60: 192 type=119 (ANGLES) 106 104 115 60: 193 type=118 (ANGLES) 104 106 107 60: 194 type=118 (ANGLES) 104 106 108 60: 195 type=120 (ANGLES) 104 106 109 60: 196 type=121 (ANGLES) 107 106 108 60: 197 type=118 (ANGLES) 107 106 109 60: 198 type=118 (ANGLES) 108 106 109 60: 199 type=118 (ANGLES) 106 109 110 60: 200 type=118 (ANGLES) 106 109 111 60: 201 type=119 (ANGLES) 106 109 112 60: 202 type=121 (ANGLES) 110 109 111 60: 203 type=116 (ANGLES) 110 109 112 60: 204 type=116 (ANGLES) 111 109 112 60: 205 type=138 (ANGLES) 109 112 113 60: 206 type=138 (ANGLES) 109 112 114 60: 207 type=139 (ANGLES) 113 112 114 60: 208 type=122 (ANGLES) 104 115 116 60: 209 type=123 (ANGLES) 104 115 117 60: 210 type=124 (ANGLES) 116 115 117 60: 211 type=125 (ANGLES) 115 117 118 60: 212 type=126 (ANGLES) 115 117 119 60: 213 type=127 (ANGLES) 118 117 119 60: 214 type=116 (ANGLES) 117 119 120 60: 215 type=128 (ANGLES) 117 119 121 60: 216 type=129 (ANGLES) 117 119 134 60: 217 type=118 (ANGLES) 120 119 121 60: 218 type=116 (ANGLES) 120 119 134 60: 219 type=119 (ANGLES) 121 119 134 60: 220 type=118 (ANGLES) 119 121 122 60: 221 type=118 (ANGLES) 119 121 123 60: 222 type=120 (ANGLES) 119 121 124 60: 223 type=121 (ANGLES) 122 121 123 60: 224 type=118 (ANGLES) 122 121 124 60: 225 type=118 (ANGLES) 123 121 124 60: 226 type=118 (ANGLES) 121 124 125 60: 227 type=120 (ANGLES) 121 124 126 60: 228 type=120 (ANGLES) 121 124 130 60: 229 type=118 (ANGLES) 125 124 126 60: 230 type=118 (ANGLES) 125 124 130 60: 231 type=120 (ANGLES) 126 124 130 60: 232 type=118 (ANGLES) 124 126 127 60: 233 type=118 (ANGLES) 124 126 128 60: 234 type=118 (ANGLES) 124 126 129 60: 235 type=121 (ANGLES) 127 126 128 60: 236 type=121 (ANGLES) 127 126 129 60: 237 type=121 (ANGLES) 128 126 129 60: 238 type=118 (ANGLES) 124 130 131 60: 239 type=118 (ANGLES) 124 130 132 60: 240 type=118 (ANGLES) 124 130 133 60: 241 type=121 (ANGLES) 131 130 132 60: 242 type=121 (ANGLES) 131 130 133 60: 243 type=121 (ANGLES) 132 130 133 60: 244 type=122 (ANGLES) 119 134 135 60: 245 type=123 (ANGLES) 119 134 136 60: 246 type=124 (ANGLES) 135 134 136 60: 247 type=125 (ANGLES) 134 136 137 60: 248 type=126 (ANGLES) 134 136 138 60: 249 type=127 (ANGLES) 137 136 138 60: 250 type=116 (ANGLES) 136 138 139 60: 251 type=128 (ANGLES) 136 138 140 60: 252 type=129 (ANGLES) 136 138 144 60: 253 type=118 (ANGLES) 139 138 140 60: 254 type=116 (ANGLES) 139 138 144 60: 255 type=119 (ANGLES) 140 138 144 60: 256 type=118 (ANGLES) 138 140 141 60: 257 type=118 (ANGLES) 138 140 142 60: 258 type=118 (ANGLES) 138 140 143 60: 259 type=121 (ANGLES) 141 140 142 60: 260 type=121 (ANGLES) 141 140 143 60: 261 type=121 (ANGLES) 142 140 143 60: 262 type=122 (ANGLES) 138 144 145 60: 263 type=123 (ANGLES) 138 144 146 60: 264 type=124 (ANGLES) 145 144 146 60: 265 type=125 (ANGLES) 144 146 147 60: 266 type=126 (ANGLES) 144 146 148 60: 267 type=127 (ANGLES) 147 146 148 60: 268 type=116 (ANGLES) 146 148 149 60: 269 type=128 (ANGLES) 146 148 150 60: 270 type=129 (ANGLES) 146 148 154 60: 271 type=118 (ANGLES) 149 148 150 60: 272 type=116 (ANGLES) 149 148 154 60: 273 type=119 (ANGLES) 150 148 154 60: 274 type=118 (ANGLES) 148 150 151 60: 275 type=118 (ANGLES) 148 150 152 60: 276 type=118 (ANGLES) 148 150 153 60: 277 type=121 (ANGLES) 151 150 152 60: 278 type=121 (ANGLES) 151 150 153 60: 279 type=121 (ANGLES) 152 150 153 60: 280 type=122 (ANGLES) 148 154 155 60: G96Angle: 60: nr: 0 60: Restr. Angles: 60: nr: 0 60: Lin. Angle: 60: nr: 0 60: Bond-Cross: 60: nr: 0 60: BA-Cross: 60: nr: 0 60: U-B: 60: nr: 0 60: Quartic Angles: 60: nr: 0 60: Tab. Angles: 60: nr: 0 60: Proper Dih.: 60: nr: 145 60: iatoms: 60: 0 type=140 (PDIHS) 4 24 22 23 60: 1 type=141 (PDIHS) 22 26 24 25 60: 2 type=140 (PDIHS) 26 40 38 39 60: 3 type=141 (PDIHS) 38 42 40 41 60: 4 type=140 (PDIHS) 42 60 58 59 60: 5 type=142 (PDIHS) 44 47 50 48 60: 6 type=142 (PDIHS) 47 52 48 49 60: 7 type=142 (PDIHS) 47 54 50 51 60: 8 type=142 (PDIHS) 48 56 52 53 60: 9 type=142 (PDIHS) 50 56 54 55 60: 10 type=142 (PDIHS) 52 54 56 57 60: 11 type=141 (PDIHS) 58 62 60 61 60: 12 type=140 (PDIHS) 62 67 65 66 60: 13 type=141 (PDIHS) 65 69 67 68 60: 14 type=140 (PDIHS) 69 91 89 90 60: 15 type=141 (PDIHS) 77 82 80 81 60: 16 type=140 (PDIHS) 80 83 82 86 60: 17 type=141 (PDIHS) 82 84 83 85 60: 18 type=141 (PDIHS) 82 87 86 88 60: 19 type=141 (PDIHS) 89 93 91 92 60: 20 type=140 (PDIHS) 93 102 100 101 60: 21 type=141 (PDIHS) 100 104 102 103 60: 22 type=140 (PDIHS) 104 117 115 116 60: 23 type=140 (PDIHS) 109 113 112 114 60: 24 type=141 (PDIHS) 115 119 117 118 60: 25 type=140 (PDIHS) 119 136 134 135 60: 26 type=141 (PDIHS) 134 138 136 137 60: 27 type=140 (PDIHS) 138 146 144 145 60: 28 type=141 (PDIHS) 144 148 146 147 60: Ryckaert-Bell.: 60: nr: 1565 60: iatoms: 60: 0 type=143 (RBDIHS) 1 0 4 5 60: 1 type=144 (RBDIHS) 1 0 4 6 60: 2 type=144 (RBDIHS) 1 0 4 22 60: 3 type=143 (RBDIHS) 2 0 4 5 60: 4 type=144 (RBDIHS) 2 0 4 6 60: 5 type=144 (RBDIHS) 2 0 4 22 60: 6 type=143 (RBDIHS) 3 0 4 5 60: 7 type=144 (RBDIHS) 3 0 4 6 60: 8 type=144 (RBDIHS) 3 0 4 22 60: 9 type=145 (RBDIHS) 0 4 6 9 60: 10 type=146 (RBDIHS) 22 4 6 9 60: 11 type=147 (RBDIHS) 0 4 6 7 60: 12 type=147 (RBDIHS) 0 4 6 8 60: 13 type=148 (RBDIHS) 5 4 6 7 60: 14 type=148 (RBDIHS) 5 4 6 8 60: 15 type=148 (RBDIHS) 5 4 6 9 60: 16 type=149 (RBDIHS) 22 4 6 7 60: 17 type=149 (RBDIHS) 22 4 6 8 60: 18 type=150 (RBDIHS) 0 4 22 24 60: 19 type=151 (RBDIHS) 6 4 22 24 60: 20 type=148 (RBDIHS) 4 6 9 10 60: 21 type=148 (RBDIHS) 4 6 9 11 60: 22 type=152 (RBDIHS) 4 6 9 12 60: 23 type=148 (RBDIHS) 7 6 9 10 60: 24 type=148 (RBDIHS) 7 6 9 11 60: 25 type=148 (RBDIHS) 7 6 9 12 60: 26 type=148 (RBDIHS) 8 6 9 10 60: 27 type=148 (RBDIHS) 8 6 9 11 60: 28 type=148 (RBDIHS) 8 6 9 12 60: 29 type=148 (RBDIHS) 6 9 12 13 60: 30 type=148 (RBDIHS) 6 9 12 14 60: 31 type=152 (RBDIHS) 6 9 12 15 60: 32 type=148 (RBDIHS) 10 9 12 13 60: 33 type=148 (RBDIHS) 10 9 12 14 60: 34 type=148 (RBDIHS) 10 9 12 15 60: 35 type=148 (RBDIHS) 11 9 12 13 60: 36 type=148 (RBDIHS) 11 9 12 14 60: 37 type=148 (RBDIHS) 11 9 12 15 60: 38 type=148 (RBDIHS) 9 12 15 16 60: 39 type=148 (RBDIHS) 9 12 15 17 60: 40 type=153 (RBDIHS) 9 12 15 18 60: 41 type=148 (RBDIHS) 13 12 15 16 60: 42 type=148 (RBDIHS) 13 12 15 17 60: 43 type=154 (RBDIHS) 13 12 15 18 60: 44 type=148 (RBDIHS) 14 12 15 16 60: 45 type=148 (RBDIHS) 14 12 15 17 60: 46 type=154 (RBDIHS) 14 12 15 18 60: 47 type=144 (RBDIHS) 12 15 18 19 60: 48 type=144 (RBDIHS) 12 15 18 20 60: 49 type=144 (RBDIHS) 12 15 18 21 60: 50 type=143 (RBDIHS) 16 15 18 19 60: 51 type=143 (RBDIHS) 16 15 18 20 60: 52 type=143 (RBDIHS) 16 15 18 21 60: 53 type=143 (RBDIHS) 17 15 18 19 60: 54 type=143 (RBDIHS) 17 15 18 20 60: 55 type=143 (RBDIHS) 17 15 18 21 60: 56 type=155 (RBDIHS) 4 22 24 25 60: 57 type=156 (RBDIHS) 4 22 24 26 60: 58 type=155 (RBDIHS) 23 22 24 25 60: 59 type=157 (RBDIHS) 23 22 24 26 60: 60 type=158 (RBDIHS) 22 24 26 28 60: 61 type=159 (RBDIHS) 22 24 26 38 60: 62 type=160 (RBDIHS) 24 26 28 30 60: 63 type=160 (RBDIHS) 24 26 28 34 60: 64 type=161 (RBDIHS) 38 26 28 30 60: 65 type=161 (RBDIHS) 38 26 28 34 60: 66 type=147 (RBDIHS) 24 26 28 29 60: 67 type=148 (RBDIHS) 27 26 28 29 60: 68 type=148 (RBDIHS) 27 26 28 30 60: 69 type=148 (RBDIHS) 27 26 28 34 60: 70 type=149 (RBDIHS) 38 26 28 29 60: 71 type=150 (RBDIHS) 24 26 38 40 60: 72 type=151 (RBDIHS) 28 26 38 40 60: 73 type=148 (RBDIHS) 26 28 30 31 60: 74 type=148 (RBDIHS) 26 28 30 32 60: 75 type=148 (RBDIHS) 26 28 30 33 60: 76 type=148 (RBDIHS) 29 28 30 31 60: 77 type=148 (RBDIHS) 29 28 30 32 60: 78 type=148 (RBDIHS) 29 28 30 33 60: 79 type=148 (RBDIHS) 34 28 30 31 60: 80 type=148 (RBDIHS) 34 28 30 32 60: 81 type=148 (RBDIHS) 34 28 30 33 60: 82 type=148 (RBDIHS) 26 28 34 35 60: 83 type=148 (RBDIHS) 26 28 34 36 60: 84 type=148 (RBDIHS) 26 28 34 37 60: 85 type=148 (RBDIHS) 29 28 34 35 60: 86 type=148 (RBDIHS) 29 28 34 36 60: 87 type=148 (RBDIHS) 29 28 34 37 60: 88 type=148 (RBDIHS) 30 28 34 35 60: 89 type=148 (RBDIHS) 30 28 34 36 60: 90 type=148 (RBDIHS) 30 28 34 37 60: 91 type=155 (RBDIHS) 26 38 40 41 60: 92 type=156 (RBDIHS) 26 38 40 42 60: 93 type=155 (RBDIHS) 39 38 40 41 60: 94 type=157 (RBDIHS) 39 38 40 42 60: 95 type=158 (RBDIHS) 38 40 42 44 60: 96 type=159 (RBDIHS) 38 40 42 58 60: 97 type=147 (RBDIHS) 40 42 44 45 60: 98 type=147 (RBDIHS) 40 42 44 46 60: 99 type=162 (RBDIHS) 40 42 44 47 60: 100 type=148 (RBDIHS) 43 42 44 45 60: 101 type=148 (RBDIHS) 43 42 44 46 60: 102 type=163 (RBDIHS) 43 42 44 47 60: 103 type=149 (RBDIHS) 58 42 44 45 60: 104 type=149 (RBDIHS) 58 42 44 46 60: 105 type=164 (RBDIHS) 58 42 44 47 60: 106 type=150 (RBDIHS) 40 42 58 60 60: 107 type=151 (RBDIHS) 44 42 58 60 60: 108 type=165 (RBDIHS) 44 47 48 49 60: 109 type=165 (RBDIHS) 44 47 48 52 60: 110 type=165 (RBDIHS) 50 47 48 49 60: 111 type=165 (RBDIHS) 50 47 48 52 60: 112 type=165 (RBDIHS) 44 47 50 51 60: 113 type=165 (RBDIHS) 44 47 50 54 60: 114 type=165 (RBDIHS) 48 47 50 51 60: 115 type=165 (RBDIHS) 48 47 50 54 60: 116 type=165 (RBDIHS) 47 48 52 53 60: 117 type=165 (RBDIHS) 47 48 52 56 60: 118 type=165 (RBDIHS) 49 48 52 53 60: 119 type=165 (RBDIHS) 49 48 52 56 60: 120 type=165 (RBDIHS) 47 50 54 55 60: 121 type=165 (RBDIHS) 47 50 54 56 60: 122 type=165 (RBDIHS) 51 50 54 55 60: 123 type=165 (RBDIHS) 51 50 54 56 60: 124 type=165 (RBDIHS) 48 52 56 54 60: 125 type=165 (RBDIHS) 48 52 56 57 60: 126 type=165 (RBDIHS) 53 52 56 54 60: 127 type=165 (RBDIHS) 53 52 56 57 60: 128 type=165 (RBDIHS) 50 54 56 52 60: 129 type=165 (RBDIHS) 50 54 56 57 60: 130 type=165 (RBDIHS) 55 54 56 52 60: 131 type=165 (RBDIHS) 55 54 56 57 60: 132 type=155 (RBDIHS) 42 58 60 61 60: 133 type=156 (RBDIHS) 42 58 60 62 60: 134 type=155 (RBDIHS) 59 58 60 61 60: 135 type=157 (RBDIHS) 59 58 60 62 60: 136 type=159 (RBDIHS) 58 60 62 65 60: 137 type=150 (RBDIHS) 60 62 65 67 60: 138 type=155 (RBDIHS) 62 65 67 68 60: 139 type=156 (RBDIHS) 62 65 67 69 60: 140 type=155 (RBDIHS) 66 65 67 68 60: 141 type=157 (RBDIHS) 66 65 67 69 60: 142 type=158 (RBDIHS) 65 67 69 71 60: 143 type=159 (RBDIHS) 65 67 69 89 60: 144 type=166 (RBDIHS) 67 69 71 74 60: 145 type=167 (RBDIHS) 89 69 71 74 60: 146 type=147 (RBDIHS) 67 69 71 72 60: 147 type=147 (RBDIHS) 67 69 71 73 60: 148 type=148 (RBDIHS) 70 69 71 72 60: 149 type=148 (RBDIHS) 70 69 71 73 60: 150 type=148 (RBDIHS) 70 69 71 74 60: 151 type=149 (RBDIHS) 89 69 71 72 60: 152 type=149 (RBDIHS) 89 69 71 73 60: 153 type=150 (RBDIHS) 67 69 89 91 60: 154 type=151 (RBDIHS) 71 69 89 91 60: 155 type=148 (RBDIHS) 69 71 74 75 60: 156 type=148 (RBDIHS) 69 71 74 76 60: 157 type=152 (RBDIHS) 69 71 74 77 60: 158 type=148 (RBDIHS) 72 71 74 75 60: 159 type=148 (RBDIHS) 72 71 74 76 60: 160 type=148 (RBDIHS) 72 71 74 77 60: 161 type=148 (RBDIHS) 73 71 74 75 60: 162 type=148 (RBDIHS) 73 71 74 76 60: 163 type=148 (RBDIHS) 73 71 74 77 60: 164 type=148 (RBDIHS) 71 74 77 78 60: 165 type=148 (RBDIHS) 71 74 77 79 60: 166 type=153 (RBDIHS) 71 74 77 80 60: 167 type=148 (RBDIHS) 75 74 77 78 60: 168 type=148 (RBDIHS) 75 74 77 79 60: 169 type=168 (RBDIHS) 75 74 77 80 60: 170 type=148 (RBDIHS) 76 74 77 78 60: 171 type=148 (RBDIHS) 76 74 77 79 60: 172 type=168 (RBDIHS) 76 74 77 80 60: 173 type=169 (RBDIHS) 74 77 80 81 60: 174 type=170 (RBDIHS) 74 77 80 82 60: 175 type=171 (RBDIHS) 78 77 80 82 60: 176 type=171 (RBDIHS) 79 77 80 82 60: 177 type=172 (RBDIHS) 77 80 82 83 60: 178 type=172 (RBDIHS) 77 80 82 86 60: 179 type=173 (RBDIHS) 81 80 82 83 60: 180 type=173 (RBDIHS) 81 80 82 86 60: 181 type=173 (RBDIHS) 80 82 83 84 60: 182 type=173 (RBDIHS) 80 82 83 85 60: 183 type=173 (RBDIHS) 86 82 83 84 60: 184 type=173 (RBDIHS) 86 82 83 85 60: 185 type=173 (RBDIHS) 80 82 86 87 60: 186 type=173 (RBDIHS) 80 82 86 88 60: 187 type=173 (RBDIHS) 83 82 86 87 60: 188 type=173 (RBDIHS) 83 82 86 88 60: 189 type=155 (RBDIHS) 69 89 91 92 60: 190 type=156 (RBDIHS) 69 89 91 93 60: 191 type=155 (RBDIHS) 90 89 91 92 60: 192 type=157 (RBDIHS) 90 89 91 93 60: 193 type=158 (RBDIHS) 89 91 93 95 60: 194 type=159 (RBDIHS) 89 91 93 100 60: 195 type=174 (RBDIHS) 91 93 95 98 60: 196 type=175 (RBDIHS) 100 93 95 98 60: 197 type=147 (RBDIHS) 91 93 95 96 60: 198 type=147 (RBDIHS) 91 93 95 97 60: 199 type=148 (RBDIHS) 94 93 95 96 60: 200 type=148 (RBDIHS) 94 93 95 97 60: 201 type=176 (RBDIHS) 94 93 95 98 60: 202 type=149 (RBDIHS) 100 93 95 96 60: 203 type=149 (RBDIHS) 100 93 95 97 60: 204 type=150 (RBDIHS) 91 93 100 102 60: 205 type=151 (RBDIHS) 95 93 100 102 60: 206 type=177 (RBDIHS) 93 95 98 99 60: 207 type=178 (RBDIHS) 96 95 98 99 60: 208 type=178 (RBDIHS) 97 95 98 99 60: 209 type=155 (RBDIHS) 93 100 102 103 60: 210 type=156 (RBDIHS) 93 100 102 104 60: 211 type=155 (RBDIHS) 101 100 102 103 60: 212 type=157 (RBDIHS) 101 100 102 104 60: 213 type=158 (RBDIHS) 100 102 104 106 60: 214 type=159 (RBDIHS) 100 102 104 115 60: 215 type=179 (RBDIHS) 102 104 106 109 60: 216 type=180 (RBDIHS) 115 104 106 109 60: 217 type=147 (RBDIHS) 102 104 106 107 60: 218 type=147 (RBDIHS) 102 104 106 108 60: 219 type=148 (RBDIHS) 105 104 106 107 60: 220 type=148 (RBDIHS) 105 104 106 108 60: 221 type=148 (RBDIHS) 105 104 106 109 60: 222 type=149 (RBDIHS) 115 104 106 107 60: 223 type=149 (RBDIHS) 115 104 106 108 60: 224 type=150 (RBDIHS) 102 104 115 117 60: 225 type=151 (RBDIHS) 106 104 115 117 60: 226 type=148 (RBDIHS) 104 106 109 110 60: 227 type=148 (RBDIHS) 104 106 109 111 60: 228 type=181 (RBDIHS) 104 106 109 112 60: 229 type=148 (RBDIHS) 107 106 109 110 60: 230 type=148 (RBDIHS) 107 106 109 111 60: 231 type=182 (RBDIHS) 107 106 109 112 60: 232 type=148 (RBDIHS) 108 106 109 110 60: 233 type=148 (RBDIHS) 108 106 109 111 60: 234 type=182 (RBDIHS) 108 106 109 112 60: 235 type=183 (RBDIHS) 106 109 112 113 60: 236 type=183 (RBDIHS) 106 109 112 114 60: 237 type=155 (RBDIHS) 104 115 117 118 60: 238 type=156 (RBDIHS) 104 115 117 119 60: 239 type=155 (RBDIHS) 116 115 117 118 60: 240 type=157 (RBDIHS) 116 115 117 119 60: 241 type=158 (RBDIHS) 115 117 119 121 60: 242 type=159 (RBDIHS) 115 117 119 134 60: 243 type=184 (RBDIHS) 117 119 121 124 60: 244 type=185 (RBDIHS) 134 119 121 124 60: 245 type=147 (RBDIHS) 117 119 121 122 60: 246 type=147 (RBDIHS) 117 119 121 123 60: 247 type=148 (RBDIHS) 120 119 121 122 60: 248 type=148 (RBDIHS) 120 119 121 123 60: 249 type=148 (RBDIHS) 120 119 121 124 60: 250 type=149 (RBDIHS) 134 119 121 122 60: 251 type=149 (RBDIHS) 134 119 121 123 60: 252 type=150 (RBDIHS) 117 119 134 136 60: 253 type=151 (RBDIHS) 121 119 134 136 60: 254 type=148 (RBDIHS) 119 121 124 125 60: 255 type=152 (RBDIHS) 119 121 124 126 60: 256 type=152 (RBDIHS) 119 121 124 130 60: 257 type=148 (RBDIHS) 122 121 124 125 60: 258 type=148 (RBDIHS) 122 121 124 126 60: 259 type=148 (RBDIHS) 122 121 124 130 60: 260 type=148 (RBDIHS) 123 121 124 125 60: 261 type=148 (RBDIHS) 123 121 124 126 60: 262 type=148 (RBDIHS) 123 121 124 130 60: 263 type=148 (RBDIHS) 121 124 126 127 60: 264 type=148 (RBDIHS) 121 124 126 128 60: 265 type=148 (RBDIHS) 121 124 126 129 60: 266 type=148 (RBDIHS) 125 124 126 127 60: 267 type=148 (RBDIHS) 125 124 126 128 60: 268 type=148 (RBDIHS) 125 124 126 129 60: 269 type=148 (RBDIHS) 130 124 126 127 60: 270 type=148 (RBDIHS) 130 124 126 128 60: 271 type=148 (RBDIHS) 130 124 126 129 60: 272 type=148 (RBDIHS) 121 124 130 131 60: 273 type=148 (RBDIHS) 121 124 130 132 60: 274 type=148 (RBDIHS) 121 124 130 133 60: 275 type=148 (RBDIHS) 125 124 130 131 60: 276 type=148 (RBDIHS) 125 124 130 132 60: 277 type=148 (RBDIHS) 125 124 130 133 60: 278 type=148 (RBDIHS) 126 124 130 131 60: 279 type=148 (RBDIHS) 126 124 130 132 60: 280 type=148 (RBDIHS) 126 124 130 133 60: 281 type=155 (RBDIHS) 119 134 136 137 60: 282 type=156 (RBDIHS) 119 134 136 138 60: 283 type=155 (RBDIHS) 135 134 136 137 60: 284 type=157 (RBDIHS) 135 134 136 138 60: 285 type=158 (RBDIHS) 134 136 138 140 60: 286 type=159 (RBDIHS) 134 136 138 144 60: 287 type=147 (RBDIHS) 136 138 140 141 60: 288 type=147 (RBDIHS) 136 138 140 142 60: 289 type=147 (RBDIHS) 136 138 140 143 60: 290 type=148 (RBDIHS) 139 138 140 141 60: 291 type=148 (RBDIHS) 139 138 140 142 60: 292 type=148 (RBDIHS) 139 138 140 143 60: 293 type=149 (RBDIHS) 144 138 140 141 60: 294 type=149 (RBDIHS) 144 138 140 142 60: 295 type=149 (RBDIHS) 144 138 140 143 60: 296 type=150 (RBDIHS) 136 138 144 146 60: 297 type=151 (RBDIHS) 140 138 144 146 60: 298 type=155 (RBDIHS) 138 144 146 147 60: 299 type=156 (RBDIHS) 138 144 146 148 60: 300 type=155 (RBDIHS) 145 144 146 147 60: 301 type=157 (RBDIHS) 145 144 146 148 60: 302 type=158 (RBDIHS) 144 146 148 150 60: 303 type=159 (RBDIHS) 144 146 148 154 60: 304 type=147 (RBDIHS) 146 148 150 151 60: 305 type=147 (RBDIHS) 146 148 150 152 60: 306 type=147 (RBDIHS) 146 148 150 153 60: 307 type=148 (RBDIHS) 149 148 150 151 60: 308 type=148 (RBDIHS) 149 148 150 152 60: 309 type=148 (RBDIHS) 149 148 150 153 60: 310 type=149 (RBDIHS) 154 148 150 151 60: 311 type=149 (RBDIHS) 154 148 150 152 60: 312 type=149 (RBDIHS) 154 148 150 153 60: Restr. Dih.: 60: nr: 0 60: CBT Dih.: 60: nr: 0 60: Fourier Dih.: 60: nr: 0 60: Improper Dih.: 60: nr: 0 60: Per. Imp. Dih.: 60: nr: 0 60: Tab. Dih.: 60: nr: 0 60: CMAP Dih.: 60: nr: 0 60: GB 1-2 Pol.: 60: nr: 0 60: GB 1-3 Pol.: 60: nr: 0 60: GB 1-4 Pol.: 60: nr: 0 60: GB Polariz.: 60: nr: 0 60: Nonpolar Sol.: 60: nr: 0 60: LJ-14: 60: nr: 1197 60: iatoms: 60: 0 type=186 (LJ14) 0 7 60: 1 type=186 (LJ14) 0 8 60: 2 type=187 (LJ14) 0 9 60: 3 type=188 (LJ14) 0 23 60: 4 type=189 (LJ14) 0 24 60: 5 type=190 (LJ14) 1 5 60: 6 type=190 (LJ14) 1 6 60: 7 type=190 (LJ14) 1 22 60: 8 type=190 (LJ14) 2 5 60: 9 type=190 (LJ14) 2 6 60: 10 type=190 (LJ14) 2 22 60: 11 type=190 (LJ14) 3 5 60: 12 type=190 (LJ14) 3 6 60: 13 type=190 (LJ14) 3 22 60: 14 type=191 (LJ14) 4 10 60: 15 type=191 (LJ14) 4 11 60: 16 type=192 (LJ14) 4 12 60: 17 type=190 (LJ14) 4 25 60: 18 type=192 (LJ14) 4 26 60: 19 type=193 (LJ14) 5 7 60: 20 type=193 (LJ14) 5 8 60: 21 type=191 (LJ14) 5 9 60: 22 type=194 (LJ14) 5 23 60: 23 type=186 (LJ14) 5 24 60: 24 type=191 (LJ14) 6 13 60: 25 type=191 (LJ14) 6 14 60: 26 type=192 (LJ14) 6 15 60: 27 type=195 (LJ14) 6 23 60: 28 type=187 (LJ14) 6 24 60: 29 type=193 (LJ14) 7 10 60: 30 type=193 (LJ14) 7 11 60: 31 type=191 (LJ14) 7 12 60: 32 type=196 (LJ14) 7 22 60: 33 type=193 (LJ14) 8 10 60: 34 type=193 (LJ14) 8 11 60: 35 type=191 (LJ14) 8 12 60: 36 type=196 (LJ14) 8 22 60: 37 type=191 (LJ14) 9 16 60: 38 type=191 (LJ14) 9 17 60: 39 type=187 (LJ14) 9 18 60: 40 type=197 (LJ14) 9 22 60: 41 type=193 (LJ14) 10 13 60: 42 type=193 (LJ14) 10 14 60: 43 type=191 (LJ14) 10 15 60: 44 type=193 (LJ14) 11 13 60: 45 type=193 (LJ14) 11 14 60: 46 type=191 (LJ14) 11 15 60: 47 type=190 (LJ14) 12 19 60: 48 type=190 (LJ14) 12 20 60: 49 type=190 (LJ14) 12 21 60: 50 type=193 (LJ14) 13 16 60: 51 type=193 (LJ14) 13 17 60: 52 type=186 (LJ14) 13 18 60: 53 type=193 (LJ14) 14 16 60: 54 type=193 (LJ14) 14 17 60: 55 type=186 (LJ14) 14 18 60: 56 type=190 (LJ14) 16 19 60: 57 type=190 (LJ14) 16 20 60: 58 type=190 (LJ14) 16 21 60: 59 type=190 (LJ14) 17 19 60: 60 type=190 (LJ14) 17 20 60: 61 type=190 (LJ14) 17 21 60: 62 type=196 (LJ14) 22 27 60: 63 type=197 (LJ14) 22 28 60: 64 type=198 (LJ14) 22 38 60: 65 type=190 (LJ14) 23 25 60: 66 type=195 (LJ14) 23 26 60: 67 type=186 (LJ14) 24 29 60: 68 type=187 (LJ14) 24 30 60: 69 type=187 (LJ14) 24 34 60: 70 type=188 (LJ14) 24 39 60: 71 type=189 (LJ14) 24 40 60: 72 type=190 (LJ14) 25 27 60: 73 type=190 (LJ14) 25 28 60: 74 type=190 (LJ14) 25 38 60: 75 type=191 (LJ14) 26 31 60: 76 type=191 (LJ14) 26 32 60: 77 type=191 (LJ14) 26 33 60: 78 type=191 (LJ14) 26 35 60: 79 type=191 (LJ14) 26 36 60: 80 type=191 (LJ14) 26 37 60: 81 type=190 (LJ14) 26 41 60: 82 type=192 (LJ14) 26 42 60: 83 type=193 (LJ14) 27 29 60: 84 type=191 (LJ14) 27 30 60: 85 type=191 (LJ14) 27 34 60: 86 type=194 (LJ14) 27 39 60: 87 type=186 (LJ14) 27 40 60: 88 type=195 (LJ14) 28 39 60: 89 type=187 (LJ14) 28 40 60: 90 type=193 (LJ14) 29 31 60: 91 type=193 (LJ14) 29 32 60: 92 type=193 (LJ14) 29 33 60: 93 type=193 (LJ14) 29 35 60: 94 type=193 (LJ14) 29 36 60: 95 type=193 (LJ14) 29 37 60: 96 type=196 (LJ14) 29 38 60: 97 type=191 (LJ14) 30 35 60: 98 type=191 (LJ14) 30 36 60: 99 type=191 (LJ14) 30 37 60: 100 type=197 (LJ14) 30 38 60: 101 type=191 (LJ14) 31 34 60: 102 type=191 (LJ14) 32 34 60: 103 type=191 (LJ14) 33 34 60: 104 type=197 (LJ14) 34 38 60: 105 type=196 (LJ14) 38 43 60: 106 type=197 (LJ14) 38 44 60: 107 type=198 (LJ14) 38 58 60: 108 type=190 (LJ14) 39 41 60: 109 type=195 (LJ14) 39 42 60: 110 type=186 (LJ14) 40 45 60: 111 type=186 (LJ14) 40 46 60: 112 type=199 (LJ14) 40 47 60: 113 type=188 (LJ14) 40 59 60: 114 type=189 (LJ14) 40 60 60: 115 type=190 (LJ14) 41 43 60: 116 type=190 (LJ14) 41 44 60: 117 type=190 (LJ14) 41 58 60: 118 type=200 (LJ14) 42 48 60: 119 type=200 (LJ14) 42 50 60: 120 type=190 (LJ14) 42 61 60: 121 type=192 (LJ14) 42 62 60: 122 type=193 (LJ14) 43 45 60: 123 type=193 (LJ14) 43 46 60: 124 type=201 (LJ14) 43 47 60: 125 type=194 (LJ14) 43 59 60: 126 type=186 (LJ14) 43 60 60: 127 type=202 (LJ14) 44 49 60: 128 type=202 (LJ14) 44 51 60: 129 type=200 (LJ14) 44 52 60: 130 type=200 (LJ14) 44 54 60: 131 type=195 (LJ14) 44 59 60: 132 type=187 (LJ14) 44 60 60: 133 type=201 (LJ14) 45 48 60: 134 type=201 (LJ14) 45 50 60: 135 type=196 (LJ14) 45 58 60: 136 type=201 (LJ14) 46 48 60: 137 type=201 (LJ14) 46 50 60: 138 type=196 (LJ14) 46 58 60: 139 type=203 (LJ14) 47 53 60: 140 type=203 (LJ14) 47 55 60: 141 type=204 (LJ14) 47 56 60: 142 type=205 (LJ14) 47 58 60: 143 type=203 (LJ14) 48 51 60: 144 type=204 (LJ14) 48 54 60: 145 type=203 (LJ14) 48 57 60: 146 type=203 (LJ14) 49 50 60: 147 type=206 (LJ14) 49 53 60: 148 type=203 (LJ14) 49 56 60: 149 type=204 (LJ14) 50 52 60: 150 type=203 (LJ14) 50 57 60: 151 type=206 (LJ14) 51 55 60: 152 type=203 (LJ14) 51 56 60: 153 type=203 (LJ14) 52 55 60: 154 type=203 (LJ14) 53 54 60: 155 type=206 (LJ14) 53 57 60: 156 type=206 (LJ14) 55 57 60: 157 type=196 (LJ14) 58 63 60: 158 type=196 (LJ14) 58 64 60: 159 type=198 (LJ14) 58 65 60: 160 type=190 (LJ14) 59 61 60: 161 type=195 (LJ14) 59 62 60: 162 type=188 (LJ14) 60 66 60: 163 type=189 (LJ14) 60 67 60: 164 type=190 (LJ14) 61 63 60: 165 type=190 (LJ14) 61 64 60: 166 type=190 (LJ14) 61 65 60: 167 type=190 (LJ14) 62 68 60: 168 type=192 (LJ14) 62 69 60: 169 type=194 (LJ14) 63 66 60: 170 type=186 (LJ14) 63 67 60: 171 type=194 (LJ14) 64 66 60: 172 type=186 (LJ14) 64 67 60: 173 type=196 (LJ14) 65 70 60: 174 type=197 (LJ14) 65 71 60: 175 type=198 (LJ14) 65 89 60: 176 type=190 (LJ14) 66 68 60: 177 type=195 (LJ14) 66 69 60: 178 type=186 (LJ14) 67 72 60: 179 type=186 (LJ14) 67 73 60: 180 type=187 (LJ14) 67 74 60: 181 type=188 (LJ14) 67 90 60: 182 type=189 (LJ14) 67 91 60: 183 type=190 (LJ14) 68 70 60: 184 type=190 (LJ14) 68 71 60: 185 type=190 (LJ14) 68 89 60: 186 type=191 (LJ14) 69 75 60: 187 type=191 (LJ14) 69 76 60: 188 type=192 (LJ14) 69 77 60: 189 type=190 (LJ14) 69 92 60: 190 type=192 (LJ14) 69 93 60: 191 type=193 (LJ14) 70 72 60: 192 type=193 (LJ14) 70 73 60: 193 type=191 (LJ14) 70 74 60: 194 type=194 (LJ14) 70 90 60: 195 type=186 (LJ14) 70 91 60: 196 type=191 (LJ14) 71 78 60: 197 type=191 (LJ14) 71 79 60: 198 type=187 (LJ14) 71 80 60: 199 type=195 (LJ14) 71 90 60: 200 type=187 (LJ14) 71 91 60: 201 type=193 (LJ14) 72 75 60: 202 type=193 (LJ14) 72 76 60: 203 type=191 (LJ14) 72 77 60: 204 type=196 (LJ14) 72 89 60: 205 type=193 (LJ14) 73 75 60: 206 type=193 (LJ14) 73 76 60: 207 type=191 (LJ14) 73 77 60: 208 type=196 (LJ14) 73 89 60: 209 type=190 (LJ14) 74 81 60: 210 type=207 (LJ14) 74 82 60: 211 type=197 (LJ14) 74 89 60: 212 type=193 (LJ14) 75 78 60: 213 type=193 (LJ14) 75 79 60: 214 type=186 (LJ14) 75 80 60: 215 type=193 (LJ14) 76 78 60: 216 type=193 (LJ14) 76 79 60: 217 type=186 (LJ14) 76 80 60: 218 type=187 (LJ14) 77 83 60: 219 type=187 (LJ14) 77 86 60: 220 type=190 (LJ14) 78 81 60: 221 type=208 (LJ14) 78 82 60: 222 type=190 (LJ14) 79 81 60: 223 type=208 (LJ14) 79 82 60: 224 type=190 (LJ14) 80 84 60: 225 type=190 (LJ14) 80 85 60: 226 type=190 (LJ14) 80 87 60: 227 type=190 (LJ14) 80 88 60: 228 type=190 (LJ14) 81 83 60: 229 type=190 (LJ14) 81 86 60: 230 type=190 (LJ14) 83 87 60: 231 type=190 (LJ14) 83 88 60: 232 type=190 (LJ14) 84 86 60: 233 type=190 (LJ14) 85 86 60: 234 type=196 (LJ14) 89 94 60: 235 type=197 (LJ14) 89 95 60: 236 type=198 (LJ14) 89 100 60: 237 type=190 (LJ14) 90 92 60: 238 type=195 (LJ14) 90 93 60: 239 type=186 (LJ14) 91 96 60: 240 type=186 (LJ14) 91 97 60: 241 type=209 (LJ14) 91 98 60: 242 type=188 (LJ14) 91 101 60: 243 type=189 (LJ14) 91 102 60: 244 type=190 (LJ14) 92 94 60: 245 type=190 (LJ14) 92 95 60: 246 type=190 (LJ14) 92 100 60: 247 type=190 (LJ14) 93 99 60: 248 type=190 (LJ14) 93 103 60: 249 type=192 (LJ14) 93 104 60: 250 type=193 (LJ14) 94 96 60: 251 type=193 (LJ14) 94 97 60: 252 type=210 (LJ14) 94 98 60: 253 type=194 (LJ14) 94 101 60: 254 type=186 (LJ14) 94 102 60: 255 type=195 (LJ14) 95 101 60: 256 type=187 (LJ14) 95 102 60: 257 type=190 (LJ14) 96 99 60: 258 type=196 (LJ14) 96 100 60: 259 type=190 (LJ14) 97 99 60: 260 type=196 (LJ14) 97 100 60: 261 type=211 (LJ14) 98 100 60: 262 type=196 (LJ14) 100 105 60: 263 type=197 (LJ14) 100 106 60: 264 type=198 (LJ14) 100 115 60: 265 type=190 (LJ14) 101 103 60: 266 type=195 (LJ14) 101 104 60: 267 type=186 (LJ14) 102 107 60: 268 type=186 (LJ14) 102 108 60: 269 type=187 (LJ14) 102 109 60: 270 type=188 (LJ14) 102 116 60: 271 type=189 (LJ14) 102 117 60: 272 type=190 (LJ14) 103 105 60: 273 type=190 (LJ14) 103 106 60: 274 type=190 (LJ14) 103 115 60: 275 type=191 (LJ14) 104 110 60: 276 type=191 (LJ14) 104 111 60: 277 type=197 (LJ14) 104 112 60: 278 type=190 (LJ14) 104 118 60: 279 type=192 (LJ14) 104 119 60: 280 type=193 (LJ14) 105 107 60: 281 type=193 (LJ14) 105 108 60: 282 type=191 (LJ14) 105 109 60: 283 type=194 (LJ14) 105 116 60: 284 type=186 (LJ14) 105 117 60: 285 type=195 (LJ14) 106 113 60: 286 type=195 (LJ14) 106 114 60: 287 type=195 (LJ14) 106 116 60: 288 type=187 (LJ14) 106 117 60: 289 type=193 (LJ14) 107 110 60: 290 type=193 (LJ14) 107 111 60: 291 type=196 (LJ14) 107 112 60: 292 type=196 (LJ14) 107 115 60: 293 type=193 (LJ14) 108 110 60: 294 type=193 (LJ14) 108 111 60: 295 type=196 (LJ14) 108 112 60: 296 type=196 (LJ14) 108 115 60: 297 type=197 (LJ14) 109 115 60: 298 type=194 (LJ14) 110 113 60: 299 type=194 (LJ14) 110 114 60: 300 type=194 (LJ14) 111 113 60: 301 type=194 (LJ14) 111 114 60: 302 type=196 (LJ14) 115 120 60: 303 type=197 (LJ14) 115 121 60: 304 type=198 (LJ14) 115 134 60: 305 type=190 (LJ14) 116 118 60: 306 type=195 (LJ14) 116 119 60: 307 type=186 (LJ14) 117 122 60: 308 type=186 (LJ14) 117 123 60: 309 type=187 (LJ14) 117 124 60: 310 type=188 (LJ14) 117 135 60: 311 type=189 (LJ14) 117 136 60: 312 type=190 (LJ14) 118 120 60: 313 type=190 (LJ14) 118 121 60: 314 type=190 (LJ14) 118 134 60: 315 type=191 (LJ14) 119 125 60: 316 type=192 (LJ14) 119 126 60: 317 type=192 (LJ14) 119 130 60: 318 type=190 (LJ14) 119 137 60: 319 type=192 (LJ14) 119 138 60: 320 type=193 (LJ14) 120 122 60: 321 type=193 (LJ14) 120 123 60: 322 type=191 (LJ14) 120 124 60: 323 type=194 (LJ14) 120 135 60: 324 type=186 (LJ14) 120 136 60: 325 type=191 (LJ14) 121 127 60: 326 type=191 (LJ14) 121 128 60: 327 type=191 (LJ14) 121 129 60: 328 type=191 (LJ14) 121 131 60: 329 type=191 (LJ14) 121 132 60: 330 type=191 (LJ14) 121 133 60: 331 type=195 (LJ14) 121 135 60: 332 type=187 (LJ14) 121 136 60: 333 type=193 (LJ14) 122 125 60: 334 type=191 (LJ14) 122 126 60: 335 type=191 (LJ14) 122 130 60: 336 type=196 (LJ14) 122 134 60: 337 type=193 (LJ14) 123 125 60: 338 type=191 (LJ14) 123 126 60: 339 type=191 (LJ14) 123 130 60: 340 type=196 (LJ14) 123 134 60: 341 type=197 (LJ14) 124 134 60: 342 type=193 (LJ14) 125 127 60: 343 type=193 (LJ14) 125 128 60: 344 type=193 (LJ14) 125 129 60: 345 type=193 (LJ14) 125 131 60: 346 type=193 (LJ14) 125 132 60: 347 type=193 (LJ14) 125 133 60: 348 type=191 (LJ14) 126 131 60: 349 type=191 (LJ14) 126 132 60: 350 type=191 (LJ14) 126 133 60: 351 type=191 (LJ14) 127 130 60: 352 type=191 (LJ14) 128 130 60: 353 type=191 (LJ14) 129 130 60: 354 type=196 (LJ14) 134 139 60: 355 type=197 (LJ14) 134 140 60: 356 type=198 (LJ14) 134 144 60: 357 type=190 (LJ14) 135 137 60: 358 type=195 (LJ14) 135 138 60: 359 type=186 (LJ14) 136 141 60: 360 type=186 (LJ14) 136 142 60: 361 type=186 (LJ14) 136 143 60: 362 type=188 (LJ14) 136 145 60: 363 type=189 (LJ14) 136 146 60: 364 type=190 (LJ14) 137 139 60: 365 type=190 (LJ14) 137 140 60: 366 type=190 (LJ14) 137 144 60: 367 type=190 (LJ14) 138 147 60: 368 type=192 (LJ14) 138 148 60: 369 type=193 (LJ14) 139 141 60: 370 type=193 (LJ14) 139 142 60: 371 type=193 (LJ14) 139 143 60: 372 type=194 (LJ14) 139 145 60: 373 type=186 (LJ14) 139 146 60: 374 type=195 (LJ14) 140 145 60: 375 type=187 (LJ14) 140 146 60: 376 type=196 (LJ14) 141 144 60: 377 type=196 (LJ14) 142 144 60: 378 type=196 (LJ14) 143 144 60: 379 type=196 (LJ14) 144 149 60: 380 type=197 (LJ14) 144 150 60: 381 type=198 (LJ14) 144 154 60: 382 type=190 (LJ14) 145 147 60: 383 type=195 (LJ14) 145 148 60: 384 type=186 (LJ14) 146 151 60: 385 type=186 (LJ14) 146 152 60: 386 type=186 (LJ14) 146 153 60: 387 type=188 (LJ14) 146 155 60: 388 type=190 (LJ14) 147 149 60: 389 type=190 (LJ14) 147 150 60: 390 type=190 (LJ14) 147 154 60: 391 type=193 (LJ14) 149 151 60: 392 type=193 (LJ14) 149 152 60: 393 type=193 (LJ14) 149 153 60: 394 type=194 (LJ14) 149 155 60: 395 type=195 (LJ14) 150 155 60: 396 type=196 (LJ14) 151 154 60: 397 type=196 (LJ14) 152 154 60: 398 type=196 (LJ14) 153 154 60: Coulomb-14: 60: nr: 0 60: LJC-14 q: 60: nr: 0 60: LJC Pairs NB: 60: nr: 0 60: LJ (SR): 60: nr: 0 60: Buck.ham (SR): 60: nr: 0 60: LJ: 60: nr: 0 60: B.ham: 60: nr: 0 60: Disper. corr.: 60: nr: 0 60: Coulomb (SR): 60: nr: 0 60: Coul: 60: nr: 0 60: RF excl.: 60: nr: 0 60: Coul. recip.: 60: nr: 0 60: LJ recip.: 60: nr: 0 60: DPD: 60: nr: 0 60: Polarization: 60: nr: 0 60: Water Pol.: 60: nr: 0 60: Thole Pol.: 60: nr: 0 60: Anharm. Pol.: 60: nr: 0 60: Position Rest.: 60: nr: 0 60: Flat-b. P-R.: 60: nr: 0 60: Dis. Rest.: 60: nr: 0 60: D.R.Viol. (nm): 60: nr: 0 60: Orient. Rest.: 60: nr: 0 60: Ori. R. RMSD: 60: nr: 0 60: Angle Rest.: 60: nr: 0 60: Angle Rest. Z: 60: nr: 0 60: Dih. Rest.: 60: nr: 0 60: Dih. Rest. Vi.: 60: nr: 0 60: Constraint: 60: nr: 0 60: Constr. No Co.: 60: nr: 0 60: Settle: 60: nr: 0 60: Virtual site 1: 60: nr: 0 60: Virtual site 2: 60: nr: 0 60: Virt. site 2fd: 60: nr: 0 60: Virtual site 3: 60: nr: 0 60: Virt. site 3fd: 60: nr: 0 60: Vir. site 3fad: 60: nr: 0 60: Vir. site 3out: 60: nr: 0 60: Virt. site 4fd: 60: nr: 0 60: Vir. site 4fdn: 60: nr: 0 60: Virtual site N: 60: nr: 0 60: COM Pull En.: 60: nr: 0 60: Dens. fitting: 60: nr: 0 60: Quantum En.: 60: nr: 0 60: Potential: 60: nr: 0 60: Kinetic En.: 60: nr: 0 60: Total Energy: 60: nr: 0 60: Conserved En.: 60: nr: 0 60: Temperature: 60: nr: 0 60: Vir. Temp.: 60: nr: 0 60: Pres. DC: 60: nr: 0 60: Pressure: 60: nr: 0 60: dH/dl constr.: 60: nr: 0 60: dVremain/dl: 60: nr: 0 60: dEkin/dl: 60: nr: 0 60: dVcoul/dl: 60: nr: 0 60: dVvdw/dl: 60: nr: 0 60: dVbonded/dl: 60: nr: 0 60: dVrestraint/dl: 60: nr: 0 60: dVtemp/dl: 60: nr: 0 60: grp[T-Coupling ] nr=1, name=[ rest] 60: grp[Energy Mon. ] nr=1, name=[ rest] 60: grp[Acc. not used] nr=1, name=[ rest] 60: grp[Freeze ] nr=1, name=[ rest] 60: grp[User1 ] nr=1, name=[ rest] 60: grp[User2 ] nr=1, name=[ rest] 60: grp[VCM ] nr=1, name=[ rest] 60: grp[Compressed X] nr=1, name=[ rest] 60: grp[Or. Res. Fit] nr=1, name=[ rest] 60: grp[QMMM ] nr=1, name=[ rest] 60: grpname (11): 60: grpname[0]={name="System"} 60: grpname[1]={name="Protein"} 60: grpname[2]={name="Protein-H"} 60: grpname[3]={name="C-alpha"} 60: grpname[4]={name="Backbone"} 60: grpname[5]={name="MainChain"} 60: grpname[6]={name="MainChain+Cb"} 60: grpname[7]={name="MainChain+H"} 60: grpname[8]={name="SideChain"} 60: grpname[9]={name="SideChain-H"} 60: grpname[10]={name="rest"} 60: groups T-Cou Energ Acc. Freez User1 User2 VCM Compr Or. R QMMM 60: allocated 0 0 0 0 0 0 0 0 0 0 60: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0 60: box (3x3): 60: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00} 60: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00} 60: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00} 60: box_rel (3x3): 60: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: boxv (3x3): 60: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: pres_prev (3x3): 60: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: svir_prev (3x3): 60: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: fvir_prev (3x3): 60: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: nosehoover_xi: not available 60: x (156x3): 60: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00} 60: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00} 60: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00} 60: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00} 60: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00} 60: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00} 60: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00} 60: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00} 60: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01} 60: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01} 60: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01} 60: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00} 60: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01} 60: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01} 60: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01} 60: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01} 60: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01} 60: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01} 60: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01} 60: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01} 60: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01} 60: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01} 60: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00} 60: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00} 60: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00} 60: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00} 60: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00} 60: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01} 60: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00} 60: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00} 60: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00} 60: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00} 60: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01} 60: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01} 60: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00} 60: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00} 60: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00} 60: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00} 60: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01} 60: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01} 60: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01} 60: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01} 60: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01} 60: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01} 60: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01} 60: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01} 60: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01} 60: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01} 60: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01} 60: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01} 60: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01} 60: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01} 60: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01} 60: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01} 60: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01} 60: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01} 60: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01} 60: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01} 60: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01} 60: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01} 60: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01} 60: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01} 60: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01} 60: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01} 60: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01} 60: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01} 60: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01} 60: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01} 60: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01} 60: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01} 60: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01} 60: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01} 60: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01} 60: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01} 60: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02} 60: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02} 60: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02} 60: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02} 60: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02} 60: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01} 60: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02} 60: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01} 60: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02} 60: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01} 60: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01} 60: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01} 60: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02} 60: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01} 60: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02} 60: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01} 60: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02} 60: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01} 60: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01} 60: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02} 60: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02} 60: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02} 60: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01} 60: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02} 60: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02} 60: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02} 60: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02} 60: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02} 60: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01} 60: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01} 60: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01} 60: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01} 60: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01} 60: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01} 60: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01} 60: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01} 60: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01} 60: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01} 60: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01} 60: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01} 60: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01} 60: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01} 60: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01} 60: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01} 60: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01} 60: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01} 60: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01} 60: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01} 60: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01} 60: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01} 60: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01} 60: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02} 60: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01} 60: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01} 60: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01} 60: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01} 60: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01} 60: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01} 60: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01} 60: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01} 60: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02} 60: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02} 60: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02} 60: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02} 60: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01} 60: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01} 60: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01} 60: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01} 60: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01} 60: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01} 60: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01} 60: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01} 60: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01} 60: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01} 60: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01} 60: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01} 60: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01} 60: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01} 60: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01} 60: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02} 60: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01} 60: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01} 60: v (156x3): 60: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: Group statistics 60: T-Coupling : 156 (total 156 atoms) 60: Energy Mon. : 156 (total 156 atoms) 60: Acc. not used: 156 (total 156 atoms) 60: Freeze : 156 (total 156 atoms) 60: User1 : 156 (total 156 atoms) 60: User2 : 156 (total 156 atoms) 60: VCM : 156 (total 156 atoms) 60: Compressed X: 156 (total 156 atoms) 60: Or. Res. Fit: 156 (total 156 atoms) 60: QMMM : 156 (total 156 atoms) 60: [ OK ] DumpTest.WorksWithTpr (39 ms) 60: [ RUN ] DumpTest.WorksWithTprAndMdpWriting 60: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 60: [ OK ] DumpTest.WorksWithTprAndMdpWriting (0 ms) 60: [----------] 2 tests from DumpTest (41 ms total) 60: 60: [----------] 3 tests from HelpwritingTest 60: [ RUN ] HelpwritingTest.ConvertTprWritesHelp 60: [ OK ] HelpwritingTest.ConvertTprWritesHelp (0 ms) 60: [ RUN ] HelpwritingTest.DumpWritesHelp 60: [ OK ] HelpwritingTest.DumpWritesHelp (0 ms) 60: [ RUN ] HelpwritingTest.ReportMethodsWritesHelp 60: [ OK ] HelpwritingTest.ReportMethodsWritesHelp (0 ms) 60: [----------] 3 tests from HelpwritingTest (0 ms total) 60: 60: [----------] 7 tests from GmxMakeNdx 60: [ RUN ] GmxMakeNdx.WritesDefaultProteinIndexGroups 60: 60: Reading structure file 60: Going to read 0 old index file(s) 60: Analysing residue names: 60: There are: 16 Protein residues 60: Analysing Protein... 60: 60: 0 System : 256 atoms 60: 1 Protein : 256 atoms 60: 2 Protein-H : 139 atoms 60: 3 C-alpha : 16 atoms 60: 4 Backbone : 48 atoms 60: 5 MainChain : 63 atoms 60: 6 MainChain+Cb : 78 atoms 60: 7 MainChain+H : 81 atoms 60: 8 SideChain : 175 atoms 60: 9 SideChain-H : 76 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: [ OK ] GmxMakeNdx.WritesDefaultProteinIndexGroups (2 ms) 60: [ RUN ] GmxMakeNdx.HandlesNoStructureInput 60: Going to read 1 old index file(s) 60: Deducing 22 atoms in the system from indices in the index file 60: 60: 0 System : 22 atoms 60: 1 Protein : 22 atoms 60: 2 Protein-H : 10 atoms 60: 3 C-alpha : 1 atoms 60: 4 Backbone : 5 atoms 60: 5 MainChain : 7 atoms 60: 6 MainChain+Cb : 8 atoms 60: 7 MainChain+H : 9 atoms 60: 8 SideChain : 13 atoms 60: 9 SideChain-H : 3 atoms 60: 10 CA : 1 atoms 60: 11 C_&_r_1 : 1 atoms 60: 12 C_&_r_2 : 1 atoms 60: 13 N_&_r_2 : 1 atoms 60: 14 N_&_r_3 : 1 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: Copied index group 1 'Protein' 60: Copied index group 2 'Protein-H' 60: Merged two groups with OR: 22 10 -> 22 60: 60: > 60: [ OK ] GmxMakeNdx.HandlesNoStructureInput (1 ms) 60: [ RUN ] GmxMakeNdx.HandlesNotProtein 60: Going to read 1 old index file(s) 60: Deducing 6 atoms in the system from indices in the index file 60: 60: 0 System : 6 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: [ OK ] GmxMakeNdx.HandlesNotProtein (0 ms) 60: [ RUN ] GmxMakeNdx.HandlesEmptyIndexResult 60: Going to read 1 old index file(s) 60: Deducing 22 atoms in the system from indices in the index file 60: 60: 0 System : 22 atoms 60: 1 Protein : 22 atoms 60: 2 Protein-H : 10 atoms 60: 3 C-alpha : 1 atoms 60: 4 Backbone : 5 atoms 60: 5 MainChain : 7 atoms 60: 6 MainChain+Cb : 8 atoms 60: 7 MainChain+H : 9 atoms 60: 8 SideChain : 13 atoms 60: 9 SideChain-H : 3 atoms 60: 10 CA : 1 atoms 60: 11 C_&_r_1 : 1 atoms 60: 12 C_&_r_2 : 1 atoms 60: 13 N_&_r_2 : 1 atoms 60: 14 N_&_r_3 : 1 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: Copied index group 4 'Backbone' 60: Copied index group 8 'SideChain' 60: Merged two groups with AND: 5 13 -> 0 60: Group is empty 60: 60: > 60: [ OK ] GmxMakeNdx.HandlesEmptyIndexResult (0 ms) 60: [ RUN ] GmxMakeNdx.HandlesEmptyIndexFile 60: Going to read 1 old index file(s) 60: Deducing 6 atoms in the system from indices in the index file 60: 60: 0 System : 6 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: Removed group 0 'System' 60: 60: > 60: [ OK ] GmxMakeNdx.HandlesEmptyIndexFile (3 ms) 60: [ RUN ] GmxMakeNdx.Splitres 60: 60: Reading structure file 60: Going to read 0 old index file(s) 60: Analysing residue names: 60: There are: 2 Water residues 60: 60: 0 System : 6 atoms 60: 1 Water : 6 atoms 60: 2 SOL : 6 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: Splitting group 1 'Water' into residues 60: 60: > 60: [ OK ] GmxMakeNdx.Splitres (0 ms) 60: [ RUN ] GmxMakeNdx.Splitat 60: 60: Reading structure file 60: Going to read 0 old index file(s) 60: Analysing residue names: 60: There are: 2 Water residues 60: 60: 0 System : 6 atoms 60: 1 Water : 6 atoms 60: 2 SOL : 6 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: Splitting group 1 'Water' into atoms 60: 60: > 60: [ OK ] GmxMakeNdx.Splitat (1 ms) 60: [----------] 7 tests from GmxMakeNdx (9 ms total) 60: 60: [----------] 4 tests from ReportMethodsTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Setting the LD random seed to -336626697 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated 60: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms) 60: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted 60: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms) 60: [ RUN ] ReportMethodsTest.WritesCorrectInformation 60: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 60: [ OK ] ReportMethodsTest.WritesCorrectInformation (0 ms) 60: [ RUN ] ReportMethodsTest.ToolEndToEndTest 60: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 60: section: Methods 60: subsection: Simulation system 60: A system of 1 molecules (156 atoms) was simulated. 60: 60: subsection: Simulation settings 60: A total of 0 ns were simulated with a time step of 1 fs. 60: Neighbor searching was performed every 10 steps. 60: The Cut-off algorithm was used for electrostatic interactions. 60: with a cut-off of 1 nm. 60: A single cut-off of 1.1 nm was used for Van der Waals interactions. 60: [ OK ] ReportMethodsTest.ToolEndToEndTest (0 ms) 60: [----------] 4 tests from ReportMethodsTest (5 ms total) 60: 60: [----------] 4 tests from ConvertTprTest 60: [ RUN ] ConvertTprTest.ExtendRuntimeExtensionTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended_again.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 60: Setting the LD random seed to -1143406925 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 0 60: Runtime for the run 0 ps 60: Run end step 0 60: Run end time 0 ps 60: 60: Extending remaining runtime by 100 ps 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 100000 60: Runtime for the run 100 ps 60: Run end step 100000 60: Run end time 100 ps 60: 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 100000 60: Runtime for the run 100 ps 60: Run end step 100000 60: Run end time 100 ps 60: 60: Extending remaining runtime by 100 ps 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 200000 60: Runtime for the run 200 ps 60: Run end step 200000 60: Run end time 200 ps 60: 60: [ OK ] ConvertTprTest.ExtendRuntimeExtensionTest (579 ms) 60: [ RUN ] ConvertTprTest.UntilRuntimeExtensionTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_extended.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 60: Setting the LD random seed to -608360581 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 0 60: Runtime for the run 0 ps 60: Run end step 0 60: Run end time 0 ps 60: 60: Extending remaining runtime to 100 ps 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 100000 60: Runtime for the run 100 ps 60: Run end step 100000 60: Run end time 100 ps 60: 60: [ OK ] ConvertTprTest.UntilRuntimeExtensionTest (507 ms) 60: [ RUN ] ConvertTprTest.nstepRuntimeExtensionTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 60: Setting nsteps to 102 60: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_extended.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 60: Setting the LD random seed to -131137 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 0 60: Runtime for the run 0 ps 60: Run end step 0 60: Run end time 0 ps 60: 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 102 60: Runtime for the run 0.102 ps 60: Run end step 102 60: Run end time 0.102 ps 60: 60: [ OK ] ConvertTprTest.nstepRuntimeExtensionTest (433 ms) 60: [ RUN ] ConvertTprTest.generateVelocitiesTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_new_velocities.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 60: Setting the LD random seed to -1080671242 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] ConvertTprTest.generateVelocitiesTest (593 ms) 60: [----------] 4 tests from ConvertTprTest (2114 ms total) 60: 60: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: trr version: GMX_trn_file (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr (1 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng (1 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro (1 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb (1 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 (1 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr (1 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng (1 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc (1 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro (1 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb (1 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 (1 ms) 60: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats (16 ms total) 60: 60: [----------] 30 tests from Works/TrjconvDumpTest 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 (1 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 (1 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 (1 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 (1 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 (1 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 (1 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 (1 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 (4 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 (0 ms) 60: [----------] 30 tests from Works/TrjconvDumpTest (26 ms total) 60: 60: [----------] Global test environment tear-down 60: [==========] 62 tests from 7 test suites ran. (2948 ms total) 60: [ PASSED ] 62 tests. 60/91 Test #60: ToolUnitTests ................................ Passed 3.31 sec test 61 Start 61: FileIOTests 61: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/fileio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/FileIOTests.xml" 61: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fileio/tests 61: Test timeout computed to be: 30 61: [==========] Running 413 tests from 15 test suites. 61: [----------] Global test environment set-up. 61: [----------] 4 tests from Checkpoint 61: [ RUN ] Checkpoint.ReadingThrowsWhenValueNotPresent 61: [ OK ] Checkpoint.ReadingThrowsWhenValueNotPresent (0 ms) 61: [ RUN ] Checkpoint.ReadingDoesNotThrowWhenValuePresent 61: [ OK ] Checkpoint.ReadingDoesNotThrowWhenValuePresent (0 ms) 61: [ RUN ] Checkpoint.KvtRoundTripInt64 61: [ OK ] Checkpoint.KvtRoundTripInt64 (0 ms) 61: [ RUN ] Checkpoint.KvtRoundTripReal 61: [ OK ] Checkpoint.KvtRoundTripReal (0 ms) 61: [----------] 4 tests from Checkpoint (0 ms total) 61: 61: [----------] 1 test from StructureIOTest 61: [ RUN ] StructureIOTest.ReadTpsConfRetainsChainids 61: [ OK ] StructureIOTest.ReadTpsConfRetainsChainids (0 ms) 61: [----------] 1 test from StructureIOTest (0 ms total) 61: 61: [----------] 2 tests from FileMD5Test 61: [ RUN ] FileMD5Test.CanComputeMD5 61: [ OK ] FileMD5Test.CanComputeMD5 (1 ms) 61: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 61: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 61: [----------] 2 tests from FileMD5Test (1 ms total) 61: 61: [----------] 4 tests from FileTypeTest 61: [ RUN ] FileTypeTest.CorrectValueForEmptyString 61: [ OK ] FileTypeTest.CorrectValueForEmptyString (0 ms) 61: [ RUN ] FileTypeTest.CorrectValueForNoExtension 61: [ OK ] FileTypeTest.CorrectValueForNoExtension (0 ms) 61: [ RUN ] FileTypeTest.CorrectValueForEmptyExtension 61: [ OK ] FileTypeTest.CorrectValueForEmptyExtension (0 ms) 61: [ RUN ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters 61: [ OK ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters (0 ms) 61: [----------] 4 tests from FileTypeTest (0 ms total) 61: 61: [----------] 3 tests from MrcSerializer 61: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet 61: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms) 61: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize 61: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms) 61: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip 61: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (0 ms) 61: [----------] 3 tests from MrcSerializer (0 ms total) 61: 61: [----------] 4 tests from MrcDensityMap 61: [ RUN ] MrcDensityMap.RoundTripIsIdempotent 61: [ OK ] MrcDensityMap.RoundTripIsIdempotent (0 ms) 61: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent 61: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms) 61: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile 61: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms) 61: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile 61: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (0 ms) 61: [----------] 4 tests from MrcDensityMap (0 ms total) 61: 61: [----------] 8 tests from MrcDensityMapHeaderTest 61: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader 61: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms) 61: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect 61: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms) 61: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid 61: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms) 61: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven 61: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms) 61: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined 61: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms) 61: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues 61: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms) 61: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents 61: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms) 61: [ RUN ] MrcDensityMapHeaderTest.IsSane 61: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms) 61: [----------] 8 tests from MrcDensityMapHeaderTest (0 ms total) 61: 61: [----------] 10 tests from ReadTest 61: [ RUN ] ReadTest.get_eint_ReadsInteger 61: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 61: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 61: 61: ERROR 1 [file unknown]: 61: Right hand side '0.8' for parameter 'test' in parameter file is not an 61: integer value 61: 61: 61: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 61: [ RUN ] ReadTest.get_eint_WarnsAboutString 61: 61: ERROR 1 [file unknown]: 61: Right hand side 'hello' for parameter 'test' in parameter file is not an 61: integer value 61: 61: 61: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 61: [ RUN ] ReadTest.get_eint64_ReadsInteger 61: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 61: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 61: 61: ERROR 1 [file unknown]: 61: Right hand side '0.8' for parameter 'test' in parameter file is not an 61: integer value 61: 61: 61: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 61: [ RUN ] ReadTest.get_eint64_WarnsAboutString 61: 61: ERROR 1 [file unknown]: 61: Right hand side 'hello' for parameter 'test' in parameter file is not an 61: integer value 61: 61: 61: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 61: [ RUN ] ReadTest.get_ereal_ReadsInteger 61: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 61: [ RUN ] ReadTest.get_ereal_ReadsFloat 61: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 61: [ RUN ] ReadTest.get_ereal_WarnsAboutString 61: 61: ERROR 1 [file unknown]: 61: Right hand side 'hello' for parameter 'test' in parameter file is not a 61: real value 61: 61: 61: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 61: [ RUN ] ReadTest.setStringEntry_ReturnsCorrectString 61: [ OK ] ReadTest.setStringEntry_ReturnsCorrectString (0 ms) 61: [----------] 10 tests from ReadTest (0 ms total) 61: 61: [----------] 3 tests from TimeControlTest 61: [ RUN ] TimeControlTest.UnSetHasNoValue 61: [ OK ] TimeControlTest.UnSetHasNoValue (0 ms) 61: [ RUN ] TimeControlTest.CanSetValue 61: [ OK ] TimeControlTest.CanSetValue (0 ms) 61: [ RUN ] TimeControlTest.CanUnsetValueAgain 61: [ OK ] TimeControlTest.CanUnsetValueAgain (0 ms) 61: [----------] 3 tests from TimeControlTest (0 ms total) 61: 61: [----------] 1 test from FileIOXdrSerializerTest 61: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect 61: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (0 ms) 61: [----------] 1 test from FileIOXdrSerializerTest (0 ms total) 61: 61: [----------] 1 test from TngTest 61: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 61: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 61: [----------] 1 test from TngTest (0 ms total) 61: 61: [----------] 4 tests from XvgioTest 61: [ RUN ] XvgioTest.readXvgIntWorks 61: [ OK ] XvgioTest.readXvgIntWorks (0 ms) 61: [ RUN ] XvgioTest.readXvgRealWorks 61: [ OK ] XvgioTest.readXvgRealWorks (0 ms) 61: [ RUN ] XvgioTest.readXvgIgnoreCommentLineWorks 61: [ OK ] XvgioTest.readXvgIgnoreCommentLineWorks (0 ms) 61: [ RUN ] XvgioTest.readXvgDeprecatedWorks 61: [ OK ] XvgioTest.readXvgDeprecatedWorks (0 ms) 61: [----------] 4 tests from XvgioTest (0 ms total) 61: 61: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 61: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 61: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (0 ms) 61: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 61: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (0 ms) 61: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 61: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (0 ms) 61: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 61: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (0 ms) 61: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (1 ms total) 61: 61: [----------] 360 tests from FileTypeMatch/FileTypeTest 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 (0 ms) 61: [----------] 360 tests from FileTypeMatch/FileTypeTest (1 ms total) 61: 61: [----------] 4 tests from XvgReadTimeSeries/XvgioTest 61: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 61: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 (0 ms) 61: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 61: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 (0 ms) 61: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 61: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 (0 ms) 61: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 61: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 (0 ms) 61: [----------] 4 tests from XvgReadTimeSeries/XvgioTest (0 ms total) 61: 61: [----------] Global test environment tear-down 61: [==========] 413 tests from 15 test suites ran. (6 ms total) 61: [ PASSED ] 413 tests. 61/91 Test #61: FileIOTests .................................. Passed 0.38 sec test 62 Start 62: SelectionUnitTests 62: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/selection-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/SelectionUnitTests.xml" 62: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/selection/tests 62: Test timeout computed to be: 30 62: [==========] Running 201 tests from 11 test suites. 62: [----------] Global test environment set-up. 62: [----------] 1 test from IndexGroupTest 62: [ RUN ] IndexGroupTest.RemovesDuplicates 62: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) 62: [----------] 1 test from IndexGroupTest (0 ms total) 62: 62: [----------] 15 tests from IndexBlockTest 62: [ RUN ] IndexBlockTest.CreatesUnknownBlock 62: [ OK ] IndexBlockTest.CreatesUnknownBlock (0 ms) 62: [ RUN ] IndexBlockTest.CreatesAtomBlock 62: [ OK ] IndexBlockTest.CreatesAtomBlock (0 ms) 62: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology 62: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (0 ms) 62: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology 62: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (0 ms) 62: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology 62: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms) 62: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology 62: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (0 ms) 62: [ RUN ] IndexBlockTest.CreatesSingleBlock 62: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms) 62: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive 62: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms) 62: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive 62: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) 62: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative 62: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) 62: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial 62: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) 62: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive 62: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) 62: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative 62: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) 62: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive 62: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) 62: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative 62: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) 62: [----------] 15 tests from IndexBlockTest (0 ms total) 62: 62: [----------] 11 tests from IndexMapTest 62: [ RUN ] IndexMapTest.InitializesAtomBlock 62: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms) 62: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom 62: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms) 62: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle 62: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms) 62: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue 62: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms) 62: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule 62: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms) 62: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll 62: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms) 62: [ RUN ] IndexMapTest.InitializesMoleculeBlock 62: [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms) 62: [ RUN ] IndexMapTest.MapsSingleBlock 62: [ OK ] IndexMapTest.MapsSingleBlock (0 ms) 62: [ RUN ] IndexMapTest.MapsResidueBlocks 62: [ OK ] IndexMapTest.MapsResidueBlocks (0 ms) 62: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask 62: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (0 ms) 62: [ RUN ] IndexMapTest.HandlesMultipleRequests 62: [ OK ] IndexMapTest.HandlesMultipleRequests (0 ms) 62: [----------] 11 tests from IndexMapTest (0 ms total) 62: 62: [----------] 3 tests from IndexGroupsAndNamesTest 62: [ RUN ] IndexGroupsAndNamesTest.containsNames 62: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms) 62: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing 62: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms) 62: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect 62: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms) 62: [----------] 3 tests from IndexGroupsAndNamesTest (0 ms total) 62: 62: [----------] 15 tests from NeighborhoodSearchTest 62: [ RUN ] NeighborhoodSearchTest.SimpleSearch 62: [ OK ] NeighborhoodSearchTest.SimpleSearch (16 ms) 62: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 62: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (16 ms) 62: [ RUN ] NeighborhoodSearchTest.GridSearchBox 62: [ OK ] NeighborhoodSearchTest.GridSearchBox (1 ms) 62: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 62: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (9 ms) 62: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 62: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (2 ms) 62: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 62: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (0 ms) 62: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 62: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (1 ms) 62: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 62: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) 62: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 62: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (37 ms) 62: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches 62: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms) 62: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC 62: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) 62: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC 62: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) 62: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs 62: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) 62: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions 62: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (2 ms) 62: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 62: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (0 ms) 62: [----------] 15 tests from NeighborhoodSearchTest (98 ms total) 62: 62: [----------] 13 tests from PositionCalculationTest 62: [ RUN ] PositionCalculationTest.ComputesAtomPositions 62: [ OK ] PositionCalculationTest.ComputesAtomPositions (0 ms) 62: [ RUN ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex 62: [ OK ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex (0 ms) 62: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions 62: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (0 ms) 62: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions 62: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (0 ms) 62: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions 62: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms) 62: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions 62: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms) 62: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole 62: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms) 62: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax 62: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (0 ms) 62: [ RUN ] PositionCalculationTest.ComputesPositionMask 62: [ OK ] PositionCalculationTest.ComputesPositionMask (0 ms) 62: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms 62: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (0 ms) 62: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 62: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms) 62: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations 62: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (0 ms) 62: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations 62: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (0 ms) 62: [----------] 13 tests from PositionCalculationTest (1 ms total) 62: 62: [----------] 33 tests from SelectionCollectionTest 62: [ RUN ] SelectionCollectionTest.HandlesNoSelections 62: [ OK ] SelectionCollectionTest.HandlesNoSelections (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType 62: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests 62: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry 62: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (0 ms) 62: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile 62: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace 62: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions 62: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue 62: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 62: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 62: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 62: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 62: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 62: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 62: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference 62: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed 62: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup 62: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed 62: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 62: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (0 ms) 62: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo 62: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (0 ms) 62: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes 62: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (0 ms) 62: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo 62: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (0 ms) 62: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation 62: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (0 ms) 62: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 62: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (0 ms) 62: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 62: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets 62: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 62: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 62: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 62: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (0 ms) 62: [ RUN ] SelectionCollectionTest.RetrieveValidSelection 62: [ OK ] SelectionCollectionTest.RetrieveValidSelection (0 ms) 62: [ RUN ] SelectionCollectionTest.RetrieveInvalidSelection 62: [ OK ] SelectionCollectionTest.RetrieveInvalidSelection (0 ms) 62: [ RUN ] SelectionCollectionTest.CanCopyEmptyCollection 62: [ OK ] SelectionCollectionTest.CanCopyEmptyCollection (0 ms) 62: [ RUN ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately 62: [ OK ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately (0 ms) 62: [----------] 33 tests from SelectionCollectionTest (11 ms total) 62: 62: [----------] 14 tests from SelectionCollectionInteractiveTest 62: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput 62: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (0 ms) 62: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation 62: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (0 ms) 62: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput 62: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (0 ms) 62: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput 62: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (0 ms) 62: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups 62: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (0 ms) 62: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections 62: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (0 ms) 62: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus 62: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (0 ms) 62: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus 62: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (0 ms) 62: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus 62: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (0 ms) 62: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline 62: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (0 ms) 62: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections 62: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (0 ms) 62: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine 62: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (0 ms) 62: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput 62: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (0 ms) 62: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively 62: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (0 ms) 62: [----------] 14 tests from SelectionCollectionInteractiveTest (3 ms total) 62: 62: [----------] 70 tests from SelectionCollectionDataTest 62: [ RUN ] SelectionCollectionDataTest.HandlesAllNone 62: [ OK ] SelectionCollectionDataTest.HandlesAllNone (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr 62: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesResnr 62: [ OK ] SelectionCollectionDataTest.HandlesResnr (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesResIndex 62: [ OK ] SelectionCollectionDataTest.HandlesResIndex (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex 62: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesAtomname 62: [ OK ] SelectionCollectionDataTest.HandlesAtomname (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname 62: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype 62: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesChain 62: [ OK ] SelectionCollectionDataTest.HandlesChain (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesMass 62: [ OK ] SelectionCollectionDataTest.HandlesMass (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesCharge 62: [ OK ] SelectionCollectionDataTest.HandlesCharge (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc 62: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode 62: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy 62: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesBeta 62: [ OK ] SelectionCollectionDataTest.HandlesBeta (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesResname 62: [ OK ] SelectionCollectionDataTest.HandlesResname (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords 62: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue 62: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName 62: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords 62: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 62: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword 62: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword 62: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword 62: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (1 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 62: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 62: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 62: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (0 ms) 62: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 62: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (0 ms) 62: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 62: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 62: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 62: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 62: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 62: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 62: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed 62: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions 62: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers 62: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions 62: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges 62: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges 62: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode 62: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching 62: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching 62: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 62: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 62: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions 62: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame 62: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords 62: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods 62: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions 62: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic 62: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons 62: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 62: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 62: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 62: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 62: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 62: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 62: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 62: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis 62: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables 62: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables 62: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables 62: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups 62: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups 62: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 62: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (0 ms) 62: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation 62: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation (0 ms) 62: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation 62: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation (0 ms) 62: [ RUN ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent 62: [ OK ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent (0 ms) 62: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation 62: [ OK ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation (0 ms) 62: [----------] 70 tests from SelectionCollectionDataTest (57 ms total) 62: 62: [----------] 17 tests from SelectionOptionTest 62: [ RUN ] SelectionOptionTest.ParsesSimpleSelection 62: [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms) 62: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired 62: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (0 ms) 62: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired 62: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (0 ms) 62: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired 62: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (0 ms) 62: [ RUN ] SelectionOptionTest.ChecksEmptySelections 62: [ OK ] SelectionOptionTest.ChecksEmptySelections (0 ms) 62: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections 62: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (0 ms) 62: [ RUN ] SelectionOptionTest.HandlesTooManySelections 62: [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms) 62: [ RUN ] SelectionOptionTest.HandlesTooFewSelections 62: [ OK ] SelectionOptionTest.HandlesTooFewSelections (0 ms) 62: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText 62: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (0 ms) 62: [ RUN ] SelectionOptionTest.HandlesAdjuster 62: [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms) 62: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster 62: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms) 62: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster 62: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (0 ms) 62: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster 62: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (0 ms) 62: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection 62: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms) 62: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections 62: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (0 ms) 62: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection 62: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (0 ms) 62: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster 62: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms) 62: [----------] 17 tests from SelectionOptionTest (3 ms total) 62: 62: [----------] 9 tests from SelectionFileOptionTest 62: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile 62: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (0 ms) 62: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions 62: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (0 ms) 62: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile 62: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms) 62: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile 62: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (0 ms) 62: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet 62: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (0 ms) 62: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile 62: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (0 ms) 62: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile 62: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms) 62: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile 62: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (0 ms) 62: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles 62: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (0 ms) 62: [----------] 9 tests from SelectionFileOptionTest (1 ms total) 62: 62: [----------] Global test environment tear-down 62: [==========] 201 tests from 11 test suites ran. (180 ms total) 62: [ PASSED ] 201 tests. 62/91 Test #62: SelectionUnitTests ........................... Passed 0.54 sec test 63 Start 63: MdrunOutputTests 63: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunOutputTests.xml" 63: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 63: Test timeout computed to be: 600 63: [==========] Running 12 tests from 5 test suites. 63: [----------] Global test environment set-up. 63: [----------] 1 test from MdrunTest 63: [ RUN ] MdrunTest.WritesHelp 63: [ OK ] MdrunTest.WritesHelp (30 ms) 63: [----------] 1 test from MdrunTest (31 ms total) 63: 63: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput 63: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group rest is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI process 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 1 steps, 0.0 ps. 63: Setting the LD random seed to -553765129 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.104 0.052 199.8 63: (ns/day) (hour/ns) 63: Performance: 3.333 7.200 63: Reading frame 0 time 0.000 63: # Atoms 6 63: Reading frame 1 time 0.001 Last frame 1 time 0.001 63: 63: 63: Item #frames Timestep (ps) 63: Step 2 0.001 63: Time 2 0.001 63: Lambda 0 63: Coords 2 0.001 63: Velocities 0 63: Forces 0 63: Box 2 0.001 63: Checking file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc 63: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (82 ms) 63: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group rest is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI process 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 1 steps, 0.0 ps. 63: Setting the LD random seed to -571254855 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.022 0.011 199.2 63: (ns/day) (hour/ns) 63: Performance: 15.752 1.524 63: Reading frame 0 time 0.000 63: # Atoms 6 63: Reading frame 1 time 0.001 Last frame 1 time 0.001 63: 63: 63: Item #frames Timestep (ps) 63: Step 2 0.001 63: Time 2 0.001 63: Lambda 0 63: Coords 2 0.001 63: Velocities 0 63: Forces 0 63: Box 2 0.001 63: Checking file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc 63: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (19 ms) 63: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group rest is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 2 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI process 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 1 steps, 0.0 ps. 63: Setting the LD random seed to -69476545 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 34 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.094 0.047 199.8 63: (ns/day) (hour/ns) 63: Performance: 3.679 6.524 63: Reading frame 0 time 0.000 63: # Atoms 3 63: Reading frame 1 time 0.001 Last frame 1 time 0.001 63: 63: 63: Item #frames Timestep (ps) 63: Step 2 0.001 63: Time 2 0.001 63: Lambda 0 63: Coords 2 0.001 63: Velocities 0 63: Forces 0 63: Box 2 0.001 63: Checking file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc 63: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (101 ms) 63: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (205 ms total) 63: 63: [----------] 2 tests from Argon12/OutputFiles 63: [ RUN ] Argon12/OutputFiles.FilesArePresent/0 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI process 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.049 0.025 199.3 63: (ns/day) (hour/ns) 63: Performance: 59.539 0.403 63: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (43 ms) 63: [ RUN ] Argon12/OutputFiles.FilesArePresent/1 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI process 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.037 0.019 199.6 63: (ns/day) (hour/ns) 63: Performance: 78.898 0.304 63: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (32 ms) 63: [----------] 2 tests from Argon12/OutputFiles (81 ms total) 63: 63: [----------] 3 tests from MdrunCanWrite/Trajectories 63: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 63: Number of degrees of freedom in T-Coupling group System is 12.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There was 1 NOTE 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 63: 63: Using 1 MPI process 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc-and-methanol' 63: 6 steps, 0.0 ps. 63: Setting the LD random seed to -35258369 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.071 0.035 199.8 63: (ns/day) (hour/ns) 63: Performance: 17.078 1.405 63: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (60 ms) 63: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 63: Number of degrees of freedom in T-Coupling group System is 12.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There was 1 NOTE 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 63: 63: Using 1 MPI process 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc-and-methanol' 63: 6 steps, 0.0 ps. 63: Setting the LD random seed to -2199809 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.046 0.023 199.6 63: (ns/day) (hour/ns) 63: Performance: 26.485 0.906 63: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (35 ms) 63: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 63: Number of degrees of freedom in T-Coupling group System is 12.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There was 1 NOTE 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 63: 63: Using 1 MPI process 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc-and-methanol' 63: 6 steps, 0.0 ps. 63: Setting the LD random seed to -4260163 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.077 0.039 199.7 63: (ns/day) (hour/ns) 63: Performance: 15.588 1.540 63: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (55 ms) 63: [----------] 3 tests from MdrunCanWrite/Trajectories (152 ms total) 63: 63: [----------] 3 tests from MdrunCanWrite/NptTrajectories 63: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 63: Number of degrees of freedom in T-Coupling group System is 12.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There was 1 NOTE 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 63: 63: Using 1 MPI process 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc-and-methanol' 63: 2 steps, 0.0 ps. 63: Setting the LD random seed to 1868382127 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.064 0.032 199.7 63: (ns/day) (hour/ns) 63: Performance: 8.043 2.984 63: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (64 ms) 63: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 63: 63: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 63: The Berendsen barostat does not generate any strictly correct ensemble, 63: and should not be used for new production simulations (in our opinion). 63: We recommend using the C-rescale barostat instead. 63: 63: Number of degrees of freedom in T-Coupling group System is 12.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There was 1 NOTE 63: 63: There was 1 WARNING 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 63: 63: Using 1 MPI process 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc-and-methanol' 63: 2 steps, 0.0 ps. 63: Setting the LD random seed to -1611934049 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.017 0.008 198.9 63: (ns/day) (hour/ns) 63: Performance: 31.074 0.772 63: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (20 ms) 63: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 63: Number of degrees of freedom in T-Coupling group System is 12.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There was 1 NOTE 63: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 63: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 63: 63: Using 1 MPI process 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc-and-methanol' 63: 2 steps, 0.0 ps. 63: Setting the LD random seed to -35303476 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.135 0.068 199.9 63: (ns/day) (hour/ns) 63: Performance: 3.834 6.260 63: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (82 ms) 63: [----------] 3 tests from MdrunCanWrite/NptTrajectories (168 ms total) 63: 63: [----------] Global test environment tear-down 63: [==========] 12 tests from 5 test suites ran. (784 ms total) 63: [ PASSED ] 12 tests. 63/91 Test #63: MdrunOutputTests ............................. Passed 1.17 sec test 64 Start 64: MdrunModulesTests 64: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunModulesTests.xml" 64: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 64: Test timeout computed to be: 600 64: [==========] Running 15 tests from 3 test suites. 64: [----------] Global test environment set-up. 64: [----------] 9 tests from DensityFittingTest 64: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct 64: Number of degrees of freedom in T-Coupling group rest is 33.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Steepest Descents: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 2 64: 64: Energy minimization reached the maximum number of steps before the forces 64: reached the requested precision Fmax < 10. 64: 64: writing lowest energy coordinates. 64: 64: Steepest Descents did not converge to Fmax < 10 in 3 steps. 64: Potential Energy = -3.8565254e+03 64: Maximum force = 4.5099883e+03 on atom 3 64: Norm of force = 1.6816849e+03 64: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to 1032846326 64: 64: Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (16 ms) 64: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation 64: Number of degrees of freedom in T-Coupling group rest is 33.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Steepest Descents: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 2 64: 64: Energy minimization reached the maximum number of steps before the forces 64: reached the requested precision Fmax < 10. 64: 64: writing lowest energy coordinates. 64: 64: Steepest Descents did not converge to Fmax < 10 in 3 steps. 64: Potential Energy = -9.8207725e+03 64: Maximum force = 7.3954834e+03 on atom 2 64: Norm of force = 2.7825089e+03 64: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -1484788929 64: 64: Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation (56 ms) 64: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff 64: [ OK ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff (0 ms) 64: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix 64: Number of degrees of freedom in T-Coupling group rest is 33.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Overriding nsteps with value passed on the command line: 4 steps 64: 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Steepest Descents: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 4 64: 64: Energy minimization reached the maximum number of steps before the forces 64: reached the requested precision Fmax < 10. 64: 64: writing lowest energy coordinates. 64: 64: Steepest Descents did not converge to Fmax < 10 in 5 steps. 64: Potential Energy = -1.0954993e+04 64: Maximum force = 7.4724790e+03 on atom 2 64: Norm of force = 2.7758003e+03 64: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Setting the LD random seed to -539820297 64: 64: Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix (23 ms) 64: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff 64: [ OK ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff (0 ms) 64: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix 64: Number of degrees of freedom in T-Coupling group rest is 33.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Steepest Descents: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 2 64: 64: Energy minimization reached the maximum number of steps before the forces 64: reached the requested precision Fmax < 10. 64: 64: writing lowest energy coordinates. 64: 64: Steepest Descents did not converge to Fmax < 10 in 3 steps. 64: Potential Energy = -3.8565254e+03 64: Maximum force = 4.5099883e+03 on atom 3 64: Norm of force = 1.6816849e+03 64: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to 1975516587 64: 64: Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix (8 ms) 64: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy 64: Number of degrees of freedom in T-Coupling group rest is 33.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Steepest Descents: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 2 64: 64: Energy minimization reached the maximum number of steps before the forces 64: reached the requested precision Fmax < 10. 64: 64: writing lowest energy coordinates. 64: 64: Steepest Descents did not converge to Fmax < 10 in 3 steps. 64: Potential Energy = -2.7138664e+04 64: Maximum force = 6.7827656e+03 on atom 2 64: Norm of force = 1.9608866e+03 64: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to 2146950559 64: 64: Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (31 ms) 64: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch 64: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (0 ms) 64: [ RUN ] DensityFittingTest.CheckpointWorks 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (2) 64: 64: Number of degrees of freedom in T-Coupling group rest is 33.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 64: NVE simulation: will use the initial temperature of 68.810 K for 64: determining the Verlet buffer size 64: 64: 64: There were 2 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Argon' 64: 2 steps, 0.0 ps. 64: Setting the LD random seed to 2108620735 64: 64: Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.031 0.016 199.4 64: (ns/day) (hour/ns) 64: Performance: 16.538 1.451 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps 64: Can not increase nstlist because an NVE ensemble is used 64: 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Argon' 64: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps). 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.045 0.022 199.6 64: (ns/day) (hour/ns) 64: Performance: 19.275 1.245 64: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (55 ms) 64: [----------] 9 tests from DensityFittingTest (192 ms total) 64: 64: [----------] 4 tests from MimicTest 64: [ RUN ] MimicTest.OneQuantumMol 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group rest is 21.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 64: NVE simulation with an initial temperature of zero: will use a Verlet 64: buffer of 10%. Check your energy drift! 64: 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/4water.gro' 64: 64: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 64: Reading frame 0 time 0.000 Last frame 0 time 0.000 64: 64: NOTE: 19 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.000 0.000 185.7 64: (ns/day) (hour/ns) 64: Performance: 432.960 0.055 64: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1174555409 64: 64: Generated 10 of the 10 non-bonded parameter combinations 64: 64: Generated 10 of the 10 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MimicTest.OneQuantumMol (8 ms) 64: [ RUN ] MimicTest.AllQuantumMol 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group rest is 21.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 64: NVE simulation with an initial temperature of zero: will use a Verlet 64: buffer of 10%. Check your energy drift! 64: 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/4water.gro' 64: 64: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 64: Reading frame 0 time 0.000 Last frame 0 time 0.000 64: 64: NOTE: 16 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.000 0.000 184.9 64: (ns/day) (hour/ns) 64: Performance: 489.052 0.049 64: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -69636249 64: 64: Generated 10 of the 10 non-bonded parameter combinations 64: 64: Generated 10 of the 10 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MimicTest.AllQuantumMol (7 ms) 64: [ RUN ] MimicTest.TwoQuantumMol 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group rest is 21.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 64: NVE simulation with an initial temperature of zero: will use a Verlet 64: buffer of 10%. Check your energy drift! 64: 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/4water.gro' 64: 64: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 64: Reading frame 0 time 0.000 Last frame 0 time 0.000 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.001 0.000 185.4 64: (ns/day) (hour/ns) 64: Performance: 319.284 0.075 64: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1573058 64: 64: Generated 10 of the 10 non-bonded parameter combinations 64: 64: Generated 10 of the 10 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MimicTest.TwoQuantumMol (15 ms) 64: [ RUN ] MimicTest.BondCuts 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group rest is 66.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 64: NVE simulation: will use the initial temperature of 300.368 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/ala.gro' 64: 64: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 64: Reading frame 0 time 0.000 Last frame 0 time 0.000 64: 64: NOTE: 12 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.001 0.000 192.6 64: (ns/day) (hour/ns) 64: Performance: 205.319 0.117 64: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1478165537 64: 64: Generated 2211 of the 2211 non-bonded parameter combinations 64: 64: Generated 2211 of the 2211 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MimicTest.BondCuts (24 ms) 64: [----------] 4 tests from MimicTest (57 ms total) 64: 64: [----------] 2 tests from WithIntegrator/ImdTest 64: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0 64: Generating 1-4 interactions: fudge = 1 64: 64: NOTE 1 [file glycine_vacuo.top, line 12]: 64: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an 64: estimated oscillational period of 1.0e-02 ps, which is less than 10 times 64: the time step of 2.0e-03 ps. 64: Maybe you forgot to change the constraints mdp option. 64: 64: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 64: Number of degrees of freedom in T-Coupling group System is 27.00 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 2 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Changing nstlist from 10 to 25, rlist from 1.071 to 1.232 64: 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: IMD: Enabled. This simulation will accept incoming IMD connections. 64: IMD: Pulling from IMD remote is enabled (-imdpull). 64: IMD: Setting port for connection requests to 0. 64: IMD: Setting up incoming socket. 64: IMD: Listening for IMD connection on port 59281. 64: IMD: -imdwait not set, starting simulation. 64: starting mdrun 'Glycine' 64: 2 steps, 0.0 ps. 64: Setting the LD random seed to -8685570 64: 64: Generated 20503 of the 20503 non-bonded parameter combinations 64: 64: Generated 17396 of the 20503 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Glycine' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.071 nm, buffer size 0.071 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.026 0.013 199.4 64: (ns/day) (hour/ns) 64: Performance: 40.516 0.592 64: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (112 ms) 64: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 64: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not 64: apply to steep. 64: 64: Generating 1-4 interactions: fudge = 1 64: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 64: Number of degrees of freedom in T-Coupling group System is 27.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 2 NOTEs 64: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: IMD: Enabled. This simulation will accept incoming IMD connections. 64: IMD: Pulling from IMD remote is enabled (-imdpull). 64: IMD: Setting port for connection requests to 0. 64: IMD: Setting up incoming socket. 64: IMD: Listening for IMD connection on port 57445. 64: IMD: -imdwait not set, starting simulation. 64: 64: Steepest Descents: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 2 64: 64: Energy minimization reached the maximum number of steps before the forces 64: reached the requested precision Fmax < 10. 64: 64: writing lowest energy coordinates. 64: 64: Steepest Descents did not converge to Fmax < 10 in 3 steps. 64: Potential Energy = 1.1977064e+03 64: Maximum force = 1.7794877e+04 on atom 9 64: Norm of force = 7.8732901e+03 64: Setting the LD random seed to -69240719 64: 64: Generated 20503 of the 20503 non-bonded parameter combinations 64: 64: Generated 17396 of the 20503 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Glycine' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (122 ms) 64: [----------] 2 tests from WithIntegrator/ImdTest (236 ms total) 64: 64: [----------] Global test environment tear-down 64: [==========] 15 tests from 3 test suites ran. (620 ms total) 64: [ PASSED ] 15 tests. 64/91 Test #64: MdrunModulesTests ............................ Passed 0.96 sec test 65 Start 65: MdrunIOTests 65: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunIOTests.xml" 65: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 65: Test timeout computed to be: 600 65: [==========] Running 76 tests from 13 test suites. 65: [----------] Global test environment set-up. 65: [----------] 9 tests from GromppTest 65: [ RUN ] GromppTest.EmptyMdpFileWorks 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: Number of degrees of freedom in T-Coupling group rest is 12.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 65: NVE simulation: will use the initial temperature of 1046.791 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: Setting the LD random seed to 2146825727 65: 65: Generated 8 of the 10 non-bonded parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'Methanol' 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] GromppTest.EmptyMdpFileWorks (3 ms) 65: [ RUN ] GromppTest.SimulatedAnnealingWorks 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: Simulated annealing for group rest: Periodic, 4 timepoints 65: Time (ps) Temperature (K) 65: 0.0 298.0 65: 2.0 320.0 65: 4.0 320.0 65: 6.0 298.0 65: Number of degrees of freedom in T-Coupling group rest is 12.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 65: NVE simulation: will use the initial temperature of 1046.791 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: Setting the LD random seed to -134217865 65: 65: Generated 8 of the 10 non-bonded parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'Methanol' 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] GromppTest.SimulatedAnnealingWorks (6 ms) 65: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: Simulated annealing for group Methanol: Single, 3 timepoints 65: Time (ps) Temperature (K) 65: 0.0 298.0 65: 3.0 280.0 65: 6.0- 270.0 65: Simulated annealing for group SOL: Periodic, 4 timepoints 65: Time (ps) Temperature (K) 65: 0.0 298.0 65: 2.0 320.0 65: 4.0 320.0 65: 6.0 298.0 65: Number of degrees of freedom in T-Coupling group Methanol is 7.20 65: Number of degrees of freedom in T-Coupling group SOL is 4.80 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 65: NVE simulation: will use the initial temperature of 1046.791 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: Setting the LD random seed to -1157693986 65: 65: Generated 8 of the 10 non-bonded parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'Methanol' 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (6 ms) 65: [ RUN ] GromppTest.DeathTestHandlesNoMaxwarnError 65: [ OK ] GromppTest.DeathTestHandlesNoMaxwarnError (0 ms) 65: [ RUN ] GromppTest.HandlesMaxwarn 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 65: The Berendsen thermostat does not generate the correct kinetic energy 65: distribution, and should not be used for new production simulations (in 65: our opinion). We would recommend the V-rescale thermostat. 65: 65: Number of degrees of freedom in T-Coupling group System is 12.00 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 2 NOTEs 65: 65: There was 1 WARNING 65: Setting the LD random seed to -234883217 65: 65: Generated 8 of the 10 non-bonded parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'Methanol' 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] GromppTest.HandlesMaxwarn (2 ms) 65: [ RUN ] GromppTest.MaxwarnShouldBePositive 65: [ OK ] GromppTest.MaxwarnShouldBePositive (8 ms) 65: [ RUN ] GromppTest.ValidTransformationCoord 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: Pull group 1 'SOL' has 3 atoms 65: Pull group 2 'Methanol' has 3 atoms 65: Number of degrees of freedom in T-Coupling group rest is 12.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 65: NVE simulation: will use the initial temperature of 1046.791 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: Pull group natoms pbc atom distance at start reference at t=0 65: 1 3 5 65: 2 3 2 0.613 nm 0.000 nm 65: 1 3 5 65: 2 3 2 0.613 nm 0.000 nm 65: 65: There were 3 NOTEs 65: Setting the LD random seed to -269615178 65: 65: Generated 8 of the 10 non-bonded parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'Methanol' 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] GromppTest.ValidTransformationCoord (3 ms) 65: [ RUN ] GromppTest.InvalidTransformationCoord 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: Pull group 1 'SOL' has 3 atoms 65: Pull group 2 'Methanol' has 3 atoms 65: Number of degrees of freedom in T-Coupling group rest is 12.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 65: NVE simulation: will use the initial temperature of 1046.791 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: Pull group natoms pbc atom distance at start reference at t=0 65: 1 3 5 65: 2 3 2 0.613 nm 0.000 nm 65: 1 3 5 65: 2 3 2 Setting the LD random seed to -235016476 65: 65: Generated 8 of the 10 non-bonded parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'Methanol' 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: [ OK ] GromppTest.InvalidTransformationCoord (11 ms) 65: [ RUN ] GromppTest.RejectCRescaleAndAnisotropic 65: [ OK ] GromppTest.RejectCRescaleAndAnisotropic (0 ms) 65: [----------] 9 tests from GromppTest (47 ms total) 65: 65: [----------] 6 tests from MdrunTerminationTest 65: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There was 1 NOTE 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 2 steps, 0.0 ps. 65: Setting the LD random seed to -1146295937 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.046 0.023 199.5 65: (ns/day) (hour/ns) 65: Performance: 11.159 2.151 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Setting nsteps to 4 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 65: Input file: 65: Run start step 0 65: Run start time 0 ps 65: Step to be made during run 2 65: Runtime for the run 0.002 ps 65: Run end step 2 65: Run end time 0.002 ps 65: 65: 65: Output file: 65: Run start step 0 65: Run start time 0 ps 65: Step to be made during run 4 65: Runtime for the run 0.004 ps 65: Run end step 4 65: Run end time 0.004 ps 65: 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.036 0.018 199.7 65: (ns/day) (hour/ns) 65: Performance: 14.485 1.657 65: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (49 ms) 65: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There was 1 NOTE 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 10 to 1, rlist from 1.032 to 1 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 100 steps, 0.1 ps. 65: 65: Step 5: Run time exceeded 0.000 hours, will terminate the run within 200 steps 65: Setting the LD random seed to -1619559620 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.059 0.029 199.6 65: (ns/day) (hour/ns) 65: Performance: 296.967 0.081 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Setting nsteps to 102 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). 65: Input file: 65: Run start step 0 65: Run start time 0 ps 65: Step to be made during run 100 65: Runtime for the run 0.1 ps 65: Run end step 100 65: Run end time 0.1 ps 65: 65: 65: Output file: 65: Run start step 0 65: Run start time 0 ps 65: Step to be made during run 102 65: Runtime for the run 0.102 ps 65: Run end step 102 65: Run end time 0.102 ps 65: 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.017 0.008 198.9 65: (ns/day) (hour/ns) 65: Performance: 30.669 0.783 65: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (49 ms) 65: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There was 1 NOTE 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 2 steps, 0.0 ps. 65: Setting the LD random seed to -270402273 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 23 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.069 0.035 199.7 65: (ns/day) (hour/ns) 65: Performance: 7.459 3.218 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Setting nsteps to 4 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 65: Input file: 65: Run start step 0 65: Run start time 0 ps 65: Step to be made during run 2 65: Runtime for the run 0.002 ps 65: Run end step 2 65: Run end time 0.002 ps 65: 65: 65: Output file: 65: Run start step 0 65: Run start time 0 ps 65: Step to be made during run 4 65: Runtime for the run 0.004 ps 65: Run end step 4 65: Run end time 0.004 ps 65: 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.510 0.255 200.0 65: (ns/day) (hour/ns) 65: Performance: 1.017 23.600 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Setting nsteps to 6 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps). 65: Input file: 65: Run start step 0 65: Run start time 0 ps 65: Step to be made during run 4 65: Runtime for the run 0.004 ps 65: Run end step 4 65: Run end time 0.004 ps 65: 65: 65: Output file: 65: Run start step 0 65: Run start time 0 ps 65: Step to be made during run 6 65: Runtime for the run 0.006 ps 65: Run end step 6 65: Run end time 0.006 ps 65: 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.018 0.009 199.5 65: (ns/day) (hour/ns) 65: Performance: 28.315 0.848 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Setting nsteps to 8 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). 65: Input file: 65: Run start step 0 65: Run start time 0 ps 65: Step to be made during run 6 65: Runtime for the run 0.006 ps 65: Run end step 6 65: Run end time 0.006 ps 65: 65: 65: Output file: 65: Run start step 0 65: Run start time 0 ps 65: Step to be made during run 8 65: Runtime for the run 0.008 ps 65: Run end step 8 65: Run end time 0.008 ps 65: 65: 65: Writing final coordinates. 65: 65: NOTE: 16 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.488 0.244 200.0 65: (ns/day) (hour/ns) 65: Performance: 1.062 22.596 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: NOTE: 27 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.000 0.000 174.2 65: (ns/day) (hour/ns) 65: Performance: 707.789 0.034 65: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (686 ms) 65: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There was 1 NOTE 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 2 steps, 0.0 ps. 65: Setting the LD random seed to -780419113 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.032 0.016 199.2 65: (ns/day) (hour/ns) 65: Performance: 16.108 1.490 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Setting nsteps to 4 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 4 steps, 0.0 ps. 65: Input file: 65: Run start step 0 65: Run start time 0 ps 65: Step to be made during run 2 65: Runtime for the run 0.002 ps 65: Run end step 2 65: Run end time 0.002 ps 65: 65: 65: Output file: 65: Run start step 0 65: Run start time 0 ps 65: Step to be made during run 4 65: Runtime for the run 0.004 ps 65: Run end step 4 65: Run end time 0.004 ps 65: 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.030 0.015 199.6 65: (ns/day) (hour/ns) 65: Performance: 28.626 0.838 65: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (53 ms) 65: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There was 1 NOTE 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 2 steps, 0.0 ps. 65: Setting the LD random seed to 1409267198 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.044 0.022 199.6 65: (ns/day) (hour/ns) 65: Performance: 11.765 2.040 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Setting nsteps to 4 65: Input file: 65: Run start step 0 65: Run start time 0 ps 65: Step to be made during run 2 65: Runtime for the run 0.002 ps 65: Run end step 2 65: Run end time 0.002 ps 65: 65: 65: Output file: 65: Run start step 0 65: Run start time 0 ps 65: Step to be made during run 4 65: Runtime for the run 0.004 ps 65: Run end step 4 65: Run end time 0.004 ps 65: 65: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (32 ms) 65: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There was 1 NOTE 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 2 steps, 0.0 ps. 65: Setting the LD random seed to 1876946761 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.036 0.018 199.5 65: (ns/day) (hour/ns) 65: Performance: 14.478 1.658 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Setting nsteps to 4 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 65: Input file: 65: Run start step 0 65: Run start time 0 ps 65: Step to be made during run 2 65: Runtime for the run 0.002 ps 65: Run end step 2 65: Run end time 0.002 ps 65: 65: 65: Output file: 65: Run start step 0 65: Run start time 0 ps 65: Step to be made during run 4 65: Runtime for the run 0.004 ps 65: Run end step 4 65: Run end time 0.004 ps 65: 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.135 0.068 199.9 65: (ns/day) (hour/ns) 65: Performance: 3.826 6.272 65: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (102 ms) 65: [----------] 6 tests from MdrunTerminationTest (978 ms total) 65: 65: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks 65: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 65: NVE simulation: will use the initial temperature of 2573.591 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps. 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.029 0.014 199.6 65: (ns/day) (hour/ns) 65: Performance: 102.057 0.235 65: trr version: GMX_trn_file (single precision) 65: 65: 65: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (18 ms) 65: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 65: NVE simulation: will use the initial temperature of 2573.591 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps. 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.097 0.048 199.8 65: (ns/day) (hour/ns) 65: Performance: 30.363 0.790 65: 65: 65: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (74 ms) 65: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (92 ms total) 65: 65: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: NVE simulation: will use the initial temperature of 68.810 K for 65: determining the Verlet buffer size 65: 65: 65: There were 3 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: NVE simulation: will use the initial temperature of 68.810 K for 65: determining the Verlet buffer size 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.030 0.015 199.2 65: (ns/day) (hour/ns) 65: Performance: 97.169 0.247 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.029 0.015 199.4 65: (ns/day) (hour/ns) 65: Performance: 52.710 0.455 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.039 0.020 199.6 65: (ns/day) (hour/ns) 65: Performance: 39.487 0.608 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (68 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: NVE simulation: will use the initial temperature of 68.810 K for 65: determining the Verlet buffer size 65: 65: 65: There were 3 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: NVE simulation: will use the initial temperature of 68.810 K for 65: determining the Verlet buffer size 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.039 0.020 199.4 65: (ns/day) (hour/ns) 65: Performance: 74.917 0.320 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.029 0.014 199.1 65: (ns/day) (hour/ns) 65: Performance: 54.194 0.443 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.035 0.017 199.6 65: (ns/day) (hour/ns) 65: Performance: 44.525 0.539 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (77 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: NVE simulation: will use the initial temperature of 68.810 K for 65: determining the Verlet buffer size 65: 65: 65: There were 3 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: NVE simulation: will use the initial temperature of 68.810 K for 65: determining the Verlet buffer size 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.044 0.022 199.8 65: (ns/day) (hour/ns) 65: Performance: 66.099 0.363 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.021 0.011 199.7 65: (ns/day) (hour/ns) 65: Performance: 73.363 0.327 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.030 0.015 199.4 65: (ns/day) (hour/ns) 65: Performance: 51.027 0.470 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (74 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: NVE simulation: will use the initial temperature of 68.810 K for 65: determining the Verlet buffer size 65: 65: 65: There were 3 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: NVE simulation: will use the initial temperature of 68.810 K for 65: determining the Verlet buffer size 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.047 0.024 199.7 65: (ns/day) (hour/ns) 65: Performance: 62.415 0.385 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.023 0.012 199.7 65: (ns/day) (hour/ns) 65: Performance: 67.428 0.356 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: NOTE: 15 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.052 0.026 199.6 65: (ns/day) (hour/ns) 65: Performance: 29.714 0.808 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (85 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.040 0.020 199.6 65: (ns/day) (hour/ns) 65: Performance: 72.598 0.331 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.046 0.023 199.5 65: (ns/day) (hour/ns) 65: Performance: 33.848 0.709 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.083 0.042 199.6 65: (ns/day) (hour/ns) 65: Performance: 18.597 1.291 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (99 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.036 0.018 199.6 65: (ns/day) (hour/ns) 65: Performance: 80.471 0.298 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.039 0.020 199.6 65: (ns/day) (hour/ns) 65: Performance: 39.378 0.609 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.043 0.022 199.7 65: (ns/day) (hour/ns) 65: Performance: 35.819 0.670 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (96 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.039 0.020 199.7 65: (ns/day) (hour/ns) 65: Performance: 74.521 0.322 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.036 0.018 199.7 65: (ns/day) (hour/ns) 65: Performance: 42.829 0.560 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.022 0.011 199.6 65: (ns/day) (hour/ns) 65: Performance: 69.913 0.343 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (79 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.045 0.022 199.6 65: (ns/day) (hour/ns) 65: Performance: 65.718 0.365 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.031 0.015 199.5 65: (ns/day) (hour/ns) 65: Performance: 50.521 0.475 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.043 0.022 199.6 65: (ns/day) (hour/ns) 65: Performance: 35.943 0.668 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (80 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 65: NVE simulation: will use the initial temperature of 2573.591 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 65: NVE simulation: will use the initial temperature of 2573.591 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps. 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 67 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.108 0.054 199.8 65: (ns/day) (hour/ns) 65: Performance: 27.133 0.885 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.031 0.016 199.4 65: (ns/day) (hour/ns) 65: Performance: 49.417 0.486 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.040 0.020 199.5 65: (ns/day) (hour/ns) 65: Performance: 39.024 0.615 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (139 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 65: NVE simulation: will use the initial temperature of 2573.591 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 65: NVE simulation: will use the initial temperature of 2573.591 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps. 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.037 0.019 199.1 65: (ns/day) (hour/ns) 65: Performance: 79.390 0.302 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.030 0.015 199.1 65: (ns/day) (hour/ns) 65: Performance: 51.158 0.469 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.052 0.026 199.7 65: (ns/day) (hour/ns) 65: Performance: 29.808 0.805 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (75 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 65: NVE simulation: will use the initial temperature of 2573.591 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 65: NVE simulation: will use the initial temperature of 2573.591 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps. 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.043 0.022 199.5 65: (ns/day) (hour/ns) 65: Performance: 67.617 0.355 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.031 0.016 199.7 65: (ns/day) (hour/ns) 65: Performance: 49.703 0.483 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.027 0.014 199.6 65: (ns/day) (hour/ns) 65: Performance: 57.543 0.417 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (64 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 65: NVE simulation: will use the initial temperature of 2573.591 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 65: NVE simulation: will use the initial temperature of 2573.591 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps. 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 24 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.369 0.184 199.9 65: (ns/day) (hour/ns) 65: Performance: 7.968 3.012 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.688 0.344 200.0 65: (ns/day) (hour/ns) 65: Performance: 2.260 10.619 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.021 0.011 199.6 65: (ns/day) (hour/ns) 65: Performance: 73.684 0.326 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (587 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps. 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.028 0.014 199.3 65: (ns/day) (hour/ns) 65: Performance: 103.184 0.233 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.045 0.022 199.5 65: (ns/day) (hour/ns) 65: Performance: 34.619 0.693 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.029 0.014 199.4 65: (ns/day) (hour/ns) 65: Performance: 54.309 0.442 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 (65 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps. 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.049 0.025 199.6 65: (ns/day) (hour/ns) 65: Performance: 59.359 0.404 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.038 0.019 199.4 65: (ns/day) (hour/ns) 65: Performance: 40.373 0.594 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.040 0.020 199.2 65: (ns/day) (hour/ns) 65: Performance: 38.268 0.627 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 (97 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps. 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.038 0.019 199.6 65: (ns/day) (hour/ns) 65: Performance: 76.704 0.313 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.027 0.013 199.6 65: (ns/day) (hour/ns) 65: Performance: 58.461 0.411 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.021 0.011 199.6 65: (ns/day) (hour/ns) 65: Performance: 72.307 0.332 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 (90 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps. 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.030 0.015 199.5 65: (ns/day) (hour/ns) 65: Performance: 96.129 0.250 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.024 0.012 199.5 65: (ns/day) (hour/ns) 65: Performance: 65.982 0.364 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.050 0.025 199.7 65: (ns/day) (hour/ns) 65: Performance: 31.114 0.771 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 (74 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file unknown]: 65: You are using constraints on all bonds, whereas the forcefield has been 65: parametrized only with constraints involving hydrogen atoms. We suggest 65: using constraints = h-bonds instead, this will also improve performance. 65: 65: Number of degrees of freedom in T-Coupling group System is 23.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 65: NVE simulation: will use the initial temperature of 456.887 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 65: There are 9 non-linear virtual site constructions. Their contribution to 65: the energy error is approximated. In most cases this does not affect the 65: error significantly. 65: 65: 65: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 6 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file unknown]: 65: You are using constraints on all bonds, whereas the forcefield has been 65: parametrized only with constraints involving hydrogen atoms. We suggest 65: using constraints = h-bonds instead, this will also improve performance. 65: 65: Number of degrees of freedom in T-Coupling group System is 23.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 65: NVE simulation: will use the initial temperature of 456.887 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 65: There are 9 non-linear virtual site constructions. Their contribution to 65: the energy error is approximated. In most cases this does not affect the 65: error significantly. 65: 65: 65: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 6 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 16 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 65: 65: turning all bonds into constraints... 65: 65: Cleaning up constraints and constant bonded interactions with virtual sites 65: 65: Removed 18 Angles with virtual sites, 21 left 65: 65: Removed 10 Proper Dih.s with virtual sites, 44 left 65: 65: Converted 15 Constraints with virtual sites to connections, 7 left 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 65: 65: turning all bonds into constraints... 65: 65: Cleaning up constraints and constant bonded interactions with virtual sites 65: 65: Removed 18 Angles with virtual sites, 21 left 65: 65: Removed 10 Proper Dih.s with virtual sites, 44 left 65: 65: Converted 15 Constraints with virtual sites to connections, 7 left 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.027 0.013 199.1 65: (ns/day) (hour/ns) 65: Performance: 108.983 0.220 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.113 0.056 199.7 65: (ns/day) (hour/ns) 65: Performance: 13.785 1.741 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.036 0.018 199.3 65: (ns/day) (hour/ns) 65: Performance: 43.635 0.550 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 (121 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file unknown]: 65: You are using constraints on all bonds, whereas the forcefield has been 65: parametrized only with constraints involving hydrogen atoms. We suggest 65: using constraints = h-bonds instead, this will also improve performance. 65: 65: Number of degrees of freedom in T-Coupling group System is 23.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 65: NVE simulation: will use the initial temperature of 456.887 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 65: There are 9 non-linear virtual site constructions. Their contribution to 65: the energy error is approximated. In most cases this does not affect the 65: error significantly. 65: 65: 65: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 6 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file unknown]: 65: You are using constraints on all bonds, whereas the forcefield has been 65: parametrized only with constraints involving hydrogen atoms. We suggest 65: using constraints = h-bonds instead, this will also improve performance. 65: 65: Number of degrees of freedom in T-Coupling group System is 23.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 65: NVE simulation: will use the initial temperature of 456.887 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 65: There are 9 non-linear virtual site constructions. Their contribution to 65: the energy error is approximated. In most cases this does not affect the 65: error significantly. 65: 65: 65: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 6 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 16 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 65: 65: turning all bonds into constraints... 65: 65: Cleaning up constraints and constant bonded interactions with virtual sites 65: 65: Removed 18 Angles with virtual sites, 21 left 65: 65: Removed 10 Proper Dih.s with virtual sites, 44 left 65: 65: Converted 15 Constraints with virtual sites to connections, 7 left 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 65: 65: turning all bonds into constraints... 65: 65: Cleaning up constraints and constant bonded interactions with virtual sites 65: 65: Removed 18 Angles with virtual sites, 21 left 65: 65: Removed 10 Proper Dih.s with virtual sites, 44 left 65: 65: Converted 15 Constraints with virtual sites to connections, 7 left 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.056 0.028 199.5 65: (ns/day) (hour/ns) 65: Performance: 52.435 0.458 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.037 0.019 199.0 65: (ns/day) (hour/ns) 65: Performance: 41.911 0.573 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.087 0.044 199.6 65: (ns/day) (hour/ns) 65: Performance: 17.818 1.347 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 (148 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file unknown]: 65: You are using constraints on all bonds, whereas the forcefield has been 65: parametrized only with constraints involving hydrogen atoms. We suggest 65: using constraints = h-bonds instead, this will also improve performance. 65: 65: Number of degrees of freedom in T-Coupling group System is 23.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 65: NVE simulation: will use the initial temperature of 456.887 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 65: There are 9 non-linear virtual site constructions. Their contribution to 65: the energy error is approximated. In most cases this does not affect the 65: error significantly. 65: 65: 65: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 6 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file unknown]: 65: You are using constraints on all bonds, whereas the forcefield has been 65: parametrized only with constraints involving hydrogen atoms. We suggest 65: using constraints = h-bonds instead, this will also improve performance. 65: 65: Number of degrees of freedom in T-Coupling group System is 23.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 65: NVE simulation: will use the initial temperature of 456.887 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 65: There are 9 non-linear virtual site constructions. Their contribution to 65: the energy error is approximated. In most cases this does not affect the 65: error significantly. 65: 65: 65: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 6 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 16 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 65: 65: turning all bonds into constraints... 65: 65: Cleaning up constraints and constant bonded interactions with virtual sites 65: 65: Removed 18 Angles with virtual sites, 21 left 65: 65: Removed 10 Proper Dih.s with virtual sites, 44 left 65: 65: Converted 15 Constraints with virtual sites to connections, 7 left 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 65: 65: turning all bonds into constraints... 65: 65: Cleaning up constraints and constant bonded interactions with virtual sites 65: 65: Removed 18 Angles with virtual sites, 21 left 65: 65: Removed 10 Proper Dih.s with virtual sites, 44 left 65: 65: Converted 15 Constraints with virtual sites to connections, 7 left 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.035 0.018 199.3 65: (ns/day) (hour/ns) 65: Performance: 83.216 0.288 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.096 0.048 199.7 65: (ns/day) (hour/ns) 65: Performance: 16.220 1.480 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.046 0.023 199.3 65: (ns/day) (hour/ns) 65: Performance: 33.738 0.711 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 (420 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file unknown]: 65: You are using constraints on all bonds, whereas the forcefield has been 65: parametrized only with constraints involving hydrogen atoms. We suggest 65: using constraints = h-bonds instead, this will also improve performance. 65: 65: Number of degrees of freedom in T-Coupling group System is 23.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 65: NVE simulation: will use the initial temperature of 456.887 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 65: There are 9 non-linear virtual site constructions. Their contribution to 65: the energy error is approximated. In most cases this does not affect the 65: error significantly. 65: 65: 65: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 6 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file unknown]: 65: You are using constraints on all bonds, whereas the forcefield has been 65: parametrized only with constraints involving hydrogen atoms. We suggest 65: using constraints = h-bonds instead, this will also improve performance. 65: 65: Number of degrees of freedom in T-Coupling group System is 23.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 65: NVE simulation: will use the initial temperature of 456.887 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 65: There are 9 non-linear virtual site constructions. Their contribution to 65: the energy error is approximated. In most cases this does not affect the 65: error significantly. 65: 65: 65: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 6 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 16 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 65: 65: turning all bonds into constraints... 65: 65: Cleaning up constraints and constant bonded interactions with virtual sites 65: 65: Removed 18 Angles with virtual sites, 21 left 65: 65: Removed 10 Proper Dih.s with virtual sites, 44 left 65: 65: Converted 15 Constraints with virtual sites to connections, 7 left 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 65: 65: turning all bonds into constraints... 65: 65: Cleaning up constraints and constant bonded interactions with virtual sites 65: 65: Removed 18 Angles with virtual sites, 21 left 65: 65: Removed 10 Proper Dih.s with virtual sites, 44 left 65: 65: Converted 15 Constraints with virtual sites to connections, 7 left 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.109 0.055 199.7 65: (ns/day) (hour/ns) 65: Performance: 26.920 0.892 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.032 0.016 199.3 65: (ns/day) (hour/ns) 65: Performance: 48.533 0.495 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.028 0.014 199.1 65: (ns/day) (hour/ns) 65: Performance: 55.467 0.433 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 (113 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file unknown]: 65: You are using constraints on all bonds, whereas the forcefield has been 65: parametrized only with constraints involving hydrogen atoms. We suggest 65: using constraints = h-bonds instead, this will also improve performance. 65: 65: Number of degrees of freedom in T-Coupling group System is 23.00 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 65: There are 9 non-linear virtual site constructions. Their contribution to 65: the energy error is approximated. In most cases this does not affect the 65: error significantly. 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 5 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file unknown]: 65: You are using constraints on all bonds, whereas the forcefield has been 65: parametrized only with constraints involving hydrogen atoms. We suggest 65: using constraints = h-bonds instead, this will also improve performance. 65: 65: Number of degrees of freedom in T-Coupling group System is 23.00 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 65: There are 9 non-linear virtual site constructions. Their contribution to 65: the energy error is approximated. In most cases this does not affect the 65: error significantly. 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 5 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 16 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 65: 65: turning all bonds into constraints... 65: 65: Cleaning up constraints and constant bonded interactions with virtual sites 65: 65: Removed 18 Angles with virtual sites, 21 left 65: 65: Removed 10 Proper Dih.s with virtual sites, 44 left 65: 65: Converted 15 Constraints with virtual sites to connections, 7 left 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 65: 65: turning all bonds into constraints... 65: 65: Cleaning up constraints and constant bonded interactions with virtual sites 65: 65: Removed 18 Angles with virtual sites, 21 left 65: 65: Removed 10 Proper Dih.s with virtual sites, 44 left 65: 65: Converted 15 Constraints with virtual sites to connections, 7 left 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.918 0.459 200.0 65: (ns/day) (hour/ns) 65: Performance: 3.198 7.504 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.057 0.028 199.5 65: (ns/day) (hour/ns) 65: Performance: 27.326 0.878 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: NOTE: 16 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.152 0.076 199.9 65: (ns/day) (hour/ns) 65: Performance: 10.244 2.343 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 (926 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file unknown]: 65: You are using constraints on all bonds, whereas the forcefield has been 65: parametrized only with constraints involving hydrogen atoms. We suggest 65: using constraints = h-bonds instead, this will also improve performance. 65: 65: Number of degrees of freedom in T-Coupling group System is 23.00 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 65: There are 9 non-linear virtual site constructions. Their contribution to 65: the energy error is approximated. In most cases this does not affect the 65: error significantly. 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 5 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file unknown]: 65: You are using constraints on all bonds, whereas the forcefield has been 65: parametrized only with constraints involving hydrogen atoms. We suggest 65: using constraints = h-bonds instead, this will also improve performance. 65: 65: Number of degrees of freedom in T-Coupling group System is 23.00 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 65: There are 9 non-linear virtual site constructions. Their contribution to 65: the energy error is approximated. In most cases this does not affect the 65: error significantly. 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 5 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 65: 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 16 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 65: 65: turning all bonds into constraints... 65: 65: Cleaning up constraints and constant bonded interactions with virtual sites 65: 65: Removed 18 Angles with virtual sites, 21 left 65: 65: Removed 10 Proper Dih.s with virtual sites, 44 left 65: 65: Converted 15 Constraints with virtual sites to connections, 7 left 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 65: 65: turning all bonds into constraints... 65: 65: Cleaning up constraints and constant bonded interactions with virtual sites 65: 65: Removed 18 Angles with virtual sites, 21 left 65: 65: Removed 10 Proper Dih.s with virtual sites, 44 left 65: 65: Converted 15 Constraints with virtual sites to connections, 7 left 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.044 0.022 199.6 65: (ns/day) (hour/ns) 65: Performance: 67.365 0.356 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 65: 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.093 0.046 199.8 65: (ns/day) (hour/ns) 65: Performance: 16.765 1.432 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 65: 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 1.196 0.598 200.0 65: (ns/day) (hour/ns) 65: Performance: 1.300 18.461 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 (897 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file unknown]: 65: You are using constraints on all bonds, whereas the forcefield has been 65: parametrized only with constraints involving hydrogen atoms. We suggest 65: using constraints = h-bonds instead, this will also improve performance. 65: 65: Number of degrees of freedom in T-Coupling group System is 23.00 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 65: There are 9 non-linear virtual site constructions. Their contribution to 65: the energy error is approximated. In most cases this does not affect the 65: error significantly. 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 5 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file unknown]: 65: You are using constraints on all bonds, whereas the forcefield has been 65: parametrized only with constraints involving hydrogen atoms. We suggest 65: using constraints = h-bonds instead, this will also improve performance. 65: 65: Number of degrees of freedom in T-Coupling group System is 23.00 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 65: There are 9 non-linear virtual site constructions. Their contribution to 65: the energy error is approximated. In most cases this does not affect the 65: error significantly. 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 5 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 16 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 65: 65: turning all bonds into constraints... 65: 65: Cleaning up constraints and constant bonded interactions with virtual sites 65: 65: Removed 18 Angles with virtual sites, 21 left 65: 65: Removed 10 Proper Dih.s with virtual sites, 44 left 65: 65: Converted 15 Constraints with virtual sites to connections, 7 left 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 65: 65: turning all bonds into constraints... 65: 65: Cleaning up constraints and constant bonded interactions with virtual sites 65: 65: Removed 18 Angles with virtual sites, 21 left 65: 65: Removed 10 Proper Dih.s with virtual sites, 44 left 65: 65: Converted 15 Constraints with virtual sites to connections, 7 left 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.040 0.020 199.6 65: (ns/day) (hour/ns) 65: Performance: 73.030 0.329 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.047 0.023 199.6 65: (ns/day) (hour/ns) 65: Performance: 33.312 0.720 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.045 0.023 199.6 65: (ns/day) (hour/ns) 65: Performance: 34.127 0.703 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 (174 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file unknown]: 65: You are using constraints on all bonds, whereas the forcefield has been 65: parametrized only with constraints involving hydrogen atoms. We suggest 65: using constraints = h-bonds instead, this will also improve performance. 65: 65: Number of degrees of freedom in T-Coupling group System is 23.00 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 65: There are 9 non-linear virtual site constructions. Their contribution to 65: the energy error is approximated. In most cases this does not affect the 65: error significantly. 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 5 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file unknown]: 65: You are using constraints on all bonds, whereas the forcefield has been 65: parametrized only with constraints involving hydrogen atoms. We suggest 65: using constraints = h-bonds instead, this will also improve performance. 65: 65: Number of degrees of freedom in T-Coupling group System is 23.00 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 65: There are 9 non-linear virtual site constructions. Their contribution to 65: the energy error is approximated. In most cases this does not affect the 65: error significantly. 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 5 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 65: 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 16 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 65: 65: turning all bonds into constraints... 65: 65: Cleaning up constraints and constant bonded interactions with virtual sites 65: 65: Removed 18 Angles with virtual sites, 21 left 65: 65: Removed 10 Proper Dih.s with virtual sites, 44 left 65: 65: Converted 15 Constraints with virtual sites to connections, 7 left 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 65: 65: turning all bonds into constraints... 65: 65: Cleaning up constraints and constant bonded interactions with virtual sites 65: 65: Removed 18 Angles with virtual sites, 21 left 65: 65: Removed 10 Proper Dih.s with virtual sites, 44 left 65: 65: Converted 15 Constraints with virtual sites to connections, 7 left 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.029 0.015 199.2 65: (ns/day) (hour/ns) 65: Performance: 101.023 0.238 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 65: 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.042 0.021 199.4 65: (ns/day) (hour/ns) 65: Performance: 37.295 0.644 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 65: 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.040 0.020 199.7 65: (ns/day) (hour/ns) 65: Performance: 38.536 0.623 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 (178 ms) 65: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (4849 ms total) 65: 65: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact 65: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 79.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: NVE simulation: will use the initial temperature of 293.480 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 79.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: NVE simulation: will use the initial temperature of 293.480 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 16 steps, 0.0 ps. 65: Generated 2485 of the 2485 non-bonded parameter combinations 65: 65: Generated 2485 of the 2485 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'nonanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 2485 of the 2485 non-bonded parameter combinations 65: 65: Generated 2485 of the 2485 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'nonanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.064 0.032 199.5 65: (ns/day) (hour/ns) 65: Performance: 45.929 0.523 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.044 0.022 198.9 65: (ns/day) (hour/ns) 65: Performance: 34.921 0.687 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: NOTE: 22 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.037 0.019 199.1 65: (ns/day) (hour/ns) 65: Performance: 41.498 0.578 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (107 ms) 65: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 79.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: NVE simulation: will use the initial temperature of 293.480 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 79.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: NVE simulation: will use the initial temperature of 293.480 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 16 steps, 0.0 ps. 65: Generated 2485 of the 2485 non-bonded parameter combinations 65: 65: Generated 2485 of the 2485 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'nonanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 293.48 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 2485 of the 2485 non-bonded parameter combinations 65: 65: Generated 2485 of the 2485 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'nonanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 293.48 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.176 0.088 199.4 65: (ns/day) (hour/ns) 65: Performance: 16.647 1.442 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.075 0.038 199.1 65: (ns/day) (hour/ns) 65: Performance: 20.560 1.167 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.104 0.052 199.2 65: (ns/day) (hour/ns) 65: Performance: 14.935 1.607 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (222 ms) 65: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 79.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: NVE simulation: will use the initial temperature of 293.480 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 79.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: NVE simulation: will use the initial temperature of 293.480 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 16 steps, 0.0 ps. 65: Generated 2485 of the 2485 non-bonded parameter combinations 65: 65: Generated 2485 of the 2485 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'nonanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 2485 of the 2485 non-bonded parameter combinations 65: 65: Generated 2485 of the 2485 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'nonanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.056 0.028 199.8 65: (ns/day) (hour/ns) 65: Performance: 52.754 0.455 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.045 0.023 199.8 65: (ns/day) (hour/ns) 65: Performance: 34.213 0.701 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.076 0.038 199.8 65: (ns/day) (hour/ns) 65: Performance: 20.460 1.173 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (123 ms) 65: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 79.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: NVE simulation: will use the initial temperature of 293.480 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 79.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: NVE simulation: will use the initial temperature of 293.480 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 16 steps, 0.0 ps. 65: Generated 2485 of the 2485 non-bonded parameter combinations 65: 65: Generated 2485 of the 2485 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'nonanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 293.48 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 2485 of the 2485 non-bonded parameter combinations 65: 65: Generated 2485 of the 2485 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'nonanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 293.48 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.081 0.040 199.7 65: (ns/day) (hour/ns) 65: Performance: 36.428 0.659 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.095 0.048 199.7 65: (ns/day) (hour/ns) 65: Performance: 16.281 1.474 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.091 0.045 199.4 65: (ns/day) (hour/ns) 65: Performance: 17.091 1.404 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (207 ms) 65: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 79.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 79.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 16 steps, 0.0 ps. 65: Generated 2485 of the 2485 non-bonded parameter combinations 65: 65: Generated 2485 of the 2485 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'nonanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 2485 of the 2485 non-bonded parameter combinations 65: 65: Generated 2485 of the 2485 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'nonanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.076 0.038 199.4 65: (ns/day) (hour/ns) 65: Performance: 38.555 0.622 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.067 0.034 199.4 65: (ns/day) (hour/ns) 65: Performance: 23.104 1.039 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.067 0.034 199.6 65: (ns/day) (hour/ns) 65: Performance: 23.072 1.040 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (147 ms) 65: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 79.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 79.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 16 steps, 0.0 ps. 65: Generated 2485 of the 2485 non-bonded parameter combinations 65: 65: Generated 2485 of the 2485 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'nonanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 2485 of the 2485 non-bonded parameter combinations 65: 65: Generated 2485 of the 2485 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'nonanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.061 0.030 199.5 65: (ns/day) (hour/ns) 65: Performance: 48.337 0.497 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.057 0.029 199.3 65: (ns/day) (hour/ns) 65: Performance: 27.044 0.887 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.049 0.024 199.6 65: (ns/day) (hour/ns) 65: Performance: 31.796 0.755 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (236 ms) 65: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 79.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 79.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 16 steps, 0.0 ps. 65: Generated 2485 of the 2485 non-bonded parameter combinations 65: 65: Generated 2485 of the 2485 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'nonanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 2485 of the 2485 non-bonded parameter combinations 65: 65: Generated 2485 of the 2485 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'nonanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.123 0.062 199.7 65: (ns/day) (hour/ns) 65: Performance: 23.838 1.007 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.061 0.031 199.3 65: (ns/day) (hour/ns) 65: Performance: 25.327 0.948 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.056 0.028 199.5 65: (ns/day) (hour/ns) 65: Performance: 27.915 0.860 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (179 ms) 65: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 79.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 79.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 20, rlist from 0.749 to 0.843 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 16 steps, 0.0 ps. 65: Generated 2485 of the 2485 non-bonded parameter combinations 65: 65: Generated 2485 of the 2485 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'nonanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 2485 of the 2485 non-bonded parameter combinations 65: 65: Generated 2485 of the 2485 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'nonanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.032 0.016 199.3 65: (ns/day) (hour/ns) 65: Performance: 91.695 0.262 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 20, rlist from 0.749 to 0.843 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.042 0.021 199.0 65: (ns/day) (hour/ns) 65: Performance: 37.164 0.646 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 20, rlist from 0.749 to 0.843 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.060 0.030 199.6 65: (ns/day) (hour/ns) 65: Performance: 26.007 0.923 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (167 ms) 65: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (1393 ms total) 65: 65: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact 65: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.032 0.016 199.3 65: (ns/day) (hour/ns) 65: Performance: 92.557 0.259 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.048 0.024 199.6 65: (ns/day) (hour/ns) 65: Performance: 32.365 0.742 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.054 0.027 199.6 65: (ns/day) (hour/ns) 65: Performance: 28.584 0.840 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (77 ms) 65: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.044 0.022 199.5 65: (ns/day) (hour/ns) 65: Performance: 66.557 0.361 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.036 0.018 199.5 65: (ns/day) (hour/ns) 65: Performance: 43.150 0.556 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.046 0.023 199.6 65: (ns/day) (hour/ns) 65: Performance: 33.409 0.718 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (74 ms) 65: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 65: 1 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 3 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 65: 1 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.078 0.039 199.7 65: (ns/day) (hour/ns) 65: Performance: 37.499 0.640 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.032 0.016 199.3 65: (ns/day) (hour/ns) 65: Performance: 48.306 0.497 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.030 0.015 199.1 65: (ns/day) (hour/ns) 65: Performance: 51.748 0.464 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (121 ms) 65: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 65: 1 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 3 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 65: 1 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.032 0.016 199.6 65: (ns/day) (hour/ns) 65: Performance: 91.409 0.263 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.028 0.014 199.6 65: (ns/day) (hour/ns) 65: Performance: 55.866 0.430 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.034 0.017 199.6 65: (ns/day) (hour/ns) 65: Performance: 45.730 0.525 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (59 ms) 65: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.083 0.042 199.7 65: (ns/day) (hour/ns) 65: Performance: 35.341 0.679 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: NOTE: 33 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.097 0.048 199.8 65: (ns/day) (hour/ns) 65: Performance: 16.039 1.496 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.048 0.024 199.1 65: (ns/day) (hour/ns) 65: Performance: 32.172 0.746 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (160 ms) 65: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.041 0.020 199.8 65: (ns/day) (hour/ns) 65: Performance: 72.281 0.332 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.029 0.014 199.8 65: (ns/day) (hour/ns) 65: Performance: 53.718 0.447 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.037 0.019 199.2 65: (ns/day) (hour/ns) 65: Performance: 41.999 0.571 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (70 ms) 65: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.077 0.038 199.8 65: (ns/day) (hour/ns) 65: Performance: 38.249 0.627 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.026 0.013 199.6 65: (ns/day) (hour/ns) 65: Performance: 59.487 0.403 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.060 0.030 199.3 65: (ns/day) (hour/ns) 65: Performance: 25.946 0.925 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (129 ms) 65: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.042 0.021 199.7 65: (ns/day) (hour/ns) 65: Performance: 69.065 0.347 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.147 0.074 199.8 65: (ns/day) (hour/ns) 65: Performance: 10.537 2.278 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.051 0.026 199.1 65: (ns/day) (hour/ns) 65: Performance: 30.244 0.794 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (132 ms) 65: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact (825 ms total) 65: 65: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact 65: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: NVE simulation: will use the initial temperature of 68.810 K for 65: determining the Verlet buffer size 65: 65: 65: There were 3 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: NVE simulation: will use the initial temperature of 68.810 K for 65: determining the Verlet buffer size 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.040 0.020 199.7 65: (ns/day) (hour/ns) 65: Performance: 74.043 0.324 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.053 0.027 199.4 65: (ns/day) (hour/ns) 65: Performance: 29.015 0.827 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.076 0.038 199.5 65: (ns/day) (hour/ns) 65: Performance: 20.439 1.174 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (113 ms) 65: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: NVE simulation: will use the initial temperature of 68.810 K for 65: determining the Verlet buffer size 65: 65: 65: There were 3 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: NVE simulation: will use the initial temperature of 68.810 K for 65: determining the Verlet buffer size 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.050 0.025 199.7 65: (ns/day) (hour/ns) 65: Performance: 58.589 0.410 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.033 0.017 199.6 65: (ns/day) (hour/ns) 65: Performance: 46.337 0.518 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.038 0.019 199.5 65: (ns/day) (hour/ns) 65: Performance: 40.606 0.591 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (87 ms) 65: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact (200 ms total) 65: 65: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact 65: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.095 0.048 199.8 65: (ns/day) (hour/ns) 65: Performance: 30.919 0.776 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.036 0.018 199.5 65: (ns/day) (hour/ns) 65: Performance: 43.177 0.556 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.027 0.013 199.4 65: (ns/day) (hour/ns) 65: Performance: 58.137 0.413 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (129 ms) 65: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.056 0.028 199.6 65: (ns/day) (hour/ns) 65: Performance: 52.771 0.455 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.034 0.017 199.5 65: (ns/day) (hour/ns) 65: Performance: 45.028 0.533 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.031 0.015 199.3 65: (ns/day) (hour/ns) 65: Performance: 50.688 0.473 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (77 ms) 65: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 65: 1 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 3 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 65: 1 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.056 0.028 199.6 65: (ns/day) (hour/ns) 65: Performance: 52.795 0.455 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.033 0.017 199.4 65: (ns/day) (hour/ns) 65: Performance: 46.591 0.515 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.033 0.016 199.6 65: (ns/day) (hour/ns) 65: Performance: 47.635 0.504 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (80 ms) 65: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 65: 1 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 3 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 65: 1 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.040 0.020 199.5 65: (ns/day) (hour/ns) 65: Performance: 73.079 0.328 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.046 0.023 199.7 65: (ns/day) (hour/ns) 65: Performance: 33.649 0.713 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.052 0.026 199.6 65: (ns/day) (hour/ns) 65: Performance: 29.853 0.804 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (108 ms) 65: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.056 0.028 199.7 65: (ns/day) (hour/ns) 65: Performance: 52.644 0.456 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.062 0.031 199.7 65: (ns/day) (hour/ns) 65: Performance: 25.189 0.953 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.049 0.025 199.4 65: (ns/day) (hour/ns) 65: Performance: 31.569 0.760 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (111 ms) 65: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.056 0.028 199.7 65: (ns/day) (hour/ns) 65: Performance: 52.322 0.459 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.047 0.024 199.7 65: (ns/day) (hour/ns) 65: Performance: 32.730 0.733 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.047 0.024 199.4 65: (ns/day) (hour/ns) 65: Performance: 32.815 0.731 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (108 ms) 65: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 65: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (0 ms) 65: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.035 0.018 199.6 65: (ns/day) (hour/ns) 65: Performance: 82.728 0.290 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: NOTE: 25 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.065 0.032 199.7 65: (ns/day) (hour/ns) 65: Performance: 23.997 1.000 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: NOTE: 28 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.087 0.044 199.5 65: (ns/day) (hour/ns) 65: Performance: 17.772 1.350 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (123 ms) 65: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact (740 ms total) 65: 65: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact 65: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.056 0.028 199.5 65: (ns/day) (hour/ns) 65: Performance: 52.172 0.460 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.068 0.034 199.7 65: (ns/day) (hour/ns) 65: Performance: 22.711 1.057 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.035 0.017 199.4 65: (ns/day) (hour/ns) 65: Performance: 44.548 0.539 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (96 ms) 65: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (96 ms total) 65: 65: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact 65: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Pull group 1 'FirstWaterMolecule' has 3 atoms 65: Pull group 2 'SecondWaterMolecule' has 3 atoms 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: NVE simulation: will use the initial temperature of 2573.591 K for 65: determining the Verlet buffer size 65: 65: Pull group natoms pbc atom distance at start reference at t=0 65: 1 3 2 65: 2 3 5 1.112 nm 1.000 nm 65: 65: There were 3 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Pull group 1 'FirstWaterMolecule' has 3 atoms 65: Pull group 2 'SecondWaterMolecule' has 3 atoms 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: NVE simulation: will use the initial temperature of 2573.591 K for 65: determining the Verlet buffer size 65: 65: Pull group natoms pbc atom distance at start reference at t=0 65: 1 3 2 65: 2 3 5 1.112 nm 1.000 nm 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps. 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.057 0.029 199.6 65: (ns/day) (hour/ns) 65: Performance: 51.532 0.466 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.058 0.029 199.6 65: (ns/day) (hour/ns) 65: Performance: 26.780 0.896 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.065 0.033 199.7 65: (ns/day) (hour/ns) 65: Performance: 23.812 1.008 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (133 ms) 65: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Pull group 1 'FirstWaterMolecule' has 3 atoms 65: Pull group 2 'SecondWaterMolecule' has 3 atoms 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: NVE simulation: will use the initial temperature of 2573.591 K for 65: determining the Verlet buffer size 65: 65: Pull group natoms pbc atom distance at start reference at t=0 65: 1 3 2 65: 2 3 5 1.112 nm 1.000 nm 65: 65: There were 3 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Pull group 1 'FirstWaterMolecule' has 3 atoms 65: Pull group 2 'SecondWaterMolecule' has 3 atoms 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: NVE simulation: will use the initial temperature of 2573.591 K for 65: determining the Verlet buffer size 65: 65: Pull group natoms pbc atom distance at start reference at t=0 65: 1 3 2 65: 2 3 5 1.112 nm 1.000 nm 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps. 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.061 0.031 199.7 65: (ns/day) (hour/ns) 65: Performance: 48.124 0.499 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.056 0.028 199.7 65: (ns/day) (hour/ns) 65: Performance: 27.533 0.872 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.052 0.026 199.6 65: (ns/day) (hour/ns) 65: Performance: 29.967 0.801 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (146 ms) 65: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact (280 ms total) 65: 65: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact 65: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 65: Setting the AWH bias MC random seed to 1602151413 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Pull group 1 'C_&_r_1' has 1 atoms 65: Pull group 2 'N_&_r_2' has 1 atoms 65: Pull group 3 'CA' has 1 atoms 65: Pull group 4 'C_&_r_2' has 1 atoms 65: Pull group 5 'N_&_r_3' has 1 atoms 65: Number of degrees of freedom in T-Coupling group System is 51.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: Pull group natoms pbc atom distance at start reference at t=0 65: 1 1 0 65: 2 1 0 179.098 deg 0.000 deg 65: 2 1 0 65: 3 1 0 158.667 deg 0.000 deg 65: 65: There were 3 NOTEs 65: Setting the AWH bias MC random seed to -1645002787 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Pull group 1 'C_&_r_1' has 1 atoms 65: Pull group 2 'N_&_r_2' has 1 atoms 65: Pull group 3 'CA' has 1 atoms 65: Pull group 4 'C_&_r_2' has 1 atoms 65: Pull group 5 'N_&_r_3' has 1 atoms 65: Number of degrees of freedom in T-Coupling group System is 51.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: Pull group natoms pbc atom distance at start reference at t=0 65: 1 1 0 65: 2 1 0 179.098 deg 0.000 deg 65: 2 1 0 65: 3 1 0 158.667 deg 0.000 deg 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 16 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.249 0.125 199.8 65: (ns/day) (hour/ns) 65: Performance: 11.791 2.035 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: NOTE: 27 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.120 0.060 199.7 65: (ns/day) (hour/ns) 65: Performance: 12.926 1.857 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.068 0.034 199.4 65: (ns/day) (hour/ns) 65: Performance: 22.924 1.047 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (429 ms) 65: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 65: Setting the AWH bias MC random seed to -352332450 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Pull group 1 'C_&_r_1' has 1 atoms 65: Pull group 2 'N_&_r_2' has 1 atoms 65: Pull group 3 'CA' has 1 atoms 65: Pull group 4 'C_&_r_2' has 1 atoms 65: Pull group 5 'N_&_r_3' has 1 atoms 65: Number of degrees of freedom in T-Coupling group System is 51.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: Pull group natoms pbc atom distance at start reference at t=0 65: 1 1 0 65: 2 1 0 179.098 deg 0.000 deg 65: 2 1 0 65: 3 1 0 158.667 deg 0.000 deg 65: 65: There were 3 NOTEs 65: Setting the AWH bias MC random seed to 2130636798 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Pull group 1 'C_&_r_1' has 1 atoms 65: Pull group 2 'N_&_r_2' has 1 atoms 65: Pull group 3 'CA' has 1 atoms 65: Pull group 4 'C_&_r_2' has 1 atoms 65: Pull group 5 'N_&_r_3' has 1 atoms 65: Number of degrees of freedom in T-Coupling group System is 51.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: Pull group natoms pbc atom distance at start reference at t=0 65: 1 1 0 65: 2 1 0 179.098 deg 0.000 deg 65: 2 1 0 65: 3 1 0 158.667 deg 0.000 deg 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 16 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.058 0.029 199.5 65: (ns/day) (hour/ns) 65: Performance: 50.373 0.476 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.067 0.034 199.5 65: (ns/day) (hour/ns) 65: Performance: 23.103 1.039 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.044 0.022 199.4 65: (ns/day) (hour/ns) 65: Performance: 35.330 0.679 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (154 ms) 65: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact (583 ms total) 65: 65: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact 65: [ RUN ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 79.00 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 2 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 79.00 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 2 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 16 steps, 0.0 ps. 65: Generated 2485 of the 2485 non-bonded parameter combinations 65: 65: Generated 2485 of the 2485 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'nonanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 2485 of the 2485 non-bonded parameter combinations 65: 65: Generated 2485 of the 2485 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'nonanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.098 0.049 199.9 65: (ns/day) (hour/ns) 65: Performance: 30.003 0.800 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.047 0.024 199.8 65: (ns/day) (hour/ns) 65: Performance: 32.941 0.729 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.066 0.033 199.6 65: (ns/day) (hour/ns) 65: Performance: 23.520 1.020 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (182 ms) 65: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact (182 ms total) 65: 65: [----------] 3 tests from Checking/InitialConstraintsTest 65: [ RUN ] Checking/InitialConstraintsTest.Works/0 65: Number of degrees of freedom in T-Coupling group rest is 11.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 65: NVE simulation: will use the initial temperature of 1141.954 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 2 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc-and-methanol' 65: 1 steps, 0.0 ps. 65: Setting the LD random seed to -1149953 65: 65: Generated 8 of the 10 non-bonded parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'Methanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.027 0.014 199.4 65: (ns/day) (hour/ns) 65: Performance: 12.643 1.898 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (26 ms) 65: [ RUN ] Checking/InitialConstraintsTest.Works/1 65: Number of degrees of freedom in T-Coupling group rest is 11.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 65: NVE simulation: will use the initial temperature of 1141.954 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 2 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc-and-methanol' 65: 1 steps, 0.0 ps. 65: Setting the LD random seed to 1406648186 65: 65: Generated 8 of the 10 non-bonded parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'Methanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.082 0.041 199.9 65: (ns/day) (hour/ns) 65: Performance: 4.222 5.684 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (50 ms) 65: [ RUN ] Checking/InitialConstraintsTest.Works/2 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 65: Integrator method md-vv-avek is implemented primarily for validation 65: purposes; for molecular dynamics, you should probably be using md or 65: md-vv 65: 65: Number of degrees of freedom in T-Coupling group rest is 11.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 65: NVE simulation: will use the initial temperature of 1141.954 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc-and-methanol' 65: 1 steps, 0.0 ps. 65: Setting the LD random seed to -71346179 65: 65: Generated 8 of the 10 non-bonded parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'Methanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.042 0.021 199.6 65: (ns/day) (hour/ns) 65: Performance: 8.269 2.902 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (32 ms) 65: [----------] 3 tests from Checking/InitialConstraintsTest (110 ms total) 65: 65: [----------] Global test environment tear-down 65: [==========] 76 tests from 13 test suites ran. (10845 ms total) 65: [ PASSED ] 76 tests. 65/91 Test #65: MdrunIOTests ................................. Passed 11.21 sec test 66 Start 66: MdrunTestsOneRank 66: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunTestsOneRank.xml" 66: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 66: Test timeout computed to be: 600 66: [==========] Running 28 tests from 7 test suites. 66: [----------] Global test environment set-up. 66: [----------] 1 test from CompelTest 66: [ RUN ] CompelTest.SwapCanRun 66: Setting the LD random seed to -337133641 66: 66: Generated 330891 of the 330891 non-bonded parameter combinations 66: Generating 1-4 interactions: fudge = 0.5 66: 66: Generated 330891 of the 330891 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Protein' 66: 66: turning all bonds into constraints... 66: 66: Excluding 3 bonded neighbours molecule type 'OCT' 66: 66: turning all bonds into constraints... 66: 66: Excluding 1 bonded neighbours molecule type 'NA' 66: 66: turning all bonds into constraints... 66: 66: Excluding 1 bonded neighbours molecule type 'CL' 66: 66: turning all bonds into constraints... 66: 66: Excluding 3 bonded neighbours molecule type 'Protein' 66: 66: Excluding 3 bonded neighbours molecule type 'OCT' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning all bonds into constraints... 66: Split0 group 'Ch0' contains 83 atoms. 66: Split1 group 'Ch1' contains 83 atoms. 66: Solvent group 'SOL' contains 11931 atoms. 66: Swap group 'NA+' contains 19 atoms. 66: Swap group 'CL-' contains 19 atoms. 66: Number of degrees of freedom in T-Coupling group System is 27869.00 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.316 nm, buffer size 0.316 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.262 nm, buffer size 0.262 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 1 Mb of data 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 66: Removing center of mass motion in the presence of position restraints 66: might cause artifacts. When you are using position restraints to 66: equilibrate a macro-molecule, the artifacts are usually negligible. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Update groups can not be used for this system because there are three or more consecutively coupled constraints 66: 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: SWAP: Determining initial numbers of ions per compartment. 66: SWAP: Setting pointers for checkpoint writing 66: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 66: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 66: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 66: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 66: starting mdrun 'Channel_coco in octane membrane' 66: 2 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: NOTE: 31 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.468 0.234 200.0 66: (ns/day) (hour/ns) 66: Performance: 5.536 4.335 66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 66: 66: Update groups can not be used for this system because there are three or more consecutively coupled constraints 66: 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: SWAP: Setting pointers for checkpoint writing 66: SWAP: Copying channel fluxes from checkpoint file data 66: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 66: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 66: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 66: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 66: starting mdrun 'Channel_coco in octane membrane' 66: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: NOTE: 12 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.444 0.222 200.0 66: (ns/day) (hour/ns) 66: Performance: 5.834 4.114 66: [ OK ] CompelTest.SwapCanRun (1177 ms) 66: [----------] 1 test from CompelTest (1177 ms total) 66: 66: [----------] 6 tests from BondedInteractionsTest 66: [ RUN ] BondedInteractionsTest.NormalBondWorks 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Setting the LD random seed to 1432321019 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'butane' 66: 66: This run will generate roughly 0 Mb of data 66: 66: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 66: In moleculetype 'butane' 2 atoms are not bound by a potential or 66: constraint to any other atom in the same moleculetype. Although 66: technically this might not cause issues in a simulation, this often means 66: that the user forgot to add a bond/potential/constraint or put multiple 66: molecules in the same moleculetype definition by mistake. Run with -v to 66: get information for each atom. 66: 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 66: NVE simulation with an initial temperature of zero: will use a Verlet 66: buffer of 10%. Check your energy drift! 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 66: 66: Reading frames from gro file 'A single butane', 4 atoms. 66: Reading frame 0 time 0.000 Last frame 0 time 0.000 66: 66: NOTE: 20 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.000 0.000 184.8 66: (ns/day) (hour/ns) 66: Performance: 639.132 0.038 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: 66: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 66: In moleculetype 'butane' 2 atoms are not bound by a potential or 66: constraint to any other atom in the same moleculetype. Although 66: technically this might not cause issues in a simulation, this often means 66: that the user forgot to add a bond/potential/constraint or put multiple 66: molecules in the same moleculetype definition by mistake. Run with -v to 66: get information for each atom. 66: 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 66: NVE simulation with an initial temperature of zero: will use a Verlet 66: buffer of 10%. Check your energy drift! 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: [ OK ] BondedInteractionsTest.NormalBondWorks (3 ms) 66: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 66: Setting the LD random seed to 2006876031 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'butane' 66: 66: This run will generate roughly 0 Mb of data 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 66: 66: Reading frames from gro file 'A single butane', 4 atoms. 66: Reading frame 0 time 0.000 Last frame 0 time 0.000 66: 66: NOTE: 12 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.000 0.000 189.2 66: (ns/day) (hour/ns) 66: Performance: 424.342 0.057 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: 66: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 66: In moleculetype 'butane' 4 atoms are not bound by a potential or 66: constraint to any other atom in the same moleculetype. Although 66: technically this might not cause issues in a simulation, this often means 66: that the user forgot to add a bond/potential/constraint or put multiple 66: molecules in the same moleculetype definition by mistake. Run with -v to 66: get information for each atom. 66: 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 66: NVE simulation with an initial temperature of zero: will use a Verlet 66: buffer of 10%. Check your energy drift! 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: [ OK ] BondedInteractionsTest.TabulatedBondWorks (13 ms) 66: [ RUN ] BondedInteractionsTest.NormalAngleWorks 66: Setting the LD random seed to -591795275 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'butane' 66: 66: This run will generate roughly 0 Mb of data 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 66: 66: Reading frames from gro file 'A single butane', 4 atoms. 66: Reading frame 0 time 0.000 Last frame 0 time 0.000 66: 66: NOTE: 11 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.000 0.000 188.6 66: (ns/day) (hour/ns) 66: Performance: 430.901 0.056 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: 66: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 66: In moleculetype 'butane' 4 atoms are not bound by a potential or 66: constraint to any other atom in the same moleculetype. Although 66: technically this might not cause issues in a simulation, this often means 66: that the user forgot to add a bond/potential/constraint or put multiple 66: molecules in the same moleculetype definition by mistake. Run with -v to 66: get information for each atom. 66: 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 66: NVE simulation with an initial temperature of zero: will use a Verlet 66: buffer of 10%. Check your energy drift! 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 66: 66: Reading frames from gro file 'A single butane', 4 atoms. 66: Reading frame 0 time 0.000 Last frame 0 time 0.000 66: 66: NOTE: 11 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.000 0.000 188.4 66: (ns/day) (hour/ns) 66: Performance: 439.258 0.055 66: [ OK ] BondedInteractionsTest.NormalAngleWorks (15 ms) 66: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 66: Setting the LD random seed to 2104737783 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'butane' 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (3 ms) 66: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: 66: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 66: In moleculetype 'butane' 4 atoms are not bound by a potential or 66: constraint to any other atom in the same moleculetype. Although 66: technically this might not cause issues in a simulation, this often means 66: that the user forgot to add a bond/potential/constraint or put multiple 66: molecules in the same moleculetype definition by mistake. Run with -v to 66: get information for each atom. 66: 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 66: NVE simulation with an initial temperature of zero: will use a Verlet 66: buffer of 10%. Check your energy drift! 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 66: 66: Reading frames from gro file 'A single butane', 4 atoms. 66: Reading frame 0 time 0.000 Last frame 0 time 0.000 66: 66: NOTE: 11 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.000 0.000 188.5 66: (ns/day) (hour/ns) 66: Performance: 451.855 0.053 66: Setting the LD random seed to -10491918 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'butane' 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] BondedInteractionsTest.NormalDihedralWorks (3 ms) 66: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: 66: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 66: In moleculetype 'butane' 4 atoms are not bound by a potential or 66: constraint to any other atom in the same moleculetype. Although 66: technically this might not cause issues in a simulation, this often means 66: that the user forgot to add a bond/potential/constraint or put multiple 66: molecules in the same moleculetype definition by mistake. Run with -v to 66: get information for each atom. 66: 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 66: NVE simulation with an initial temperature of zero: will use a Verlet 66: buffer of 10%. Check your energy drift! 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 66: 66: Reading frames from gro file 'A single butane', 4 atoms. 66: Reading frame 0 time 0.000 Last frame 0 time 0.000 66: 66: NOTE: 18 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.000 0.000 183.8 66: (ns/day) (hour/ns) 66: Performance: 716.182 0.034 66: Setting the LD random seed to -1145073955 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'butane' 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (10 ms) 66: [----------] 6 tests from BondedInteractionsTest (53 ms total) 66: 66: [----------] 2 tests from BoxDeformationTest 66: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 66: Setting the LD random seed to -574636129 66: 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Setting gen_seed to -940967959 66: 66: Velocities were taken from a Maxwell distribution at 0 K 66: 66: This run will generate roughly 0 Mb of data 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 66: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 66: < 0 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (10) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Number of degrees of freedom in T-Coupling group rest is 33.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 0 steps, 0.0 ps. 66: 66: NOTE: 27 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.000 0.000 163.5 66: (ns/day) (hour/ns) 66: Performance: 1485.196 0.016 66: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (4 ms) 66: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 66: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 66: < 0 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (10) 66: 66: Setting the LD random seed to -478487298 66: 66: Generated 330891 of the 330891 non-bonded parameter combinations 66: Generating 1-4 interactions: fudge = 0.5 66: 66: Generated 330891 of the 330891 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: Number of degrees of freedom in T-Coupling group rest is 1293.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 66: Calculating fourier grid dimensions for X Y Z 66: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 66: 66: 66: There were 2 NOTEs 66: Estimate for the relative computational load of the PME mesh part: 0.20 66: 66: This run will generate roughly 0 Mb of data 66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 20 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.078 0.039 199.6 66: (ns/day) (hour/ns) 66: Performance: 93.377 0.257 66: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (503 ms) 66: [----------] 2 tests from BoxDeformationTest (511 ms total) 66: 66: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 66: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 66: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 66: < 0 66: 66: Setting the LD random seed to -38879238 66: 66: Generated 2211 of the 2211 non-bonded parameter combinations 66: Generating 1-4 interactions: fudge = 0.5 66: 66: Generated 2211 of the 2211 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 66: 66: turning H bonds into constraints... 66: 66: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 66: Calculating fourier grid dimensions for X Y Z 66: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 66: 66: Estimate for the relative computational load of the PME mesh part: 0.94 66: 66: This run will generate roughly 0 Mb of data 66: 66: NOTE 2 [file ala.top, line 256]: 66: For energy conservation with LINCS, lincs_iter should be 2 or larger. 66: 66: 66: Number of degrees of freedom in T-Coupling group rest is 54.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 66: The optimal PME mesh load for parallel simulations is below 0.5 66: and for highly parallel simulations between 0.25 and 0.33, 66: for higher performance, increase the cut-off and the PME grid spacing. 66: 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'UNNAMED in water' 66: 4 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.040 0.020 199.3 66: (ns/day) (hour/ns) 66: Performance: 21.672 1.107 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 66: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 66: < 0 66: 66: Setting the LD random seed to -799055970 66: 66: Generated 2211 of the 2211 non-bonded parameter combinations 66: 66: Generated 2211 of the 2211 1-4 parameter combinations 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 66: 66: turning H bonds into constraints... 66: 66: NOTE 2 [file ala.top, line 256]: 66: For energy conservation with LINCS, lincs_iter should be 2 or larger. 66: 66: 66: Number of degrees of freedom in T-Coupling group rest is 54.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 66: The optimal PME mesh load for parallel simulations is below 0.5 66: and for highly parallel simulations between 0.25 and 0.33, 66: for higher performance, increase the cut-off and the PME grid spacing. 66: 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 66: Calculating fourier grid dimensions for X Y Z 66: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 66: 66: Estimate for the relative computational load of the PME mesh part: 0.94 66: 66: This run will generate roughly 0 Mb of data 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'UNNAMED in water' 66: 4 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: NOTE: 20 % of the run time was spent in domain decomposition, 66: 0 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.040 0.020 199.4 66: (ns/day) (hour/ns) 66: Performance: 21.489 1.117 66: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) 66: 66: 66: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (841 ms) 66: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 66: Setting the LD random seed to 1572859701 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 66: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 66: < 0 66: 66: 66: Generated 2211 of the 2211 non-bonded parameter combinations 66: Generating 1-4 interactions: fudge = 0.5 66: 66: Generated 2211 of the 2211 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 66: 66: turning H bonds into constraints... 66: 66: NOTE 2 [file ala.top, line 256]: 66: For energy conservation with LINCS, lincs_iter should be 2 or larger. 66: 66: 66: Number of degrees of freedom in T-Coupling group rest is 54.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 66: Calculating fourier grid dimensions for X Y Z 66: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 66: 66: Estimate for the relative computational load of the PME mesh part: 0.94 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 66: The optimal PME mesh load for parallel simulations is below 0.5 66: and for highly parallel simulations between 0.25 and 0.33, 66: for higher performance, increase the cut-off and the PME grid spacing. 66: 66: 66: 66: This run will generate roughly 0 Mb of data 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'UNNAMED in water' 66: 4 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.053 0.026 199.4 66: (ns/day) (hour/ns) 66: Performance: 16.396 1.464 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 66: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 66: < 0 66: 66: Setting the LD random seed to 1866393339 66: 66: Generated 2211 of the 2211 non-bonded parameter combinations 66: 66: Generated 2211 of the 2211 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 66: 66: turning H bonds into constraints... 66: 66: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 66: Calculating fourier grid dimensions for X Y Z 66: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 66: 66: Estimate for the relative computational load of the PME mesh part: 0.94 66: 66: This run will generate roughly 0 Mb of data 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 2 [file ala.top, line 256]: 66: For energy conservation with LINCS, lincs_iter should be 2 or larger. 66: 66: 66: Number of degrees of freedom in T-Coupling group rest is 54.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 66: The optimal PME mesh load for parallel simulations is below 0.5 66: and for highly parallel simulations between 0.25 and 0.33, 66: for higher performance, increase the cut-off and the PME grid spacing. 66: 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 66: Can not increase nstlist because an NVE ensemble is used 66: 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'UNNAMED in water' 66: 4 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.036 0.018 199.3 66: (ns/day) (hour/ns) 66: Performance: 23.968 1.001 66: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 66: 66: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (122 ms) 66: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (964 ms total) 66: 66: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 66: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 66: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 66: < 0 66: 66: Setting the LD random seed to -4670242 66: Generating 1-4 interactions: fudge = 0.5 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: Pull group 1 'FirstWaterMolecule' has 3 atoms 66: Pull group 2 'SecondWaterMolecule' has 3 atoms 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 3 2 66: 2 3 5 1.112 nm 1.000 nm 66: 66: There was 1 NOTE 66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: This run will generate roughly 0 Mb of data 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 4 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.071 0.036 199.6 66: (ns/day) (hour/ns) 66: Performance: 12.078 1.987 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 66: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 66: < 0 66: 66: Setting the LD random seed to -323490819 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: Generating 1-4 interactions: fudge = 0.5 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: Pull group 1 'FirstWaterMolecule' has 3 atoms 66: Pull group 2 'SecondWaterMolecule' has 3 atoms 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 3 2 66: 2 3 5 1.112 nm 1.000 nm 66: 66: There was 1 NOTE 66: 66: This run will generate roughly 0 Mb of data 66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 66: Can not increase nstlist because an NVE ensemble is used 66: 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 4 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.035 0.018 199.6 66: (ns/day) (hour/ns) 66: Performance: 24.599 0.976 66: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 66: 66: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (98 ms) 66: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (98 ms total) 66: 66: [----------] 12 tests from FreezeWorks/FreezeGroupTest 66: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 66: 66: turning H bonds into constraints... 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 66: There are 5 atoms that are fully frozen and part of COMM removal 66: group(s), removing these atoms from the COMM removal group(s) 66: 66: 66: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 66: There are 3 atoms that are frozen along less then 3 dimensions and part 66: of COMM removal group(s), due to limitations in the code these still 66: contribute to the mass of the COM along frozen dimensions and therefore 66: the COMM correction will be too small. 66: 66: Number of degrees of freedom in T-Coupling group System is 25.50 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 318.937 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 5 NOTEs 66: 66: There was 1 WARNING 66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.071 0.035 199.8 66: (ns/day) (hour/ns) 66: Performance: 21.990 1.091 66: 66: 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (56 ms) 66: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 66: Generating 1-4 interactions: fudge = 0.5 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 66: 66: turning H bonds into constraints... 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 66: There are 5 atoms that are fully frozen and part of COMM removal 66: group(s), removing these atoms from the COMM removal group(s) 66: 66: 66: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 66: There are 3 atoms that are frozen along less then 3 dimensions and part 66: of COMM removal group(s), due to limitations in the code these still 66: contribute to the mass of the COM along frozen dimensions and therefore 66: the COMM correction will be too small. 66: 66: Number of degrees of freedom in T-Coupling group System is 25.50 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 318.937 K for 66: determining the Verlet buffer size 66: 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 5 NOTEs 66: 66: There was 1 WARNING 66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.039 0.020 199.6 66: (ns/day) (hour/ns) 66: Performance: 39.390 0.609 66: 66: 66: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (27 ms) 66: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 66: 66: turning H bonds into constraints... 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 66: There are 5 atoms that are fully frozen and part of COMM removal 66: group(s), removing these atoms from the COMM removal group(s) 66: 66: 66: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 66: There are 3 atoms that are frozen along less then 3 dimensions and part 66: of COMM removal group(s), due to limitations in the code these still 66: contribute to the mass of the COM along frozen dimensions and therefore 66: the COMM correction will be too small. 66: 66: Number of degrees of freedom in T-Coupling group System is 25.50 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 66: NVE simulation: will use the initial temperature of 318.937 K for 66: determining the Verlet buffer size 66: 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 5 NOTEs 66: 66: There was 1 WARNING 66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.030 0.015 199.2 66: (ns/day) (hour/ns) 66: Performance: 51.073 0.470 66: 66: 66: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (27 ms) 66: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 66: 66: turning H bonds into constraints... 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 66: There are 5 atoms that are fully frozen and part of COMM removal 66: group(s), removing these atoms from the COMM removal group(s) 66: 66: 66: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 66: There are 3 atoms that are frozen along less then 3 dimensions and part 66: of COMM removal group(s), due to limitations in the code these still 66: contribute to the mass of the COM along frozen dimensions and therefore 66: the COMM correction will be too small. 66: 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 66: Number of degrees of freedom in T-Coupling group System is 25.50 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 66: NVE simulation: will use the initial temperature of 318.937 K for 66: determining the Verlet buffer size 66: 66: 66: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 5 NOTEs 66: 66: There was 1 WARNING 66: 66: This run will generate roughly 0 Mb of data 66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: NOTE: 25 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.096 0.048 199.6 66: (ns/day) (hour/ns) 66: Performance: 16.118 1.489 66: 66: 66: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (93 ms) 66: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 66: 66: turning H bonds into constraints... 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 66: There are 5 atoms that are fully frozen and part of COMM removal 66: group(s), removing these atoms from the COMM removal group(s) 66: 66: 66: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 66: There are 3 atoms that are frozen along less then 3 dimensions and part 66: of COMM removal group(s), due to limitations in the code these still 66: contribute to the mass of the COM along frozen dimensions and therefore 66: the COMM correction will be too small. 66: 66: Number of degrees of freedom in T-Coupling group System is 25.50 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 66: NVE simulation: will use the initial temperature of 318.937 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 5 NOTEs 66: 66: There was 1 WARNING 66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.036 0.018 199.4 66: (ns/day) (hour/ns) 66: Performance: 43.473 0.552 66: 66: 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (37 ms) 66: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 66: ./src/programs/mdrun/tests/freezegroups.cpp:194: Skipped 66: Parrinello-Rahman is not implemented in md-vv. 66: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 66: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: Generating 1-4 interactions: fudge = 0.5 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 66: 66: turning H bonds into constraints... 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 66: There are 5 atoms that are fully frozen and part of COMM removal 66: group(s), removing these atoms from the COMM removal group(s) 66: 66: 66: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 66: There are 3 atoms that are frozen along less then 3 dimensions and part 66: of COMM removal group(s), due to limitations in the code these still 66: contribute to the mass of the COM along frozen dimensions and therefore 66: the COMM correction will be too small. 66: 66: Number of degrees of freedom in T-Coupling group System is 25.50 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: This run will generate roughly 0 Mb of data 66: 66: There were 4 NOTEs 66: 66: There was 1 WARNING 66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 66: 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.041 0.021 199.6 66: (ns/day) (hour/ns) 66: Performance: 37.478 0.640 66: 66: 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (39 ms) 66: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 66: There are 5 atoms that are fully frozen and part of COMM removal 66: group(s), removing these atoms from the COMM removal group(s) 66: 66: 66: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 66: There are 3 atoms that are frozen along less then 3 dimensions and part 66: of COMM removal group(s), due to limitations in the code these still 66: contribute to the mass of the COM along frozen dimensions and therefore 66: the COMM correction will be too small. 66: 66: Number of degrees of freedom in T-Coupling group System is 25.50 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: 66: There was 1 WARNING 66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 66: 66: turning H bonds into constraints... 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 66: 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.070 0.035 199.6 66: (ns/day) (hour/ns) 66: Performance: 22.044 1.089 66: 66: 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (61 ms) 66: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 66: Generating 1-4 interactions: fudge = 0.5 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 66: 66: turning H bonds into constraints... 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 66: There are 5 atoms that are fully frozen and part of COMM removal 66: group(s), removing these atoms from the COMM removal group(s) 66: 66: 66: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 66: There are 3 atoms that are frozen along less then 3 dimensions and part 66: of COMM removal group(s), due to limitations in the code these still 66: contribute to the mass of the COM along frozen dimensions and therefore 66: the COMM correction will be too small. 66: 66: Number of degrees of freedom in T-Coupling group System is 25.50 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: 66: There was 1 WARNING 66: 66: This run will generate roughly 0 Mb of data 66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 66: 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 2.097 1.049 200.0 66: (ns/day) (hour/ns) 66: Performance: 0.742 32.365 66: 66: 66: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (1196 ms) 66: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: Generating 1-4 interactions: fudge = 0.5 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 66: 66: turning H bonds into constraints... 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 66: There are 5 atoms that are fully frozen and part of COMM removal 66: group(s), removing these atoms from the COMM removal group(s) 66: 66: 66: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 66: There are 3 atoms that are frozen along less then 3 dimensions and part 66: of COMM removal group(s), due to limitations in the code these still 66: contribute to the mass of the COM along frozen dimensions and therefore 66: the COMM correction will be too small. 66: 66: Number of degrees of freedom in T-Coupling group System is 25.50 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: 66: There was 1 WARNING 66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 66: 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.063 0.032 199.8 66: (ns/day) (hour/ns) 66: Performance: 24.618 0.975 66: 66: 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 66: There are 5 atoms that are fully frozen and part of COMM removal 66: group(s), removing these atoms from the COMM removal group(s) 66: 66: 66: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 66: There are 3 atoms that are frozen along less then 3 dimensions and part 66: of COMM removal group(s), due to limitations in the code these still 66: contribute to the mass of the COM along frozen dimensions and therefore 66: the COMM correction will be too small. 66: 66: Number of degrees of freedom in T-Coupling group System is 25.50 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: 66: There was 1 WARNING 66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (71 ms) 66: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 66: 66: turning H bonds into constraints... 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 66: 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.048 0.024 199.5 66: (ns/day) (hour/ns) 66: Performance: 32.199 0.745 66: 66: 66: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (65 ms) 66: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 66: There are 5 atoms that are fully frozen and part of COMM removal 66: group(s), removing these atoms from the COMM removal group(s) 66: 66: 66: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 66: There are 3 atoms that are frozen along less then 3 dimensions and part 66: of COMM removal group(s), due to limitations in the code these still 66: contribute to the mass of the COM along frozen dimensions and therefore 66: the COMM correction will be too small. 66: 66: Number of degrees of freedom in T-Coupling group System is 25.50 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: 66: There was 1 WARNING 66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 66: 66: turning H bonds into constraints... 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 66: 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.029 0.014 199.3 66: (ns/day) (hour/ns) 66: Performance: 54.081 0.444 66: 66: 66: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (77 ms) 66: [----------] 12 tests from FreezeWorks/FreezeGroupTest (1755 ms total) 66: 66: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 66: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Setting gen_seed to -308304609 66: 66: Velocities were taken from a Maxwell distribution at 0 K 66: 66: This run will generate roughly 0 Mb of data 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 66: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 66: < 0 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 66: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: Net Acceleration in X direction, will not be corrected 66: Net Acceleration in Y direction, will not be corrected 66: Net Acceleration in Z direction, will not be corrected 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.064 0.032 199.8 66: (ns/day) (hour/ns) 66: Performance: 48.763 0.492 66: 66: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (44 ms) 66: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 66: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 66: < 0 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Setting gen_seed to 1006327090 66: 66: Velocities were taken from a Maxwell distribution at 0 K 66: 66: This run will generate roughly 0 Mb of data 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 66: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 66: Net Acceleration in X direction, will not be corrected 66: Net Acceleration in Y direction, will not be corrected 66: Net Acceleration in Z direction, will not be corrected 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because verlet-buffer-tolerance is not set or used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.093 0.046 199.8 66: (ns/day) (hour/ns) 66: Performance: 33.486 0.717 66: 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 66: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 66: < 0 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (63 ms) 66: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 66: Generated 3 of the 3 non-bonded parameter combinations 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 66: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: Net Acceleration in X direction, will not be corrected 66: Net Acceleration in Y direction, will not be corrected 66: Net Acceleration in Z direction, will not be corrected 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Setting gen_seed to -1073153 66: 66: Velocities were taken from a Maxwell distribution at 0 K 66: 66: This run will generate roughly 0 Mb of data 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.037 0.018 199.7 66: (ns/day) (hour/ns) 66: Performance: 84.163 0.285 66: 66: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (37 ms) 66: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 66: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 66: < 0 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Setting gen_seed to -1079052631 66: 66: Velocities were taken from a Maxwell distribution at 0 K 66: 66: This run will generate roughly 0 Mb of data 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 66: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 66: Net Acceleration in X direction, will not be corrected 66: Net Acceleration in Y direction, will not be corrected 66: Net Acceleration in Z direction, will not be corrected 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because verlet-buffer-tolerance is not set or used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.032 0.016 199.6 66: (ns/day) (hour/ns) 66: Performance: 97.151 0.247 66: 66: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (49 ms) 66: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (196 ms total) 66: 66: [----------] Global test environment tear-down 66: [==========] 28 tests from 7 test suites ran. (5009 ms total) 66: [ PASSED ] 27 tests. 66: [ SKIPPED ] 1 test, listed below: 66: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 66/91 Test #66: MdrunTestsOneRank ............................ Passed 5.51 sec test 67 Start 67: MdrunTestsTwoRanks 67: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunTestsTwoRanks.xml" 67: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 67: Test timeout computed to be: 600 67: [==========] Running 28 tests from 7 test suites. 67: [----------] Global test environment set-up. 67: [----------] 1 test from CompelTest 67: [ RUN ] CompelTest.SwapCanRun 67: Setting the LD random seed to -67125250 67: 67: Generated 330891 of the 330891 non-bonded parameter combinations 67: Generating 1-4 interactions: fudge = 0.5 67: 67: Generated 330891 of the 330891 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Protein' 67: 67: turning all bonds into constraints... 67: 67: Excluding 3 bonded neighbours molecule type 'OCT' 67: 67: turning all bonds into constraints... 67: 67: Excluding 1 bonded neighbours molecule type 'NA' 67: 67: turning all bonds into constraints... 67: 67: Excluding 1 bonded neighbours molecule type 'CL' 67: 67: turning all bonds into constraints... 67: 67: Excluding 3 bonded neighbours molecule type 'Protein' 67: 67: Excluding 3 bonded neighbours molecule type 'OCT' 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: turning all bonds into constraints... 67: Split0 group 'Ch0' contains 83 atoms. 67: Split1 group 'Ch1' contains 83 atoms. 67: Solvent group 'SOL' contains 11931 atoms. 67: Swap group 'NA+' contains 19 atoms. 67: Swap group 'CL-' contains 19 atoms. 67: Number of degrees of freedom in T-Coupling group System is 27869.00 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 67: Removing center of mass motion in the presence of position restraints 67: might cause artifacts. When you are using position restraints to 67: equilibrate a macro-molecule, the artifacts are usually negligible. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 2 NOTEs 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 67: 67: Calculated rlist for 1x1 atom pair-list as 1.316 nm, buffer size 0.316 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 1.262 nm, buffer size 0.262 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 1 Mb of data 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Update groups can not be used for this system because there are three or more consecutively coupled constraints 67: 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: SWAP: Determining initial numbers of ions per compartment. 67: SWAP: Setting pointers for checkpoint writing 67: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 67: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 67: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 67: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 67: starting mdrun 'Channel_coco in octane membrane' 67: 2 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: 67: Dynamic load balancing report: 67: DLB was off during the run due to low measured imbalance. 67: Average load imbalance: 15.2%. 67: The balanceable part of the MD step is 15%, load imbalance is computed from this. 67: Part of the total run time spent waiting due to load imbalance: 2.3%. 67: 67: 67: NOTE: 27 % of the run time was spent in domain decomposition, 67: 12 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 2.273 0.568 399.9 67: (ns/day) (hour/ns) 67: Performance: 2.280 10.525 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 67: 67: Update groups can not be used for this system because there are three or more consecutively coupled constraints 67: 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: SWAP: Setting pointers for checkpoint writing 67: SWAP: Copying channel fluxes from checkpoint file data 67: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 67: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 67: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 67: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 67: starting mdrun 'Channel_coco in octane membrane' 67: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 1.367 0.350 390.9 67: (ns/day) (hour/ns) 67: Performance: 3.705 6.477 67: [ OK ] CompelTest.SwapCanRun (2216 ms) 67: [----------] 1 test from CompelTest (2216 ms total) 67: 67: [----------] 6 tests from BondedInteractionsTest 67: [ RUN ] BondedInteractionsTest.NormalBondWorks 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Setting the LD random seed to 1876831707 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'butane' 67: 67: This run will generate roughly 0 Mb of data 67: 67: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 67: In moleculetype 'butane' 2 atoms are not bound by a potential or 67: constraint to any other atom in the same moleculetype. Although 67: technically this might not cause issues in a simulation, this often means 67: that the user forgot to add a bond/potential/constraint or put multiple 67: molecules in the same moleculetype definition by mistake. Run with -v to 67: get information for each atom. 67: 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 67: 67: Reading frames from gro file 'A single butane', 4 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 60 % of the run time was spent in domain decomposition, 67: 0 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: NOTE: 18 % of the run time was spent communicating energies, 67: you might want to increase some nst* mdp options 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.224 0.056 399.8 67: (ns/day) (hour/ns) 67: Performance: 1.541 15.578 67: [ OK ] BondedInteractionsTest.NormalBondWorks (308 ms) 67: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Setting the LD random seed to 2147208815 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'butane' 67: 67: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 67: In moleculetype 'butane' 2 atoms are not bound by a potential or 67: constraint to any other atom in the same moleculetype. Although 67: technically this might not cause issues in a simulation, this often means 67: that the user forgot to add a bond/potential/constraint or put multiple 67: molecules in the same moleculetype definition by mistake. Run with -v to 67: get information for each atom. 67: 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: There were 3 NOTEs 67: 67: This run will generate roughly 0 Mb of data 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 67: 67: Reading frames from gro file 'A single butane', 4 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 13 % of the run time was spent in domain decomposition, 67: 10 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.001 0.000 367.6 67: (ns/day) (hour/ns) 67: Performance: 265.583 0.090 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: [ OK ] BondedInteractionsTest.TabulatedBondWorks (32 ms) 67: [ RUN ] BondedInteractionsTest.NormalAngleWorks 67: Setting the LD random seed to -961292439 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'butane' 67: 67: This run will generate roughly 0 Mb of data 67: 67: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 67: In moleculetype 'butane' 4 atoms are not bound by a potential or 67: constraint to any other atom in the same moleculetype. Although 67: technically this might not cause issues in a simulation, this often means 67: that the user forgot to add a bond/potential/constraint or put multiple 67: molecules in the same moleculetype definition by mistake. Run with -v to 67: get information for each atom. 67: 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 67: 67: Reading frames from gro file 'A single butane', 4 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 66 % of the run time was spent in domain decomposition, 67: 0 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: NOTE: 20 % of the run time was spent communicating energies, 67: you might want to increase some nst* mdp options 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.121 0.030 399.7 67: (ns/day) (hour/ns) 67: Performance: 2.862 8.386 67: [ OK ] BondedInteractionsTest.NormalAngleWorks (115 ms) 67: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: 67: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 67: In moleculetype 'butane' 4 atoms are not bound by a potential or 67: constraint to any other atom in the same moleculetype. Although 67: technically this might not cause issues in a simulation, this often means 67: that the user forgot to add a bond/potential/constraint or put multiple 67: molecules in the same moleculetype definition by mistake. Run with -v to 67: get information for each atom. 67: 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: Setting the LD random seed to -51905637 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'butane' 67: 67: This run will generate roughly 0 Mb of data 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 67: 67: Reading frames from gro file 'A single butane', 4 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 59 % of the run time was spent in domain decomposition, 67: 0 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: NOTE: 14 % of the run time was spent communicating energies, 67: you might want to increase some nst* mdp options 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.232 0.060 385.9 67: (ns/day) (hour/ns) 67: Performance: 1.438 16.695 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: 67: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 67: In moleculetype 'butane' 4 atoms are not bound by a potential or 67: constraint to any other atom in the same moleculetype. Although 67: technically this might not cause issues in a simulation, this often means 67: that the user forgot to add a bond/potential/constraint or put multiple 67: molecules in the same moleculetype definition by mistake. Run with -v to 67: get information for each atom. 67: 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (96 ms) 67: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 67: Setting the LD random seed to 1844682703 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'butane' 67: 67: This run will generate roughly 0 Mb of data 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 67: 67: Reading frames from gro file 'A single butane', 4 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 52 % of the run time was spent in domain decomposition, 67: 12 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: NOTE: 17 % of the run time was spent communicating energies, 67: you might want to increase some nst* mdp options 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.137 0.034 399.8 67: (ns/day) (hour/ns) 67: Performance: 2.529 9.491 67: [ OK ] BondedInteractionsTest.NormalDihedralWorks (55 ms) 67: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Setting the LD random seed to -436862977 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'butane' 67: 67: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 67: In moleculetype 'butane' 4 atoms are not bound by a potential or 67: constraint to any other atom in the same moleculetype. Although 67: technically this might not cause issues in a simulation, this often means 67: that the user forgot to add a bond/potential/constraint or put multiple 67: molecules in the same moleculetype definition by mistake. Run with -v to 67: get information for each atom. 67: 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Ch 67: This run will generate roughly 0 Mb of data 67: eck your energy drift! 67: 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 67: 67: Reading frames from gro file 'A single butane', 4 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 52 % of the run time was spent in domain decomposition, 67: 18 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: NOTE: 18 % of the run time was spent communicating energies, 67: you might want to increase some nst* mdp options 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.136 0.034 399.8 67: (ns/day) (hour/ns) 67: Performance: 2.533 9.475 67: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (55 ms) 67: [----------] 6 tests from BondedInteractionsTest (664 ms total) 67: 67: [----------] 2 tests from BoxDeformationTest 67: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 67: Setting the LD random seed to -1107313298 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: Setting gen_seed to -975831042 67: 67: Velocities were taken from a Maxwell distribution at 0 K 67: 67: This run will generate roughly 0 Mb of data 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (10) 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Argon' 67: 0 steps, 0.0 ps. 67: 67: NOTE: 60 % of the run time was spent in domain decomposition, 67: 0 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: NOTE: 13 % of the run time was spent communicating energies, 67: you might want to increase some nst* mdp options 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.240 0.072 333.6 67: (ns/day) (hour/ns) 67: Performance: 2.401 9.996 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (368 ms) 67: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (10) 67: 67: Setting the LD random seed to -1619007116 67: 67: Generated 330891 of the 330891 non-bonded parameter combinations 67: Generating 1-4 interactions: fudge = 0.5 67: 67: Generated 330891 of the 330891 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: Number of degrees of freedom in T-Coupling group rest is 1293.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 67: Calculating fourier grid dimensions for X Y Z 67: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 67: 67: Estimate for the relative computational load of the PME mesh part: 0.20 67: 67: This run will generate roughly 0 Mb of data 67: 67: There were 2 NOTEs 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 20 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: 67: Dynamic load balancing report: 67: DLB got disabled because it was unsuitable to use. 67: Average load imbalance: 23.7%. 67: The balanceable part of the MD step is 15%, load imbalance is computed from this. 67: Part of the total run time spent waiting due to load imbalance: 3.6%. 67: 67: 67: NOTE: 17 % of the run time was spent in domain decomposition, 67: 0 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 2.793 0.703 397.3 67: (ns/day) (hour/ns) 67: Performance: 5.161 4.651 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (1278 ms) 67: [----------] 2 tests from BoxDeformationTest (1654 ms total) 67: 67: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 67: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: Setting the LD random seed to -1631617093 67: 67: Generated 2211 of the 2211 non-bonded parameter combinations 67: Generating 1-4 interactions: fudge = 0.5 67: 67: Generated 2211 of the 2211 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 67: 67: turning H bonds into constraints... 67: 67: NOTE 2 [file ala.top, line 256]: 67: For energy conservation with LINCS, lincs_iter should be 2 or larger. 67: 67: 67: Number of degrees of freedom in T-Coupling group rest is 54.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 67: Calculating fourier grid dimensions for X Y Z 67: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 67: 67: Estimate for the relative computational load of the PME mesh part: 0.94 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 67: The optimal PME mesh load for parallel simulations is below 0.5 67: and for highly parallel simulations between 0.25 and 0.33, 67: for higher performance, increase the cut-off and the PME grid spacing. 67: 67: 67: 67: This run will generate roughly 0 Mb of data 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'UNNAMED in water' 67: 4 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: NOTE: 45 % of the run time was spent communicating energies, 67: you might want to increase some nst* mdp options 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.076 0.019 398.1 67: (ns/day) (hour/ns) 67: Performance: 22.700 1.057 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: Setting the LD random seed to -4292681 67: 67: Generated 2211 of the 2211 non-bonded parameter combinations 67: 67: Generated 2211 of the 2211 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 67: 67: turning H bonds into constraints... 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 2 [file ala.top, line 256]: 67: For energy conservation with LINCS, lincs_iter should be 2 or larger. 67: 67: 67: Number of degrees of freedom in T-Coupling group rest is 54.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 67: Calculating fourier grid dimensions for X Y Z 67: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 67: 67: Estimate for the relative computational load of the PME mesh part: 0.94 67: 67: This run will generate roughly 0 Mb of data 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 67: The optimal PME mesh load for parallel simulations is below 0.5 67: and for highly parallel simulations between 0.25 and 0.33, 67: for higher performance, increase the cut-off and the PME grid spacing. 67: 67: 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'UNNAMED in water' 67: 4 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: NOTE: 43 % of the run time was spent in domain decomposition, 67: 0 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSi 67: NOTE: 16 % of the run time was spent communicating energies, 67: you might want to increase some nst* mdp options 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.424 0.106 399.4 67: (ns/day) (hour/ns) 67: Performance: 4.067 5.902 67: ngleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) 67: 67: 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) 67: 67: 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 67: [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (895 ms) 67: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: Setting the LD random seed to 1553986479 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 2 [file ala.top, line 256]: 67: For energy conservation with LINCS, lincs_iter should be 2 or larger. 67: 67: 67: Number of degrees of freedom in T-Coupling group rest is 54.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 67: The optimal PME mesh load for parallel simulations is below 0.5 67: and for highly parallel simulations between 0.25 and 0.33, 67: for higher performance, increase the cut-off and the PME grid spacing. 67: 67: 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: 67: Generated 2211 of the 2211 non-bonded parameter combinations 67: 67: Generated 2211 of the 2211 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 67: 67: turning H bonds into constraints... 67: 67: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 67: Calculating fourier grid dimensions for X Y Z 67: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 67: 67: Estimate for the relative computational load of the PME mesh part: 0.94 67: 67: This run will generate roughly 0 Mb of data 67: Can not increase nstlist because an NVE ensemble is used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'UNNAMED in water' 67: 4 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: NOTE: 18 % of the run time was spent communicating energies, 67: you might want to increase some nst* mdp options 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.215 0.054 398.9 67: (ns/day) (hour/ns) 67: Performance: 8.008 2.997 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: Setting the LD random seed to 2135441086 67: 67: Generated 2211 of the 2211 non-bonded parameter combinations 67: 67: Generated 2211 of the 2211 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 67: 67: turning H bonds into constraints... 67: 67: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 67: Calculating fourier grid dimensions for X Y Z 67: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 67: 67: Estimate for the relative computational load of the PME mesh part: 0.94 67: 67: This run will generate roughly 0 Mb of data 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 2 [file ala.top, line 256]: 67: For energy conservation with LINCS, lincs_iter should be 2 or larger. 67: 67: 67: Number of degrees of freedom in T-Coupling group rest is 54.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 67: The optimal PME mesh load for parallel simulations is below 0.5 67: and for highly parallel simulations between 0.25 and 0.33, 67: for higher performance, increase the cut-off and the PME grid spacing. 67: 67: 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 67: Can not increase nstlist because an NVE ensemble is used 67: 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'UNNAMED in water' 67: 4 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: NOTE: 7 % of the run time was spent communicating energies, 67: you might want to increase some nst* mdp options 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.799 0.200 399.9 67: (ns/day) (hour/ns) 67: Performance: 2.162 11.102 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 67: 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 67: 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 67: [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (358 ms) 67: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (1254 ms total) 67: 67: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 67: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: Setting the LD random seed to -38341890 67: Generating 1-4 interactions: fudge = 0.5 67: Pull group 1 'FirstWaterMolecule' has 3 atoms 67: Pull group 2 'SecondWaterMolecule' has 3 atoms 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: turning H bonds into constraints... 67: Pull group natoms pbc atom distance at start reference at t=0 67: 1 3 2 67: 2 3 5 1.112 nm 1.000 nm 67: 67: There was 1 NOTE 67: 67: This run will generate roughly 0 Mb of data 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 4 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: NOTE: 12 % of the run time was spent in domain decomposition, 67: 5 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 2.360 0.590 399.9 67: (ns/day) (hour/ns) 67: Performance: 0.732 32.785 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: Setting the LD random seed to -698434737 67: Generating 1-4 interactions: fudge = 0.5 67: Pull group 1 'FirstWaterMolecule' has 3 atoms 67: Pull group 2 'SecondWaterMolecule' has 3 atoms 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Pull group natoms pbc atom distance at start reference at t=0 67: 1 3 2 67: 2 3 5 1.112 nm 1.000 nm 67: 67: There was 1 NOTE 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: turning H bonds into constraints... 67: 67: This run will generate roughly 0 Mb of data 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 67: Can not increase nstlist because an NVE ensemble is used 67: 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 4 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: NOTE: 10 % of the run time was spent communicating energies, 67: you might want to increase some nst* mdp options 67: 67: Core t (s) Wall t (s) (%) 67: Time: 2.288 0.572 399.9 67: (ns/day) (hour/ns) 67: Performance: 0.755 31.788 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 67: 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 67: 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (1449 ms) 67: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (1456 ms total) 67: 67: [----------] 12 tests from FreezeWorks/FreezeGroupTest 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: Generating 1-4 interactions: fudge = 0.5 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 25.50 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 67: NVE simulation: will use the initial temperature of 318.937 K for 67: determining the Verlet buffer size 67: 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 5 NOTEs 67: 67: There was 1 WARNING 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: 67: Dynamic load balancing report: 67: DLB was off during the run due to low measured imbalance. 67: Average load imbalance: 5.6%. 67: The balanceable part of the MD step is 47%, load imbalance is computed from this. 67: Part of the total run time spent waiting due to load imbalance: 2.6%. 67: 67: 67: NOTE: 46 % of the run time was spent communicating energies, 67: you might want to increase some nst* mdp options 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.151 0.044 344.4 67: (ns/day) (hour/ns) 67: Performance: 17.723 1.354 67: 67: 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (333 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: Generating 1-4 interactions: fudge = 0.5 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_Freeze 67: GroupTest_WithinTolerances_1_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 25.50 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 67: NVE simulation: will use the initial temperature of 318.937 K for 67: determining the Verlet buffer size 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: This run will generate roughly 0 Mb of data 67: 67: There were 5 NOTEs 67: 67: There was 1 WARNING 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: 67: Dynamic load balancing report: 67: DLB was off during the run due to low measured imbalance. 67: Average load imbalance: 5.2%. 67: The balanceable part of the MD step is 53%, load imbalance is computed from this. 67: Part of the total run time spent waiting due to load imbalance: 2.7%. 67: 67: 67: NOTE: 48 % of the run time was spent communicating energies, 67: you might want to increase some nst* mdp options 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.095 0.024 398.9 67: (ns/day) (hour/ns) 67: Performance: 32.488 0.739 67: 67: 67: 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (50 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: Generating 1-4 interactions: fudge = 0.5 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 25.50 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 67: NVE simulation: will use the initial temperature of 318.937 K for 67: determining the Verlet buffer size 67: 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: This run will generate roughly 0 Mb of data 67: 67: There were 5 NOTEs 67: 67: There was 1 WARNING 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: 67: Dynamic load balancing report: 67: DLB was off during the run due to low measured imbalance. 67: Average load imbalance: 5.1%. 67: The balanceable part of the MD step is 54%, load imbalance is computed from this. 67: Part of the total run time spent waiting due to load imbalance: 2.8%. 67: 67: 67: NOTE: 51 % of the run time was spent communicating energies, 67: you might want to increase some nst* mdp options 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.092 0.023 399.2 67: (ns/day) (hour/ns) 67: Performance: 33.669 0.713 67: 67: 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (48 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: Generating 1-4 interactions: fudge = 0.5 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 25.50 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 67: NVE simulation: will use the initial temperature of 318.937 K for 67: determining the Verlet buffer size 67: 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: This run will generate roughly 0 Mb of data 67: 67: There were 5 NOTEs 67: 67: There was 1 WARNING 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: 67: Dynamic load balancing report: 67: DLB was off during the run due to low measured imbalance. 67: Average load imbalance: 4.2%. 67: The balanceable part of the MD step is 59%, load imbalance is computed from this. 67: Part of the total run time spent waiting due to load imbalance: 2.5%. 67: 67: 67: NOTE: 48 % of the run time was spent communicating energies, 67: you might want to increase some nst* mdp options 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.073 0.018 398.7 67: (ns/day) (hour/ns) 67: Performance: 42.710 0.562 67: 67: 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (38 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 25.50 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 67: NVE simulation: will use the initial temperature of 318.937 K for 67: determining the Verlet buffer size 67: 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 5 NOTEs 67: 67: There was 1 WARNING 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: 67: Dynamic load balancing report: 67: DLB was off during the run due to low measured imbalance. 67: Average load imbalance: 4.1%. 67: The balanceable part of the MD step is 8%, load imbalance is computed from this. 67: Part of the total run time spent waiting due to load imbalance: 0.3%. 67: 67: 67: NOTE: 22 % of the run time was spent in domain decomposition, 67: 0 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: NOTE: 34 % of the run time was spent communicating energies, 67: you might want to increase some nst* mdp options 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.110 0.034 325.6 67: (ns/day) (hour/ns) 67: Performance: 22.929 1.047 67: 67: 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (71 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 67: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: Generating 1-4 interactions: fudge = 0.5 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 25.50 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 67: 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: NOTE: 41 % of the run time was spent communicating energies, 67: you might want to increase some nst* mdp options 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.080 0.031 260.6 67: (ns/day) (hour/ns) 67: Performance: 25.374 0.946 67: 67: 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (51 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: Generating 1-4 interactions: fudge = 0.5 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 25.50 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 67: 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: NOTE: 45 % of the run time was spent communicating energies, 67: you might want to increase some nst* mdp options 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.102 0.031 325.3 67: (ns/day) (hour/ns) 67: Performance: 24.920 0.963 67: 67: 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (59 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: Generating 1-4 interactions: fudge = 0.5 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 25.50 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 67: 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 67: 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: NOTE: 22 % of the run time was spent communicating energies, 67: you might want to increase some nst* mdp options 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.180 0.045 399.3 67: (ns/day) (hour/ns) 67: Performance: 17.232 1.393 67: 67: 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (72 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: Generating 1-4 interactions: fudge = 0.5 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 25.50 67: 67: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 67: 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: NOTE: 33 % of the run time was spent in domain decomposition, 67: 0 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: NOTE: 25 % of the run time was spent communicating energies, 67: you might want to increase some nst* mdp options 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.097 0.028 346.5 67: (ns/day) (hour/ns) 67: Performance: 27.779 0.864 67: 67: 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (132 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: Generating 1-4 interactions: fudge = 0.5 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 25.50 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 67: 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: 67: 67: NOTE: 47 % of the run time was spent communicating energies, 67: you might want to increase some nst* mdp options 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.064 0.016 398.1 67: (ns/day) (hour/ns) 67: Performance: 48.437 0.495 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (118 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 25.50 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 67: 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: NOTE: 49 % of the run time was spent communicating energies, 67: you might want to increase some nst* mdp options 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.240 0.068 352.8 67: (ns/day) (hour/ns) 67: Performance: 11.430 2.100 67: 67: 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (220 ms) 67: [----------] 12 tests from FreezeWorks/FreezeGroupTest (1201 ms total) 67: 67: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 67: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Setting gen_seed to -276858371 67: 67: Velocities were taken from a Maxwell distribution at 0 K 67: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 67: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Net Acceleration in X direction, will not be corrected 67: Net Acceleration in Y direction, will not be corrected 67: Net Acceleration in Z direction, will not be corrected 67: 67: There were 3 NOTEs 67: 67: This run will generate roughly 0 Mb of data 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 8 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: 67: Dynamic load balancing report: 67: DLB was off during the run due to low measured imbalance. 67: Average load imbalance: 6.3%. 67: The balanceable part of the MD step is 36%, load imbalance is computed from this. 67: Part of the total run time spent waiting due to load imbalance: 2.3%. 67: 67: 67: NOTE: 51 % of the run time was spent communicating energies, 67: you might want to increase some nst* mdp options 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.848 0.212 399.9 67: (ns/day) (hour/ns) 67: Performance: 7.337 3.271 67: 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 67: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 67: Net Acceleration in X direction, will not be corrected 67: Net Acceleration in Y direction, will not be corrected 67: Net Acceleration in Z direction, will not be corrected 67: 67: There were 3 NOTEs 67: 67: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (352 ms) 67: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Setting gen_seed to 1391947387 67: 67: Velocities were taken from a Maxwell distribution at 0 K 67: 67: This run will generate roughly 0 Mb of data 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because verlet-buffer-tolerance is not set or used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 8 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: 67: Dynamic load balancing report: 67: DLB was off during the run due to low measured imbalance. 67: Average load imbalance: 19.7%. 67: The balanceable part of the MD step is 38%, load imbalance is computed from this. 67: Part of the total run time spent waiting due to load imbalance: 7.4%. 67: 67: NOTE: 7.4 % of the available CPU time was lost due to load imbalance 67: in the domain decomposition. 67: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 67: You can also consider manually changing the decomposition (option -dd); 67: e.g. by using fewer domains along the box dimension in which there is 67: considerable inhomogeneity in the simulated system. 67: 67: NOTE: 22 % of the run time was spent in domain decomposition, 67: 7 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: NOTE: 6 % of the run time was spent communicating energies, 67: you might want to increase some nst* mdp options 67: 67: Core t (s) Wall t (s) (%) 67: Time: 1.456 0.372 391.4 67: (ns/day) (hour/ns) 67: Performance: 4.181 5.740 67: 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: 67: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (444 ms) 67: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 67: Generated 3 of the 3 non-bonded parameter combinations 67: Generating 1-4 interactions: fudge = 0.5 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Setting gen_seed to -193072643 67: 67: Velocities were taken from a Maxwell distribution at 0 K 67: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 67: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Net Acceleration in X direction, will not be corrected 67: Net Acceleration in Y direction, will not be corrected 67: Net Acceleration in Z direction, will not be corrected 67: 67: There were 3 NOTEs 67: 67: This run will generate roughly 0 Mb of data 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 8 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: 67: Dynamic load balancing report: 67: DLB was off during the run due to low measured imbalance. 67: Average load imbalance: 0.2%. 67: The balanceable part of the MD step is 52%, load imbalance is computed from this. 67: Part of the total run time spent waiting due to load imbalance: 0.1%. 67: 67: 67: NOTE: 48 % of the run time was spent communicating energies, 67: you might want to increase some nst* mdp options 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.057 0.014 398.9 67: (ns/day) (hour/ns) 67: Performance: 109.428 0.219 67: 67: 67: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (24 ms) 67: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 67: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 67: Net Acceleration in X direction, will not be corrected 67: Net Acceleration in Y direction, will not be corrected 67: Net Acceleration in Z direction, will not be corrected 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because verlet-buffer-tolerance is not set or used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Setting gen_seed to -134250761 67: 67: Velocities were taken from a Maxwell distribution at 0 K 67: 67: This run will generate roughly 0 Mb of data 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 8 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: 67: Dynamic load balancing report: 67: DLB was off during the run due to low measured imbalance. 67: Average load imbalance: 18.2%. 67: The balanceable part of the MD step is 38%, load imbalance is computed from this. 67: Part of the total run time spent waiting due to load imbalance: 7.0%. 67: 67: NOTE: 7.0 % of the available CPU time was lost due to load imbalance 67: in the domain decomposition. 67: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 67: You can also consider manually changing the decomposition (option -dd); 67: e.g. by using fewer domains along the box dimension in which there is 67: considerable inhomogeneity in the simulated system. 67: 67: NOTE: 14 % of the run time was spent in domain decomposition, 67: 2 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: NOTE: 16 % of the run time was spent communicating energies, 67: you might want to increase some nst* mdp options 67: 67: Core t (s) Wall t (s) (%) 67: Time: 2.050 0.512 400.0 67: (ns/day) (hour/ns) 67: Performance: 3.035 7.908 67: 67: 67: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (640 ms) 67: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (1465 ms total) 67: 67: [----------] Global test environment tear-down 67: [==========] 28 tests from 7 test suites ran. (10383 ms total) 67: [ PASSED ] 27 tests. 67: [ SKIPPED ] 1 test, listed below: 67: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 67/91 Test #67: MdrunTestsTwoRanks ........................... Passed 10.87 sec test 68 Start 68: MdrunSingleRankAlgorithmsTests 68: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-single-rank-algorithms-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunSingleRankAlgorithmsTests.xml" 68: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 68: Test timeout computed to be: 600 68: [==========] Running 5 tests from 3 test suites. 68: [----------] Global test environment set-up. 68: [----------] 1 test from DispersionCorrectionTest 68: [ RUN ] DispersionCorrectionTest.DispersionCorrectionCanRun 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 30.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 NOTEs 68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 68: Changing nstlist from 10 to 40, rlist from 1.023 to 1.158 68: 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 200 steps, 0.4 ps. 68: Setting the LD random seed to -2757890 68: 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning H bonds into constraints... 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Converted 3 Bonds with virtual sites to connections, 7 left 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 12 Constraints with virtual sites to connections, 0 left 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.038 nm, buffer size 0.038 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.023 nm, buffer size 0.023 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.087 0.044 199.8 68: (ns/day) (hour/ns) 68: Performance: 798.036 0.030 68: [ OK ] DispersionCorrectionTest.DispersionCorrectionCanRun (310 ms) 68: [----------] 1 test from DispersionCorrectionTest (310 ms total) 68: 68: [----------] 1 test from OriresTest 68: [ RUN ] OriresTest.OriresCanRun 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 518.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 68: Changing nstlist from 10 to 25, rlist from 1.07 to 1.203 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1' 68: 10 steps, 0.0 ps. 68: Setting the LD random seed to 1870353886 68: 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.070 nm, buffer size 0.070 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.031 0.016 199.5 68: (ns/day) (hour/ns) 68: Performance: 121.592 0.197 68: [ OK ] OriresTest.OriresCanRun (332 ms) 68: [----------] 1 test from OriresTest (332 ms total) 68: 68: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest 68: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 68: Number of degrees of freedom in T-Coupling group rest is 10.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 68: NVE simulation with an initial temperature of zero: will use a Verlet 68: buffer of 10%. Check your energy drift! 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 68: The optimal PME mesh load for parallel simulations is below 0.5 68: and for highly parallel simulations between 0.25 and 0.33, 68: for higher performance, increase the cut-off and the PME grid spacing. 68: 68: 68: 68: There were 2 NOTEs 68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Dipoles' 68: 20 steps, 0.1 ps. 68: Setting the LD random seed to 251059540 68: 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Dipole' 68: 68: Searching the wall atom type(s) 68: 68: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 68: Calculating fourier grid dimensions for X Y Z 68: Using a fourier grid of 20x20x40, spacing 0.200 0.200 0.200 68: 68: Estimate for the relative computational load of the PME mesh part: 1.00 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 1.462 0.731 200.0 68: (ns/day) (hour/ns) 68: Performance: 6.205 3.868 68: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 trr version: GMX_trn_file (single precision) 68: 68: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 (2003 ms) 68: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 68: Test system 'epsilon-surface-constraint' cannot run with 1 ranks. 68: The supported numbers are > 1. 68: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 (0 ms) 68: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 68: With epsilon_surface > 0 all molecules should be neutral. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 68: With epsilon_surface > 0 you can only use domain decomposition when there 68: are only small molecules with all bonds constrained (mdrun will check for 68: this). 68: 68: Number of degrees of freedom in T-Coupling group rest is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 68: NVE simulation with an initial temperature of zero: will use a Verlet 68: buffer of 10%. Check your energy drift! 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 68: The optimal PME mesh load for parallel simulations is below 0.5 68: and for highly parallel simulations between 0.25 and 0.33, 68: for higher performance, increase the cut-off and the PME grid spacing. 68: 68: 68: 68: There were 4 NOTEs 68: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Dipoles' 68: 20 steps, 0.1 ps. 68: Setting the LD random seed to -92619778 68: 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Dipole' 68: 68: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 68: Calculating fourier grid dimensions for X Y Z 68: Using a fourier grid of 20x20x20, spacing 0.200 0.200 0.200 68: 68: Estimate for the relative computational load of the PME mesh part: 1.00 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 24 % of the run time was spent in domain decomposition, 68: 0 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.105 0.053 199.7 68: (ns/day) (hour/ns) 68: Performance: 86.088 0.279 68: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 68: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 (677 ms) 68: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest (2681 ms total) 68: 68: [----------] Global test environment tear-down 68: [==========] 5 tests from 3 test suites ran. (3422 ms total) 68: [ PASSED ] 5 tests. 68/91 Test #68: MdrunSingleRankAlgorithmsTests ............... Passed 3.77 sec test 69 Start 69: Minimize1RankTests 69: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/minimize-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/Minimize1RankTests.xml" 69: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 69: Test timeout computed to be: 600 69: [==========] Running 12 tests from 2 test suites. 69: [----------] Global test environment set-up. 69: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 69: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 69: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 69: setting nstcomm equal to nstcalcenergy for less overhead 69: 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 0.5 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: This run will generate roughly 0 Mb of data 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 69: COM removal frequency is set to (4). 69: Other settings require a global communication frequency of 100. 69: Note that this will require additional global communication steps, 69: which will reduce performance when using multiple ranks. 69: Consider setting nstcomm to a multiple of 100. 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: Steepest Descents: 69: Tolerance (Fmax) = 1.00000e+01 69: Number of steps = 4 69: 69: Energy minimization reached the maximum number of steps before the forces 69: reached the requested precision Fmax < 10. 69: 69: writing lowest energy coordinates. 69: 69: Steepest Descents did not converge to Fmax < 10 in 5 steps. 69: Potential Energy = -4.7991035e+01 69: Maximum force = 1.8629774e+02 on atom 13 69: Norm of force = 8.7722025e+01 69: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (496 ms) 69: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 69: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 69: setting nstcomm equal to nstcalcenergy for less overhead 69: 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 0.5 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 69: COM removal frequency is set to (4). 69: Other settings require a global communication frequency of 100. 69: Note that this will require additional global communication steps, 69: which will reduce performance when using multiple ranks. 69: Consider setting nstcomm to a multiple of 100. 69: 69: 69: There were 4 NOTEs 69: 69: This run will generate roughly 0 Mb of data 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: Polak-Ribiere Conjugate Gradients: 69: Tolerance (Fmax) = 1.00000e+01 69: Number of steps = 4 69: F-max = 3.02331e+02 on atom 3 69: F-Norm = 1.18024e+02 69: 69: 69: Energy minimization reached the maximum number of steps before the forces 69: reached the requested precision Fmax < 10. 69: 69: writing lowest energy coordinates. 69: 69: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 69: Potential Energy = -5.5862438e+01 69: Maximum force = 4.2726288e+02 on atom 13 69: Norm of force = 1.8452569e+02 69: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (405 ms) 69: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 69: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 69: setting nstcomm equal to nstcalcenergy for less overhead 69: 69: Generated 20503 of the 20503 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 1 69: 69: Generated 17396 of the 20503 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Glycine' 69: 69: turning H bonds into constraints... 69: Number of degrees of freedom in T-Coupling group System is 22.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: This run will generate roughly 0 Mb of data 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 69: COM removal frequency is set to (4). 69: Other settings require a global communication frequency of 100. 69: Note that this will require additional global communication steps, 69: which will reduce performance when using multiple ranks. 69: Consider setting nstcomm to a multiple of 100. 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: Steepest Descents: 69: Tolerance (Fmax) = 1.00000e+01 69: Number of steps = 4 69: 69: Energy minimization reached the maximum number of steps before the forces 69: reached the requested precision Fmax < 10. 69: 69: writing lowest energy coordinates. 69: 69: Steepest Descents did not converge to Fmax < 10 in 5 steps. 69: Potential Energy = 3.1937726e+02 69: Maximum force = 9.9988652e+03 on atom 9 69: Norm of force = 4.6166996e+03 69: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (78 ms) 69: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 69: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 69: setting nstcomm equal to nstcalcenergy for less overhead 69: 69: Generated 20503 of the 20503 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 1 69: 69: Generated 17396 of the 20503 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Glycine' 69: 69: turning H bonds into constraints... 69: 69: NOTE 3 [file glycine_vacuo.top, line 12]: 69: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 69: 69: Number of degrees of freedom in T-Coupling group System is 22.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: This run will generate roughly 0 Mb of data 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 69: COM removal frequency is set to (4). 69: Other settings require a global communication frequency of 100. 69: Note that this will require additional global communication steps, 69: which will reduce performance when using multiple ranks. 69: Consider setting nstcomm to a multiple of 100. 69: 69: 69: There were 5 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: Polak-Ribiere Conjugate Gradients: 69: Tolerance (Fmax) = 1.00000e+01 69: Number of steps = 4 69: F-max = 2.41575e+04 on atom 10 69: F-Norm = 1.18451e+04 69: 69: 69: Energy minimization reached the maximum number of steps before the forces 69: reached the requested precision Fmax < 10. 69: 69: writing lowest energy coordinates. 69: 69: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 69: Potential Energy = 1.5174292e+02 69: Maximum force = 7.4208784e+03 on atom 9 69: Norm of force = 3.5692952e+03 69: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (62 ms) 69: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 69: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 69: setting nstcomm equal to nstcalcenergy for less overhead 69: 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: turning all bonds into constraints... 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Converted 15 Constraints with virtual sites to connections, 7 left 69: 69: This run will generate roughly 0 Mb of data 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file unknown]: 69: You are using constraints on all bonds, whereas the forcefield has been 69: parametrized only with constraints involving hydrogen atoms. We suggest 69: using constraints = h-bonds instead, this will also improve performance. 69: 69: Number of degrees of freedom in T-Coupling group System is 23.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 69: COM removal frequency is set to (4). 69: Other settings require a global communication frequency of 100. 69: Note that this will require additional global communication steps, 69: which will reduce performance when using multiple ranks. 69: Consider setting nstcomm to a multiple of 100. 69: 69: 69: There were 5 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: Steepest Descents: 69: Tolerance (Fmax) = 1.00000e+01 69: Number of steps = 4 69: 69: Energy minimization reached the maximum number of steps before the forces 69: reached the requested precision Fmax < 10. 69: 69: writing lowest energy coordinates. 69: 69: Steepest Descents did not converge to Fmax < 10 in 5 steps. 69: Potential Energy = -1.5698425e+02 69: Maximum force = 4.5703290e+02 on atom 17 69: Norm of force = 1.8327769e+02 69: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (8 ms) 69: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 69: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 69: setting nstcomm equal to nstcalcenergy for less overhead 69: 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 0.5 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: turning all bonds into constraints... 69: 69: NOTE 3 [file unknown]: 69: You are using constraints on all bonds, whereas the forcefield has been 69: parametrized only with constraints involving hydrogen atoms. We suggest 69: using constraints = h-bonds instead, this will also improve performance. 69: 69: 69: NOTE 4 [file unknown]: 69: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 69: 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Converted 15 Constraints with virtual sites to connections, 7 left 69: Number of degrees of freedom in T-Coupling group System is 23.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: This run will generate roughly 0 Mb of data 69: 69: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 69: COM removal frequency is set to (4). 69: Other settings require a global communication frequency of 100. 69: Note that this will require additional global communication steps, 69: which will reduce performance when using multiple ranks. 69: Consider setting nstcomm to a multiple of 100. 69: 69: 69: There were 6 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: Polak-Ribiere Conjugate Gradients: 69: Tolerance (Fmax) = 1.00000e+01 69: Number of steps = 4 69: F-max = 1.06801e+03 on atom 28 69: F-Norm = 4.26916e+02 69: 69: 69: Energy minimization reached the maximum number of steps before the forces 69: reached the requested precision Fmax < 10. 69: 69: writing lowest energy coordinates. 69: 69: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 69: Potential Energy = -1.6941193e+02 69: Maximum force = 2.1831454e+02 on atom 17 69: Norm of force = 7.9220636e+01 69: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (8 ms) 69: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (1073 ms total) 69: 69: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 69: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 69: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 69: setting nstcomm equal to nstcalcenergy for less overhead 69: 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Argon' 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 69: COM removal frequency is set to (4). 69: Other settings require a global communication frequency of 100. 69: Note that this will require additional global communication steps, 69: which will reduce performance when using multiple ranks. 69: Consider setting nstcomm to a multiple of 100. 69: 69: 69: There were 3 NOTEs 69: 69: This run will generate roughly 0 Mb of data 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: Steepest Descents: 69: Tolerance (Fmax) = 1.00000e+01 69: Number of steps = 4 69: 69: writing lowest energy coordinates. 69: 69: Steepest Descents converged to Fmax < 10 in 1 steps 69: Potential Energy = -9.7425687e-01 69: Maximum force = 4.0132279e+00 on atom 1 69: Norm of force = 1.6383933e+00 69: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 69: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 69: setting nstcomm equal to nstcalcenergy for less overhead 69: 69: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (28 ms) 69: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Argon' 69: 69: This run will generate roughly 0 Mb of data 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 69: COM removal frequency is set to (4). 69: Other settings require a global communication frequency of 100. 69: Note that this will require additional global communication steps, 69: which will reduce performance when using multiple ranks. 69: Consider setting nstcomm to a multiple of 100. 69: 69: 69: There were 3 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: Polak-Ribiere Conjugate Gradients: 69: Tolerance (Fmax) = 1.00000e+01 69: Number of steps = 4 69: F-max = 4.01323e+00 on atom 1 69: F-Norm = 1.63839e+00 69: 69: 69: writing lowest energy coordinates. 69: 69: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 69: Potential Energy = -9.9064195e-01 69: Maximum force = 2.5781672e+00 on atom 1 69: Norm of force = 1.0525324e+00 69: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 69: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 69: setting nstcomm equal to nstcalcenergy for less overhead 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 69: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 69: 69: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (8 ms) 69: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Argon' 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 69: COM removal frequency is set to (4). 69: Other settings require a global communication frequency of 100. 69: Note that this will require additional global communication steps, 69: which will reduce performance when using multiple ranks. 69: Consider setting nstcomm to a multiple of 100. 69: 69: 69: There were 3 NOTEs 69: 69: There was 1 WARNING 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: 69: This run will generate roughly 0 Mb of data 69: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: Low-Memory BFGS Minimizer: 69: Tolerance (Fmax) = 1.00000e+01 69: Number of steps = 4 69: Using 10 BFGS correction steps. 69: 69: F-max = 4.01323e+00 on atom 1 69: F-Norm = 1.63839e+00 69: 69: 69: writing lowest energy coordinates. 69: 69: Low-Memory BFGS Minimizer converged to Fmax < 10 in -1 steps 69: Potential Energy = -9.9064195e-01 69: Maximum force = 2.5781672e+00 on atom 1 69: Norm of force = 1.0525324e+00 69: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (7 ms) 69: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 69: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 69: setting nstcomm equal to nstcalcenergy for less overhead 69: 69: Generated 20503 of the 20503 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 1 69: 69: Generated 17396 of the 20503 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Glycine' 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: This run will generate roughly 0 Mb of data 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 69: COM removal frequency is set to (4). 69: Other settings require a global communication frequency of 100. 69: Note that this will require additional global communication steps, 69: which will reduce performance when using multiple ranks. 69: Consider setting nstcomm to a multiple of 100. 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: Steepest Descents: 69: Tolerance (Fmax) = 1.00000e+01 69: Number of steps = 4 69: 69: Energy minimization reached the maximum number of steps before the forces 69: reached the requested precision Fmax < 10. 69: 69: writing lowest energy coordinates. 69: 69: Steepest Descents did not converge to Fmax < 10 in 5 steps. 69: Potential Energy = 3.1939697e+02 69: Maximum force = 9.9704248e+03 on atom 9 69: Norm of force = 4.6227540e+03 69: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (87 ms) 69: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 69: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 69: setting nstcomm equal to nstcalcenergy for less overhead 69: 69: Generated 20503 of the 20503 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 1 69: 69: Generated 17396 of the 20503 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Glycine' 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 69: COM removal frequency is set to (4). 69: Other settings require a global communication frequency of 100. 69: Note that this will require additional global communication steps, 69: which will reduce performance when using multiple ranks. 69: Consider setting nstcomm to a multiple of 100. 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: 69: This run will generate roughly 0 Mb of data 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: Polak-Ribiere Conjugate Gradients: 69: Tolerance (Fmax) = 1.00000e+01 69: Number of steps = 4 69: F-max = 2.41672e+04 on atom 10 69: F-Norm = 1.19357e+04 69: 69: 69: Energy minimization reached the maximum number of steps before the forces 69: reached the requested precision Fmax < 10. 69: 69: writing lowest energy coordinates. 69: 69: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 69: Potential Energy = 1.5625757e+02 69: Maximum force = 7.5018242e+03 on atom 9 69: Norm of force = 3.6139019e+03 69: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 69: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 69: setting nstcomm equal to nstcalcenergy for less overhead 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 69: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 69: 69: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (89 ms) 69: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 69: Generated 20503 of the 20503 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 1 69: 69: Generated 17396 of the 20503 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Glycine' 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: This run will generate roughly 0 Mb of data 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 69: COM removal frequency is set to (4). 69: Other settings require a global communication frequency of 100. 69: Note that this will require additional global communication steps, 69: which will reduce performance when using multiple ranks. 69: Consider setting nstcomm to a multiple of 100. 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: Low-Memory BFGS Minimizer: 69: Tolerance (Fmax) = 1.00000e+01 69: Number of steps = 4 69: Using 10 BFGS correction steps. 69: 69: F-max = 2.41672e+04 on atom 10 69: F-Norm = 1.19357e+04 69: 69: 69: Energy minimization has stopped, but the forces have not converged to the 69: requested precision Fmax < 10 (which may not be possible for your system). It 69: stopped because the algorithm tried to make a new step whose size was too 69: small, or there was no change in the energy since last step. Either way, we 69: regard the minimization as converged to within the available machine 69: precision, given your starting configuration and EM parameters. 69: 69: Double precision normally gives you higher accuracy, but this is often not 69: needed for preparing to run molecular dynamics. 69: 69: writing lowest energy coordinates. 69: 69: Low-Memory BFGS Minimizer converged to machine precision in 0 steps, 69: but did not reach the requested Fmax < 10. 69: Potential Energy = 5.6111725e+02 69: Maximum force = 1.2685491e+04 on atom 10 69: Norm of force = 6.0643622e+03 69: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (75 ms) 69: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (297 ms total) 69: 69: [----------] Global test environment tear-down 69: [==========] 12 tests from 2 test suites ran. (1451 ms total) 69: [ PASSED ] 12 tests. 69/91 Test #69: Minimize1RankTests ........................... Passed 1.95 sec test 70 Start 70: Minimize2RankTests 70: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/minimize-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/Minimize2RankTests.xml" 70: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 70: Test timeout computed to be: 600 70: [==========] Running 12 tests from 2 test suites. 70: [----------] Global test environment set-up. 70: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 70: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generated 330891 of the 330891 non-bonded parameter combinations 70: Generating 1-4 interactions: fudge = 0.5 70: 70: Generated 330891 of the 330891 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: Number of degrees of freedom in T-Coupling group System is 27.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: This run will generate roughly 0 Mb of data 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 4 NOTEs 70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Steepest Descents: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Steepest Descents did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = -4.7991009e+01 70: Maximum force = 1.8629736e+02 on atom 13 70: Norm of force = 8.7722017e+01 70: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (532 ms) 70: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generated 330891 of the 330891 non-bonded parameter combinations 70: Generating 1-4 interactions: fudge = 0.5 70: 70: Generated 330891 of the 330891 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: Number of degrees of freedom in T-Coupling group System is 27.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: This run will generate roughly 0 Mb of data 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 4 NOTEs 70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Polak-Ribiere Conjugate Gradients: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: F-max = 3.02331e+02 on atom 3 70: F-Norm = 1.18024e+02 70: 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = -5.5862362e+01 70: Maximum force = 4.2726562e+02 on atom 13 70: Norm of force = 1.8452687e+02 70: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraint[ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (343 ms) 70: s_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generated 20503 of the 20503 non-bonded parameter combinations 70: Generating 1-4 interactions: fudge = 1 70: 70: Generated 17396 of the 20503 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Glycine' 70: 70: turning H bonds into constraints... 70: Number of degrees of freedom in T-Coupling group System is 22.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce arti 70: facts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 4 NOTEs 70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 70: This run will generate roughly 0 Mb of data 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Steepest Descents: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Steepest Descents did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = 3.1937708e+02 70: Maximum force = 9.9988643e+03 on atom 9 70: Norm of force = 4.6166993e+03 70: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 70: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (78 ms) 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generated 20503 of the 20503 non-bonded parameter combinations 70: Generating 1-4 interactions: fudge = 1 70: 70: Generated 17396 of the 20503 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Glycine' 70: 70: turning H bonds into constraints... 70: 70: NOTE 3 [file glycine_vacuo.top, line 12]: 70: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 70: 70: Number of degrees of freedom in T-Coupling group System is 22.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: This run will generate roughly 0 Mb of data 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 5 NOTEs 70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Polak-Ribiere Conjugate Gradients: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: F-max = 2.41575e+04 on atom 10 70: F-Norm = 1.18451e+04 70: 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = 1.5174438e+02 70: Maximum force = 7.4208867e+03 on atom 9 70: Norm of force = 3.5692995e+03 70: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (79 ms) 70: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: Generating 1-4 interactions: fudge = 0.5 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: turning all bonds into constraints... 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Converted 15 Constraints with virtual sites to connections, 7 left 70: 70: This run will generate roughly 0 Mb of data 70: 70: NOTE 3 [file unknown]: 70: You are using constraints on all bonds, whereas the forcefield has been 70: parametrized only with constraints involving hydrogen atoms. We suggest 70: using constraints = h-bonds instead, this will also improve performance. 70: 70: Number of degrees of freedom in T-Coupling group System is 23.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 5 NOTEs 70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 70: Update groups can not be used for this system because an incompatible virtual site type is used 70: 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Steepest Descents: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Steepest Descents did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = -1.5698413e+02 70: Maximum force = 4.5703293e+02 on atom 17 70: Norm of force = 1.8327771e+02 70: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 70: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (21 ms) 70: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: Generating 1-4 interactions: fudge = 0.5 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: turning all bonds into constraints... 70: 70: NOTE 3 [file unknown]: 70: You are using constraints on all bonds, whereas the forcefield has been 70: parametrized only with constraints involving hydrogen atoms. We suggest 70: using constraints = h-bonds instead, this will also improve performance. 70: 70: 70: NOTE 4 [file unknown]: 70: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 70: 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Converted 15 Constraints with virtual sites to connections, 7 left 70: Number of degrees of freedom in T-Coupling group System is 23.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: This run will generate roughly 0 Mb of data 70: 70: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 6 NOTEs 70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 70: Update groups can not be used for this system because an incompatible virtual site type is used 70: 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Polak-Ribiere Conjugate Gradients: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: F-max = 1.06801e+03 on atom 28 70: F-Norm = 4.26916e+02 70: 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = -1.6941205e+02 70: Maximum force = 2.1833974e+02 on atom 17 70: Norm of force = 7.9218953e+01 70: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (45 ms) 70: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (1111 ms total) 70: 70: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 70: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: This run will generate roughly 0 Mb of data 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 3 NOTEs 70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Steepest Descents: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: 70: writing lowest energy coordinates. 70: 70: Steepest Descents converged to Fmax < 10 in 1 steps 70: Potential Energy = -9.7425687e-01 70: Maximum force = 4.0132279e+00 on atom 3 70: Norm of force = 1.6383933e+00 70: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 70: Reading energy frame 0 time 0.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (32 ms) 70: Last energy frame read 0 time 0.000 [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: This run will generate roughly 0 Mb of data 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 3 NOTEs 70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Polak-Ribiere Conjugate Gradients: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (11 ms) 70: F-max = 4.01323e+00 on atom 3 70: F-Norm = 1.63839e+00 70: 70: 70: writing lowest energy coordinates. 70: 70: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 70: Potential Energy = -9.9064195e-01 70: Maximum force = 2.5781672e+00 on atom 3 70: Norm of force = 1.0525324e+00 70: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 70: 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: This run will generate roughly 0 Mb of data 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: COM removal frequency is set to (4). 70: cation frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 3 NOTEs 70: 70: There was 1 WARNING 70: Other settings require a global communi[ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (4 ms) 70: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generated 20503 of the 20503 non-bonded parameter combinations 70: Generating 1-4 interactions: fudge = 1 70: 70: Generated 17396 of the 20503 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Glycine' 70: Number of degrees of freedom in T-Coupling group System is 27.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You mi 70: ght want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 4 NOTEs 70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 70: This run will generate roughly 0 Mb of data 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Steepest Descents: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Steepest Descents did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = 3.1939685e+02 70: Maximum force = 9.9704248e+03 on atom 9 70: Norm of force = 4.6227568e+03 70: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 70: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (98 ms) 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generated 20503 of the 20503 non-bonded parameter combinations 70: Generating 1-4 interactions: fudge = 1 70: 70: Generated 17396 of the 20503 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Glycine' 70: Number of degrees of freedom in T-Coupling group System is 27.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: This run will generate roughly 0 Mb of data 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 4 NOTEs 70: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Polak-Ribiere Conjugate Gradients: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: F-max = 2.41672e+04 on atom 10 70: F-Norm = 1.19357e+04 70: 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = 1.5625764e+02 70: Maximum force = 7.5018237e+03 on atom 9 70: Norm of force = 3.6139019e+03 70: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 70: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (84 ms) 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 70: 70: Generated 20503 of the 20503 non-bonded parameter combinations 70: Generating 1-4 interactions: fudge = 1 70: 70: Generated 17396 of the 20503 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Glycine' 70: Number of degrees of freedom in T-Coupling group System is 27.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: This run will generate roughly 0 Mb of data 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (39 ms) 70: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (274 ms total) 70: 70: [----------] Global test environment tear-down 70: [==========] 12 tests from 2 test suites ran. (1478 ms total) 70: [ PASSED ] 12 tests. 70/91 Test #70: Minimize2RankTests ........................... Passed 1.93 sec test 71 Start 71: MdrunNonIntegratorTests 71: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunNonIntegratorTests.xml" 71: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 71: Test timeout computed to be: 600 71: [==========] Running 46 tests from 3 test suites. 71: [----------] Global test environment set-up. 71: [----------] 1 test from NonbondedBenchTest 71: [ RUN ] NonbondedBenchTest.BasicEndToEndTest 71: SIMD width: 4 71: System size: 3000 atoms 71: Cut-off radius: 1 nm 71: Number of threads: 1 71: Number of iterations: 1 71: Compute energies: no 71: Ewald excl. corr.: analytical 71: 71: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle 71: total useful 71: Ewald all geom. 4xM 8.597 8.5969 0.1385 0.0733 71: [ OK ] NonbondedBenchTest.BasicEndToEndTest (17 ms) 71: [----------] 1 test from NonbondedBenchTest (17 ms total) 71: 71: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest 71: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Number of degrees of freedom in T-Coupling group System is 33.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 71: NVE simulation: will use the initial temperature of 68.810 K for 71: determining the Verlet buffer size 71: 71: 71: There were 3 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Argon' 71: 16 steps, 0.0 ps. 71: Generated 1 of the 1 non-bonded parameter combinations 71: 71: Excluding 1 bonded neighbours molecule type 'Argon' 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.040 0.020 199.6 71: (ns/day) (hour/ns) 71: Performance: 73.579 0.326 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr' 71: 71: trr version: GMX_trn_file (single precision) 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 24 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.001 0.000 191.6 71: (ns/day) (hour/ns) 71: Performance: 4176.674 0.006 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (51 ms) 71: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Number of degrees of freedom in T-Coupling group System is 33.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 71: NVE simulation: will use the initial temperature of 68.810 K for 71: determining the Verlet buffer size 71: 71: 71: There were 3 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Argon' 71: 16 steps, 0.0 ps. 71: Generated 1 of the 1 non-bonded parameter combinations 71: 71: Excluding 1 bonded neighbours molecule type 'Argon' 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.066 0.033 199.8 71: (ns/day) (hour/ns) 71: Performance: 44.143 0.544 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 22 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.001 0.000 191.4 71: (ns/day) (hour/ns) 71: Performance: 4093.418 0.006 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (44 ms) 71: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Number of degrees of freedom in T-Coupling group System is 33.00 71: 71: There were 2 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 100, rlist from 0.712 to 0.744 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Argon' 71: 16 steps, 0.0 ps. 71: Generated 1 of the 1 non-bonded parameter combinations 71: 71: Excluding 1 bonded neighbours molecule type 'Argon' 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.033 0.017 199.4 71: (ns/day) (hour/ns) 71: Performance: 88.620 0.271 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 100, rlist from 0.712 to 0.744 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 21 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.001 0.000 193.7 71: (ns/day) (hour/ns) 71: Performance: 3064.972 0.008 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (27 ms) 71: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Number of degrees of freedom in T-Coupling group System is 33.00 71: 71: There were 2 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Argon' 71: 16 steps, 0.0 ps. 71: Generated 1 of the 1 non-bonded parameter combinations 71: 71: Excluding 1 bonded neighbours molecule type 'Argon' 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.036 0.018 199.6 71: (ns/day) (hour/ns) 71: Performance: 80.895 0.297 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 23 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.001 0.000 192.9 71: (ns/day) (hour/ns) 71: Performance: 4199.450 0.006 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (31 ms) 71: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 27.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 71: NVE simulation: will use the initial temperature of 398.997 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc2' 71: 16 steps, 0.0 ps. 71: Generated 330891 of the 330891 non-bonded parameter combinations 71: 71: Generated 330891 of the 330891 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.040 0.020 199.7 71: (ns/day) (hour/ns) 71: Performance: 74.148 0.324 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 24 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.001 0.000 191.8 71: (ns/day) (hour/ns) 71: Performance: 4493.504 0.005 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (275 ms) 71: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 27.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 71: NVE simulation: will use the initial temperature of 398.997 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc2' 71: 16 steps, 0.0 ps. 71: Generated 330891 of the 330891 non-bonded parameter combinations 71: 71: Generated 330891 of the 330891 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.082 0.041 199.7 71: (ns/day) (hour/ns) 71: Performance: 35.836 0.670 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 13 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.001 0.001 195.3 71: (ns/day) (hour/ns) 71: Performance: 2539.404 0.009 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (316 ms) 71: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 27.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 100, rlist from 0.735 to 0.831 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc2' 71: 16 steps, 0.0 ps. 71: Generated 330891 of the 330891 non-bonded parameter combinations 71: 71: Generated 330891 of the 330891 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.738 nm, buffer size 0.038 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.063 0.031 199.6 71: (ns/day) (hour/ns) 71: Performance: 46.740 0.513 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 100, rlist from 0.735 to 0.831 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 30 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.001 0.000 192.9 71: (ns/day) (hour/ns) 71: Performance: 4179.507 0.006 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (264 ms) 71: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 27.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc2' 71: 16 steps, 0.0 ps. 71: Generated 330891 of the 330891 non-bonded parameter combinations 71: 71: Generated 330891 of the 330891 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.069 0.035 199.6 71: (ns/day) (hour/ns) 71: Performance: 42.506 0.565 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 16 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.001 0.000 191.6 71: (ns/day) (hour/ns) 71: Performance: 4290.107 0.006 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (282 ms) 71: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: 71: NOTE 3 [file unknown]: 71: You are using constraints on all bonds, whereas the forcefield has been 71: parametrized only with constraints involving hydrogen atoms. We suggest 71: using constraints = h-bonds instead, this will also improve performance. 71: 71: Number of degrees of freedom in T-Coupling group System is 23.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 71: NVE simulation: will use the initial temperature of 456.887 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 71: There are 9 non-linear virtual site constructions. Their contribution to 71: the energy error is approximated. In most cases this does not affect the 71: error significantly. 71: 71: 71: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 6 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Update groups can not be used for this system because an incompatible virtual site type is used 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Alanine dipeptide in vacuo' 71: 16 steps, 0.0 ps. 71: Generated 2145 of the 2145 non-bonded parameter combinations 71: 71: Generated 2145 of the 2145 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 71: 71: turning all bonds into constraints... 71: 71: Cleaning up constraints and constant bonded interactions with virtual sites 71: 71: Removed 18 Angles with virtual sites, 21 left 71: 71: Removed 10 Proper Dih.s with virtual sites, 44 left 71: 71: Converted 15 Constraints with virtual sites to connections, 7 left 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.115 0.058 199.8 71: (ns/day) (hour/ns) 71: Performance: 25.440 0.943 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Update groups can not be used for this system because an incompatible virtual site type is used 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 12 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.002 0.001 194.7 71: (ns/day) (hour/ns) 71: Performance: 1723.725 0.014 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (78 ms) 71: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: 71: NOTE 3 [file unknown]: 71: You are using constraints on all bonds, whereas the forcefield has been 71: parametrized only with constraints involving hydrogen atoms. We suggest 71: using constraints = h-bonds instead, this will also improve performance. 71: 71: Number of degrees of freedom in T-Coupling group System is 23.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 71: NVE simulation: will use the initial temperature of 456.887 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 71: There are 9 non-linear virtual site constructions. Their contribution to 71: the energy error is approximated. In most cases this does not affect the 71: error significantly. 71: 71: 71: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 6 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Update groups can not be used for this system because an incompatible virtual site type is used 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Alanine dipeptide in vacuo' 71: 16 steps, 0.0 ps. 71: Generated 2145 of the 2145 non-bonded parameter combinations 71: 71: Generated 2145 of the 2145 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 71: 71: turning all bonds into constraints... 71: 71: Cleaning up constraints and constant bonded interactions with virtual sites 71: 71: Removed 18 Angles with virtual sites, 21 left 71: 71: Removed 10 Proper Dih.s with virtual sites, 44 left 71: 71: Converted 15 Constraints with virtual sites to connections, 7 left 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.029 0.015 199.4 71: (ns/day) (hour/ns) 71: Performance: 99.932 0.240 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Update groups can not be used for this system because an incompatible virtual site type is used 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 25 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.002 0.001 195.7 71: (ns/day) (hour/ns) 71: Performance: 1573.989 0.015 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (33 ms) 71: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: 71: NOTE 3 [file unknown]: 71: You are using constraints on all bonds, whereas the forcefield has been 71: parametrized only with constraints involving hydrogen atoms. We suggest 71: using constraints = h-bonds instead, this will also improve performance. 71: 71: Number of degrees of freedom in T-Coupling group System is 23.00 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 71: There are 9 non-linear virtual site constructions. Their contribution to 71: the energy error is approximated. In most cases this does not affect the 71: error significantly. 71: 71: 71: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 5 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 80, rlist from 0.748 to 0.865 71: 71: Update groups can not be used for this system because an incompatible virtual site type is used 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Alanine dipeptide in vacuo' 71: 16 steps, 0.0 ps. 71: Generated 2145 of the 2145 non-bonded parameter combinations 71: 71: Generated 2145 of the 2145 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 71: 71: turning all bonds into constraints... 71: 71: Cleaning up constraints and constant bonded interactions with virtual sites 71: 71: Removed 18 Angles with virtual sites, 21 left 71: 71: Removed 10 Proper Dih.s with virtual sites, 44 left 71: 71: Converted 15 Constraints with virtual sites to connections, 7 left 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.036 0.018 199.1 71: (ns/day) (hour/ns) 71: Performance: 80.131 0.300 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 80, rlist from 0.748 to 0.865 71: 71: Update groups can not be used for this system because an incompatible virtual site type is used 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 22 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.002 0.001 192.1 71: (ns/day) (hour/ns) 71: Performance: 1464.716 0.016 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (109 ms) 71: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: 71: NOTE 3 [file unknown]: 71: You are using constraints on all bonds, whereas the forcefield has been 71: parametrized only with constraints involving hydrogen atoms. We suggest 71: using constraints = h-bonds instead, this will also improve performance. 71: 71: Number of degrees of freedom in T-Coupling group System is 23.00 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 71: There are 9 non-linear virtual site constructions. Their contribution to 71: the energy error is approximated. In most cases this does not affect the 71: error significantly. 71: 71: 71: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 5 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 25, rlist from 0.729 to 0.81 71: 71: Update groups can not be used for this system because an incompatible virtual site type is used 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Alanine dipeptide in vacuo' 71: 16 steps, 0.0 ps. 71: Generated 2145 of the 2145 non-bonded parameter combinations 71: 71: Generated 2145 of the 2145 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 71: 71: turning all bonds into constraints... 71: 71: Cleaning up constraints and constant bonded interactions with virtual sites 71: 71: Removed 18 Angles with virtual sites, 21 left 71: 71: Removed 10 Proper Dih.s with virtual sites, 44 left 71: 71: Converted 15 Constraints with virtual sites to connections, 7 left 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.044 0.022 198.5 71: (ns/day) (hour/ns) 71: Performance: 65.897 0.364 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 25, rlist from 0.729 to 0.81 71: 71: Update groups can not be used for this system because an incompatible virtual site type is used 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 29 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.003 0.001 195.0 71: (ns/day) (hour/ns) 71: Performance: 1095.606 0.022 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (71 ms) 71: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (1589 ms total) 71: 71: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.229 0.115 199.8 71: (ns/day) (hour/ns) 71: Performance: 12.825 1.871 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 14 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.002 0.001 182.5 71: (ns/day) (hour/ns) 71: Performance: 1464.019 0.016 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (130 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.040 0.020 198.3 71: (ns/day) (hour/ns) 71: Performance: 73.197 0.328 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 13 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.002 0.001 182.8 71: (ns/day) (hour/ns) 71: Performance: 1483.408 0.016 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (38 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.075 0.037 199.5 71: (ns/day) (hour/ns) 71: Performance: 39.294 0.611 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 20 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.002 0.001 180.7 71: (ns/day) (hour/ns) 71: Performance: 1742.742 0.014 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (54 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.042 0.021 199.4 71: (ns/day) (hour/ns) 71: Performance: 70.031 0.343 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 20 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.001 0.001 181.3 71: (ns/day) (hour/ns) 71: Performance: 1903.180 0.013 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (35 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.073 0.037 199.5 71: (ns/day) (hour/ns) 71: Performance: 40.205 0.597 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 15 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.001 0.001 179.0 71: (ns/day) (hour/ns) 71: Performance: 2138.353 0.011 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (50 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.039 0.020 199.2 71: (ns/day) (hour/ns) 71: Performance: 74.587 0.322 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 23 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.002 0.001 180.9 71: (ns/day) (hour/ns) 71: Performance: 1580.450 0.015 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (35 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.040 0.020 199.3 71: (ns/day) (hour/ns) 71: Performance: 73.135 0.328 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 21 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.002 0.001 184.5 71: (ns/day) (hour/ns) 71: Performance: 1410.392 0.017 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (34 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.048 0.024 199.2 71: (ns/day) (hour/ns) 71: Performance: 61.049 0.393 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 20 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.001 0.001 178.7 71: (ns/day) (hour/ns) 71: Performance: 1896.735 0.013 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (45 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.050 0.025 199.5 71: (ns/day) (hour/ns) 71: Performance: 58.133 0.413 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 20 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.001 0.001 179.6 71: (ns/day) (hour/ns) 71: Performance: 2019.205 0.012 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (48 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.044 0.022 199.3 71: (ns/day) (hour/ns) 71: Performance: 66.132 0.363 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 20 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.001 0.001 177.9 71: (ns/day) (hour/ns) 71: Performance: 1960.100 0.012 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (39 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.061 0.031 199.2 71: (ns/day) (hour/ns) 71: Performance: 47.731 0.503 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 18 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.002 0.001 175.7 71: (ns/day) (hour/ns) 71: Performance: 1686.448 0.014 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (55 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.059 0.029 199.7 71: (ns/day) (hour/ns) 71: Performance: 49.794 0.482 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 19 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.002 0.001 176.9 71: (ns/day) (hour/ns) 71: Performance: 1574.794 0.015 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (54 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: NOTE: 34 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.144 0.072 199.9 71: (ns/day) (hour/ns) 71: Performance: 20.360 1.179 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 20 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.001 0.001 180.5 71: (ns/day) (hour/ns) 71: Performance: 1896.151 0.013 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (89 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.113 0.057 199.9 71: (ns/day) (hour/ns) 71: Performance: 25.991 0.923 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 22 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.001 0.001 179.4 71: (ns/day) (hour/ns) 71: Performance: 1882.822 0.013 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (75 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.050 0.025 199.6 71: (ns/day) (hour/ns) 71: Performance: 58.083 0.413 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 21 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.002 0.001 177.9 71: (ns/day) (hour/ns) 71: Performance: 1673.620 0.014 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (58 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.056 0.028 199.7 71: (ns/day) (hour/ns) 71: Performance: 52.522 0.457 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 20 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.001 0.001 178.7 71: (ns/day) (hour/ns) 71: Performance: 2057.647 0.012 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (49 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.056 0.028 199.6 71: (ns/day) (hour/ns) 71: Performance: 51.975 0.462 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.010 0.005 195.6 71: (ns/day) (hour/ns) 71: Performance: 301.355 0.080 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (63 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.079 0.040 199.3 71: (ns/day) (hour/ns) 71: Performance: 37.158 0.646 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 28 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.002 0.001 180.2 71: (ns/day) (hour/ns) 71: Performance: 1266.569 0.019 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (57 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.045 0.023 199.7 71: (ns/day) (hour/ns) 71: Performance: 65.240 0.368 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 21 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.002 0.001 183.1 71: (ns/day) (hour/ns) 71: Performance: 1589.831 0.015 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (46 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.075 0.038 199.9 71: (ns/day) (hour/ns) 71: Performance: 39.004 0.615 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 21 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.001 0.001 180.0 71: (ns/day) (hour/ns) 71: Performance: 2142.070 0.011 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (55 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.084 0.042 199.8 71: (ns/day) (hour/ns) 71: Performance: 34.973 0.686 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 21 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.001 0.001 179.4 71: (ns/day) (hour/ns) 71: Performance: 2151.797 0.011 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (60 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.064 0.032 198.0 71: (ns/day) (hour/ns) 71: Performance: 45.460 0.528 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 24 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.002 0.001 179.1 71: (ns/day) (hour/ns) 71: Performance: 1580.045 0.015 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (67 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.033 0.017 199.4 71: (ns/day) (hour/ns) 71: Performance: 87.780 0.273 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 13 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.001 0.001 181.8 71: (ns/day) (hour/ns) 71: Performance: 1846.147 0.013 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (59 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.044 0.022 199.6 71: (ns/day) (hour/ns) 71: Performance: 66.933 0.359 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 15 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.001 0.001 177.1 71: (ns/day) (hour/ns) 71: Performance: 2523.799 0.010 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (51 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.050 0.025 199.6 71: (ns/day) (hour/ns) 71: Performance: 58.863 0.408 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 15 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.001 0.001 174.2 71: (ns/day) (hour/ns) 71: Performance: 2387.827 0.010 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (61 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.058 0.029 199.7 71: (ns/day) (hour/ns) 71: Performance: 50.940 0.471 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 12 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.002 0.001 183.7 71: (ns/day) (hour/ns) 71: Performance: 1644.579 0.015 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (66 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.059 0.030 199.7 71: (ns/day) (hour/ns) 71: Performance: 49.588 0.484 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 13 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.001 0.001 180.3 71: (ns/day) (hour/ns) 71: Performance: 1910.854 0.013 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (60 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.042 0.021 199.6 71: (ns/day) (hour/ns) 71: Performance: 69.015 0.348 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 13 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.001 0.001 182.0 71: (ns/day) (hour/ns) 71: Performance: 1875.371 0.013 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (63 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.038 0.019 198.9 71: (ns/day) (hour/ns) 71: Performance: 77.894 0.308 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 28 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.003 0.001 186.3 71: (ns/day) (hour/ns) 71: Performance: 1066.954 0.022 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (63 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.051 0.026 199.5 71: (ns/day) (hour/ns) 71: Performance: 56.973 0.421 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 28 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.002 0.001 185.7 71: (ns/day) (hour/ns) 71: Performance: 1167.221 0.021 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (55 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.059 0.030 199.2 71: (ns/day) (hour/ns) 71: Performance: 49.321 0.487 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 20 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.003 0.001 179.5 71: (ns/day) (hour/ns) 71: Performance: 1037.312 0.023 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (61 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.049 0.025 199.2 71: (ns/day) (hour/ns) 71: Performance: 59.331 0.405 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 16 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.001 0.001 176.2 71: (ns/day) (hour/ns) 71: Performance: 2189.266 0.011 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (53 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.051 0.026 199.5 71: (ns/day) (hour/ns) 71: Performance: 57.348 0.418 71: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 16 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.002 0.001 182.1 71: (ns/day) (hour/ns) 71: Performance: 1520.383 0.016 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (57 ms) 71: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (1905 ms total) 71: 71: [----------] Global test environment tear-down 71: [==========] 46 tests from 3 test suites ran. (3572 ms total) 71: [ PASSED ] 46 tests. 71/91 Test #71: MdrunNonIntegratorTests ...................... Passed 3.89 sec test 72 Start 72: MdrunTpiTests 72: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-tpi-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunTpiTests.xml" 72: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 72: Test timeout computed to be: 600 72: [==========] Running 2 tests from 1 test suite. 72: [----------] Global test environment set-up. 72: [----------] 2 tests from Simple/TpiTest 72: [ RUN ] Simple/TpiTest.ReproducesOutput/0 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 1308.00 72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 72: TPI is not implemented for GPUs. 72: 72: Using 1 MPI process 72: Using 1 OpenMP thread 72: 72: 72: NOTE: Thread affinity was not set. 72: Reading frames from gro file '216 water molecules', 648 atoms. 72: Reading frame 0 time 0.000 mu 6.291e+01 6.291e+01 72: Last frame 0 time 0.000 72: Generated 331705 of the 331705 non-bonded parameter combinations 72: 72: Generated 331705 of the 331705 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: Excluding 3 bonded neighbours molecule type 'methane' 72: Analysing residue names: 72: There are: 216 Water residues 72: There are: 1 Other residues 72: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] Simple/TpiTest.ReproducesOutput/0 (297 ms) 72: [ RUN ] Simple/TpiTest.ReproducesOutput/1 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 1308.00 72: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 72: TPI is not implemented for GPUs. 72: 72: Using 1 MPI process 72: Using 1 OpenMP thread 72: 72: 72: NOTE: Thread affinity was not set. 72: Reading frames from gro file '216 water molecules', 648 atoms. 72: Reading frame 0 time 0.000 mu 4.535e+01 4.535e+01 72: Last frame 0 time 0.000 72: Generated 331705 of the 331705 non-bonded parameter combinations 72: 72: Generated 331705 of the 331705 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: Excluding 3 bonded neighbours molecule type 'methane' 72: Analysing residue names: 72: There are: 216 Water residues 72: There are: 1 Other residues 72: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] Simple/TpiTest.ReproducesOutput/1 (310 ms) 72: [----------] 2 tests from Simple/TpiTest (607 ms total) 72: 72: [----------] Global test environment tear-down 72: [==========] 2 tests from 1 test suite ran. (647 ms total) 72: [ PASSED ] 2 tests. 72/91 Test #72: MdrunTpiTests ................................ Passed 0.97 sec test 73 Start 73: MdrunMpiTests 73: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-mpi-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunMpiTests.xml" 73: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 73: Test timeout computed to be: 600 73: [==========] Running 16 tests from 2 test suites. 73: [----------] Global test environment set-up. 73: [----------] 4 tests from MimicTest 73: [ RUN ] MimicTest.OneQuantumMol 73: Setting the LD random seed to -4407569 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 73: For a correct single-point energy evaluation with nsteps = 0, use 73: continuation = yes to avoid constraining the input coordinates. 73: 73: 73: Generated 10 of the 10 non-bonded parameter combinations 73: 73: Generated 10 of the 10 1-4 parameter combinations 73: 73: Generating 1-4 interactions: fudge = 0.5 73: Excluding 2 bonded neighbours molecule type 'SOL' 73: 73: This run will generate roughly 0 Mb of data 73: Number of degrees of freedom in T-Coupling group rest is 21.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 73: NVE simulation with an initial temperature of zero: will use a Verlet 73: buffer of 10%. Check your energy drift! 73: 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: There were 3 NOTEs 73: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 73: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 73: Can not increase nstlist because an NVE ensemble is used 73: Using 2 MPI processes 73: Using 2 OpenMP threads per MPI process 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/4water.gro' 73: 73: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 73: Reading frame 0 time 0.000 Last frame 0 time 0.000 73: 73: NOTE: 11 % of the run time was spent in domain decomposition, 73: 8 % of the run time was spent in pair search, 73: you might want to increase nstlist (this has no effect on accuracy) 73: 73: Core t (s) Wall t (s) (%) 73: Time: 0.002 0.000 377.0 73: (ns/day) (hour/ns) 73: Performance: 191.841 0.125 73: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 73: For a correct single-point energy evaluation with nsteps = 0, use 73: continuation = yes to avoid constraining the input coordinates. 73: 73: Generating 1-4 interactions: fudge = 0.5 73: Number of degrees of freedom in T-Coupling group rest is 21.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 73: NVE simulation with an initial temperature of zero: will use a Verlet 73: buffer of 10%. Check your energy drift! 73: 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: There were 3 NOTEs 73: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] MimicTest.OneQuantumMol (63 ms) 73: [ RUN ] MimicTest.AllQuantumMol 73: Setting the LD random seed to -52737 73: 73: Generated 10 of the 10 non-bonded parameter combinations 73: 73: Generated 10 of the 10 1-4 parameter combinations 73: 73: Excluding 2 bonded neighbours molecule type 'SOL' 73: 73: This run will generate roughly 0 Mb of data 73: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 73: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 73: Can not increase nstlist because an NVE ensemble is used 73: Using 2 MPI processes 73: Using 2 OpenMP threads per MPI process 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/4water.gro' 73: 73: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 73: Reading frame 0 time 0.000 Last frame 0 time 0.000 73: 73: NOTE: 51 % of the run time was spent in domain decomposition, 73: 12 % of the run time was spent in pair search, 73: you might want to increase nstlist (this has no effect on accuracy) 73: 73: Core t (s) Wall t (s) (%) 73: Time: 0.536 0.134 399.9 73: (ns/day) (hour/ns) 73: Performance: 0.645 37.223 73: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file 73: [ OK ] MimicTest.AllQuantumMol (244 ms) 73: [ RUN ] MimicTest.TwoQuantumMol 73: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 73: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 73: For a correct single-point energy evaluation with nsteps = 0, use 73: continuation = yes to avoid constraining the input coordinates. 73: 73: Setting the LD random seed to -59016321 73: 73: Generated 10 of the 10 non-bonded parameter combinations 73: Generating 1-4 interactions: fudge = 0.5 73: 73: Generated 10 of the 10 1-4 parameter combinations 73: 73: Number of degrees of freedom in T-Coupling group rest is 21.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 73: NVE simulation with an initial temperature of zero: will use a Verlet 73: buffer of 10%. Check your energy drift! 73: 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: Excluding 2 bonded neighbours molecule type 'SOL' 73: 73: This run will generate roughly 0 Mb of data 73: 73: There were 3 NOTEs 73: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 73: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 73: Can not increase nstlist because an NVE ensemble is used 73: Using 2 MPI processes 73: Using 2 OpenMP threads per MPI process 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/4water.gro' 73: 73: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 73: Reading frame 0 time 0.000 Last frame 0 time 0.000 73: 73: NOTE: 53 % of the run time was spent in domain decomposition, 73: 24 % of the run time was spent in pair search, 73: you might want to increase nstlist (this has no effect on accuracy) 73: 73: Core t (s) Wall t (s) (%) 73: Time: 0.752 0.188 399.9 73: (ns/day) (hour/ns) 73: Performance: 0.460 52.205 73: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] MimicTest.TwoQuantumMol (278 ms) 73: [ RUN ] MimicTest.BondCuts 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 73: For a correct single-point energy evaluation with nsteps = 0, use 73: continuation = yes to avoid constraining the input coordinates. 73: 73: Setting the LD random seed to -1082687499 73: 73: Generated 2211 of the 2211 non-bonded parameter combinations 73: Generating 1-4 interactions: fudge = 0.5 73: 73: Generated 2211 of the 2211 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 73: Number of degrees of freedom in T-Coupling group rest is 66.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 73: NVE simulation: will use the initial temperature of 300.368 K for 73: determining the Verlet buffer size 73: 73: 73: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 73: 73: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 73: 73: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 73: 73: Note that mdrun will redetermine rlist based on the actual pair-list setup 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: This run will generate roughly 0 Mb of data 73: 73: There were 3 NOTEs 73: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 73: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 73: Can not increase nstlist because an NVE ensemble is used 73: Using 2 MPI processes 73: Using 2 OpenMP threads per MPI process 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/ala.gro' 73: 73: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 73: Reading frame 0 time 0.000 Last frame 0 time 0.000 73: 73: NOTE: 37 % of the run time was spent in domain decomposition, 73: 29 % of the run time was spent in pair search, 73: you might want to increase nstlist (this has no effect on accuracy) 73: 73: Core t (s) Wall t (s) (%) 73: Time: 0.609 0.152 399.9 73: (ns/day) (hour/ns) 73: Performance: 0.567 42.310 73: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] MimicTest.BondCuts (247 ms) 73: [----------] 4 tests from MimicTest (834 ms total) 73: 73: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest 73: Setting the LD random seed to -74074133 73: 73: Generated 3 of the 3 non-bonded parameter combinations 73: 73: Generated 3 of the 3 1-4 parameter combinations 73: Generating 1-4 interactions: fudge = 0.5 73: 73: Excluding 2 bonded neighbours molecule type 'SOL' 73: 73: Number of degrees of freedom in T-Coupling group rest is 9.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 73: NVE simulation with an initial temperature of zero: will use a Verlet 73: buffer of 10%. Check your energy drift! 73: 73: This run will generate roughly 0 Mb of data 73: 73: There was 1 NOTE 73: Setting the LD random seed to -542122114 73: 73: Generated 3 of the 3 non-bonded parameter combinations 73: Generating 1-4 interactions: fudge = 0.5 73: 73: Generated 3 of the 3 1-4 parameter combinations 73: 73: Excluding 2 bonded neighbours molecule type 'SOL' 73: Number of degrees of freedom in T-Coupling group System is 9.00 73: 73: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 73: 73: Calculated rlist for 1x1 atom pair-list as 1.017 nm, buffer size 0.017 nm 73: 73: Set rlist, assuming 4x4 atom pair-list, to 1.005 nm, buffer size 0.005 nm 73: 73: Note that mdrun will redetermine rlist based on the actual pair-list setup 73: 73: This run will generate roughly 0 Mb of data 73: Setting the LD random seed to -822150851 73: 73: Generated 3 of the 3 non-bonded parameter combinations 73: 73: Generated 3 of the 3 1-4 parameter combinations 73: 73: Excluding 2 bonded neighbours molecule type 'SOL' 73: 73: Generating 1-4 interactions: fudge = 0.5 73: Number of degrees of freedom in T-Coupling group rest is 9.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 73: NVE simulation with an initial temperature of zero: will use a Verlet 73: buffer of 10%. Check your energy drift! 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 73: The optimal PME mesh load for parallel simulations is below 0.5 73: and for highly parallel simulations between 0.25 and 0.33, 73: for higher performance, increase the cut-off and the PME grid spacing. 73: 73: 73: 73: There were 2 NOTEs 73: Calculating fourier grid dimensions for X Y Z 73: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 73: 73: Estimate for the relative computational load of the PME mesh part: 1.00 73: 73: This run will generate roughly 0 Mb of data 73: Setting the LD random seed to -331612201 73: 73: Generated 3 of the 3 non-bonded parameter combinations 73: Generating 1-4 interactions: fudge = 0.5 73: 73: Generated 3 of the 3 1-4 parameter combinations 73: 73: Excluding 2 bonded neighbours molecule type 'SOL' 73: 73: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 73: 73: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 73: 73: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 73: 73: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 73: 73: Note that mdrun will redetermine rlist based on the actual pair-list setup 73: Calculating fourier grid dimensions for X Y Z 73: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 73: 73: Estimate for the relative computational load of the PME mesh part: 1.00 73: 73: This run will generate roughly 0 Mb of data 73: Number of degrees of freedom in T-Coupling group System is 9.00 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 73: The optimal PME mesh load for parallel simulations is below 0.5 73: and for highly parallel simulations between 0.25 and 0.33, 73: for higher performance, increase the cut-off and the PME grid spacing. 73: 73: 73: 73: There was 1 NOTE 73: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 73: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 73: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_No.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 73: Can not increase nstlist because an NVE ensemble is used 73: Using 2 MPI processes 73: Using 2 OpenMP threads per MPI process 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: starting mdrun 'spc2' 73: 20 steps, 0.0 ps. 73: 73: Writing final coordinates. 73: 73: 73: Dynamic load balancing report: 73: DLB was off during the run due to low measured imbalance. 73: Average load imbalance: 0.5%. 73: The balanceable part of the MD step is 54%, load imbalance is computed from this. 73: Part of the total run time spent waiting due to load imbalance: 0.3%. 73: 73: 73: NOTE: 47 % of the run time was spent communicating energies, 73: you might want to increase some nst* mdp options 73: 73: Core t (s) Wall t (s) (%) 73: Time: 0.103 0.032 325.4 73: (ns/day) (hour/ns) 73: Performance: 57.191 0.420 73: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 73: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_TemperatureAndPressure.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 73: Changing nstlist from 10 to 50, rlist from 1.005 to 1.136 73: 73: Using 2 MPI processes 73: Using 2 OpenMP threads per MPI process 73: 73: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (104 ms) 73: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 73: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 73: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 73: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 73: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: starting mdrun 'spc2' 73: 20 steps, 0.0 ps. 73: 73: Writing final coordinates. 73: 73: NOTE: 35 % of the run time was spent communicating energies, 73: you might want to increase some nst* mdp options 73: 73: Core t (s) Wall t (s) (%) 73: Time: 0.094 0.024 398.8 73: (ns/day) (hour/ns) 73: Performance: 76.678 0.313 73: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (39 ms) 73: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 73: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 73: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 73: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 73: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 73: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 73: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 73: Can not increase nstlist because an NVE ensemble is used 73: Using 2 MPI processes 73: Using 2 OpenMP threads per MPI process 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: starting mdrun 'spc2' 73: 20 steps, 0.0 ps. 73: 73: Writing final coordinates. 73: 73: 73: Dynamic load balancing report: 73: DLB was turned on during the run due to measured imbalance. 73: Average load imbalance: 97.8%. 73: The balanceable part of the MD step is 4%, load imbalance is computed from this. 73: Part of the total run time spent waiting due to load imbalance: 4.2%. 73: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 73: 73: 73: NOTE: 11 % of the run time was spent in domain decomposition, 73: 5 % of the run time was spent in pair search, 73: you might want to increase nstlist (this has no effect on accuracy) 73: 73: NOTE: 12 % of the run time was spent communicating energies, 73: you might want to increase some nst* mdp options 73: 73: Core t (s) Wall t (s) (%) 73: Time: 1.703 0.434 392.7 73: (ns/day) (hour/ns) 73: Performance: 4.184 5.736 73: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (927 ms) 73: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 73: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 73: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 73: Can not increase nstlist because an NVE ensemble is used 73: Using 2 MPI processes 73: Using 2 OpenMP threads per MPI process 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: starting mdrun 'spc2' 73: 20 steps, 0.0 ps. 73: 73: Writing final coordinates. 73: 73: Core t (s) Wall t (s) (%) 73: Time: 2.688 0.684 393.1 73: (ns/day) (hour/ns) 73: Performance: 2.653 9.047 73: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (1140 ms) 73: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 73: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 73: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 73: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 73: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 73: Changing nstlist from 10 to 100, rlist from 1 to 1 73: 73: Using 2 MPI processes 73: Using 2 OpenMP threads per MPI process 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: starting mdrun 'spc2' 73: 20 steps, 0.0 ps. 73: 73: Writing final coordinates. 73: 73: Core t (s) Wall t (s) (%) 73: Time: 7.472 1.870 399.6 73: (ns/day) (hour/ns) 73: Performance: 0.970 24.735 73: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (2148 ms) 73: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 73: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 73: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 73: Changing nstlist from 10 to 100, rlist from 1 to 1 73: 73: Using 2 MPI processes 73: Using 2 OpenMP threads per MPI process 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: starting mdrun 'spc2' 73: 20 steps, 0.0 ps. 73: 73: Writing final coordinates. 73: 73: Core t (s) Wall t (s) (%) 73: Time: 0.503 0.138 365.5 73: (ns/day) (hour/ns) 73: Performance: 13.184 1.820 73: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (179 ms) 73: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 73: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 73: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest (4576 ms total) 73: 73: [----------] Global test environment tear-down 73: [==========] 16 tests from 2 test suites ran. (5571 ms total) 73: [ PASSED ] 10 tests. 73: [ SKIPPED ] 6 tests, listed below: 73: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 73: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 73: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 73: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 73: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 73: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 73/91 Test #73: MdrunMpiTests ................................ Passed 6.00 sec test 74 Start 74: MdrunMultiSimTests 74: Test command: /usr/bin/mpiexec "-n" "4" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-multisim-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunMultiSimTests.xml" 74: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 74: Test timeout computed to be: 600 74: [==========] Running 6 tests from 2 test suites. 74: [----------] Global test environment set-up. 74: [----------] 4 tests from InNvt/MultiSimTest 74: [ RUN ] InNvt/MultiSimTest.ExitsNormally/0 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 74: You have set rlist larger than the interaction cut-off, but you also have 74: verlet-buffer-tolerance > 0. Will set rlist using 74: verlet-buffer-tolerance. 74: 74: Setting the LD random seed to -1078774277 74: Generating 1-4 interactions: fudge = 0.5 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Setting gen_seed to -537133067 74: 74: Velocities were taken from a Maxwell distribution at 288 K 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 74: You have set rlist larger than the interaction cut-off, but you also have 74: verlet-buffer-tolerance > 0. Will set rlist using 74: verlet-buffer-tolerance. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 2 NOTEs 74: 74: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Setting the LD random seed to -1384150213 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: Generating 1-4 interactions: fudge = 0.5 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Setting gen_seed to -907024417 74: 74: Velocities were taken from a Maxwell distribution at 298 K 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 74: You have set rlist larger than the interaction cut-off, but you also have 74: verlet-buffer-tolerance > 0. Will set rlist using 74: verlet-buffer-tolerance. 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 2 NOTEs 74: Setting the LD random seed to -42083337 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Setting gen_seed to -1610747945 74: 74: Velocities were taken from a Maxwell distribution at 268 K 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 2 NOTEs 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 74: You have set rlist larger than the interaction cut-off, but you also have 74: verlet-buffer-tolerance > 0. Will set rlist using 74: verlet-buffer-tolerance. 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 2 NOTEs 74: Setting the LD random seed to -673190159 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Setting gen_seed to -1631612940 74: 74: Velocities were taken from a Maxwell distribution at 278 K 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormally_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormally_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 74: 74: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 74: 74: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 74: 74: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 74: 74: This is simulation 0 out of 4 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 1 MPI process 74: This is simulation 2 out of 4 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 1 MPI process 74: This is simulation 1 out of 4 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 1 MPI process 74: This is simulation 3 out of 4 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 1 MPI process 74: Using 1 OpenMP thread 74: 74: Using 1 OpenMP thread 74: 74: Using 1 OpenMP thread 74: 74: Using 1 OpenMP thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 2 steps, 0.0 ps. 74: starting mdrun 'spc2' 74: 2 steps, 0.0 ps. 74: starting mdrun 'spc2' 74: 2 steps, 0.0 ps. 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 2 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Writing final coordinates. 74: 74: Writing final coordinates. 74: 74: Writing final coordinates. 74: [ OK ] InNvt/MultiSimTest.ExitsNormally/0 (167 ms) 74: [ RUN ] InNvt/MultiSimTest.ExitsNormally/1 74: Setting the LD random seed to -88416854 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_1_input.mdp]: 74: You have set rlist larger than the interaction cut-off, but you also have 74: verlet-buffer-tolerance > 0. Will set rlist using 74: verlet-buffer-tolerance. 74: 74: Generating 1-4 interactions: fudge = 0.5 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Setting gen_seed to -208224369 74: 74: Velocities were taken from a Maxwell distribution at 298 K 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Setting the LD random seed to -76547153 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_1_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 2 NOTEs 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_1_input.mdp]: 74: You have set rlist larger than the interaction cut-off, but you also have 74: verlet-buffer-tolerance > 0. Will set rlist using 74: verlet-buffer-tolerance. 74: 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: Generating 1-4 interactions: fudge = 0.5 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Setting gen_seed to 2147291059 74: 74: Velocities were taken from a Maxwell distribution at 278 K 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: 74: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_1_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 2 NOTEs 74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 74: 74: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 74: 74: This is simulation 1 out of 2 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 2 MPI processes 74: This is simulation 0 out of 2 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 2 MPI processes 74: Using 1 OpenMP thread per MPI process 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 2 steps, 0.0 ps. 74: Using 1 OpenMP thread per MPI process 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 2 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: NOTE: 53 % of the run time was spent communicating energies, 74: you might want to increase some nst* mdp options 74: 74: Writing final coordinates. 74: 74: NOTE: 60 % of the run time was spent communicating energies, 74: you might want to increase some nst* mdp options 74: [ OK ] InNvt/MultiSimTest.ExitsNormally/1 (136 ms) 74: [ RUN ] InNvt/MultiSimTest.ExitsNormallyWithDifferentNumbersOfStepsPerSimulation/0 74: Setting the LD random seed to -1258364937 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 74: You have set rlist larger than the interaction cut-off, but you also have 74: verlet-buffer-tolerance > 0. Will set rlist using 74: verlet-buffer-tolerance. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 74: For a correct single-point energy evaluation with nsteps = 0, use 74: continuation = yes to avoid constraining the input coordinates. 74: 74: Generating 1-4 interactions: fudge = 0.5 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 74: You have set rlist larger than the interaction cut-off, but you also have 74: verlet-buffer-tolerance > 0. Will set rlist using 74: verlet-buffer-tolerance. 74: 74: Setting the LD random seed to -35663937 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: Setting the LD random seed to 1809842158 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 74: You have set rlist larger than the interaction cut-off, but you also have 74: verlet-buffer-tolerance > 0. Will set rlist using 74: verlet-buffer-tolerance. 74: 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: Generating 1-4 interactions: fudge = 0.5 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Setting gen_seed to 1924136943 74: 74: Setting gen_seed to -1124675849 74: 74: Velocities were taken from a Maxwell distribution at 288 K 74: 74: Velocities were taken from a Maxwell distribution at 298 K 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 2 NOTEs 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Setting gen_seed to -536871105 74: 74: Velocities were taken from a Maxwell distribution at 268 K 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 2 NOTEs 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 74: You have set rlist larger than the interaction cut-off, but you also have 74: verlet-buffer-tolerance > 0. Will set rlist using 74: verlet-buffer-tolerance. 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 2 NOTEs 74: Setting the LD random seed to -1174406193 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Setting gen_seed to -196609 74: 74: Velocities were taken from a Maxwell distribution at 278 K 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 74: 74: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 74: 74: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 74: 74: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 74: 74: This is simulation 2 out of 4 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 1 MPI process 74: This is simulation 0 out of 4 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 1 MPI process 74: This is simulation 1 out of 4 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 1 MPI process 74: This is simulation 3 out of 4 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 1 MPI process 74: Using 1 OpenMP thread 74: 74: Using 1 OpenMP thread 74: 74: Using 1 OpenMP thread 74: 74: Using 1 OpenMP thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 2 steps, 0.0 ps. 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 0 steps, 0.0 ps. 74: starting mdrun 'spc2' 74: 1 steps, 0.0 ps. 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 3 steps, 0.0 ps. 74: 74: Note: The number of steps is not consistent across multi simulations, 74: but we are proceeding anyway! 74: 74: Note: The number of steps is not consistent across multi simulations, 74: but we are proceeding anyway! 74: 74: Note: The number of steps is not consistent across multi simulations, 74: but we are proceeding anyway! 74: 74: Note: The number of steps is not consistent across multi simulations, 74: but we are proceeding anyway! 74: 74: Writing final coordinates. 74: 74: Writing final coordinates. 74: 74: Writing final coordinates. 74: [ OK ] InNvt/MultiSimTest.ExitsNormallyWithDifferentNumbersOfStepsPerSimulation/0 (131 ms) 74: [ RUN ] InNvt/MultiSimTest.ExitsNormallyWithDifferentNumbersOfStepsPerSimulation/1 74: Setting the LD random seed to -419448849 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Setting gen_seed to -973258837 74: 74: Velocities were taken from a Maxwell distribution at 298 K 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1_input.mdp]: 74: You have set rlist larger than the interaction cut-off, but you also have 74: verlet-buffer-tolerance > 0. Will set rlist using 74: verlet-buffer-tolerance. 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 2 NOTEs 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1_input.mdp]: 74: You have set rlist larger than the interaction cut-off, but you also have 74: verlet-buffer-tolerance > 0. Will set rlist using 74: verlet-buffer-tolerance. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1_input.mdp]: 74: For a correct single-point energy evaluation with nsteps = 0, use 74: continuation = yes to avoid constraining the input coordinates. 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Setting the LD random seed to -1912621061 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Setting gen_seed to -136905761 74: 74: Velocities were taken from a Maxwell distribution at 278 K 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 74: 74: This is simulation 0 out of 2 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 2 MPI processes 74: Using 1 OpenMP thread per MPI process 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 0 steps, 0.0 ps. 74: 74: Note: The number of steps is not consistent across multi simulations, 74: but we are proceeding anyway! 74: 74: NOTE: 26 % of the run time was spent in domain decomposition, 74: 10 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 74: 74: This is simulation 1 out of 2 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 2 MPI processes 74: Using 1 OpenMP thread per MPI process 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 1 steps, 0.0 ps. 74: 74: Note: The number of steps is not consistent across multi simulations, 74: but we are proceeding anyway! 74: 74: Writing final coordinates. 74: 74: NOTE: 50 % of the run time was spent communicating energies, 74: you might want to increase some nst* mdp options 74: [ OK ] InNvt/MultiSimTest.ExitsNormallyWithDifferentNumbersOfStepsPerSimulation/1 (33 ms) 74: [----------] 4 tests from InNvt/MultiSimTest (535 ms total) 74: 74: [----------] 2 tests from InNvt/MultiSimTerminationTest 74: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 74: You have set rlist larger than the interaction cut-off, but you also have 74: verlet-buffer-tolerance > 0. Will set rlist using 74: verlet-buffer-tolerance. 74: 74: Setting the LD random seed to -689439253 74: 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 74: You have set rlist larger than the interaction cut-off, but you also have 74: verlet-buffer-tolerance > 0. Will set rlist using 74: verlet-buffer-tolerance. 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: Setting the LD random seed to -536883226 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: Generating 1-4 interactions: fudge = 0.5 74: Generating 1-4 interactions: fudge = 0.5 74: 74: Setting gen_seed to -2103698 74: 74: Velocities were taken from a Maxwell distribution at 298 K 74: 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: Setting gen_seed to -37890 74: 74: 74: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Velocities were taken from a Maxwell distribution at 288 K 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 2 NOTEs 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 2 NOTEs 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 74: You have set rlist larger than the interaction cut-off, but you also have 74: verlet-buffer-tolerance > 0. Will set rlist using 74: verlet-buffer-tolerance. 74: 74: Setting the LD random seed to 2143124538 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Setting gen_seed to -814488581 74: 74: Velocities were taken from a Maxwell distribution at 278 K 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Setting the LD random seed to 2027077622 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 2 NOTEs 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 74: You have set rlist larger than the interaction cut-off, but you also have 74: verlet-buffer-tolerance > 0. Will set rlist using 74: verlet-buffer-tolerance. 74: 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Setting gen_seed to -1627395203 74: 74: Velocities were taken from a Maxwell distribution at 268 K 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 2 NOTEs 74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 74: 74: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 74: 74: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 74: 74: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 74: 74: This is simulation 0 out of 4 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: This is simulation 2 out of 4 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 1 MPI process 74: 74: Using 1 MPI process 74: This is simulation 1 out of 4 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 1 MPI process 74: This is simulation 3 out of 4 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 1 MPI process 74: Using 1 OpenMP thread 74: 74: Using 1 OpenMP thread 74: 74: Using 1 OpenMP thread 74: 74: Using 1 OpenMP thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in cas 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: e you run multiple jobs). 74: starting mdrun 'spc2' 74: 100 steps, 0.1 ps. 74: starting mdrun 'spc2' 74: 100 steps, 0.1 ps. 74: starting mdrun 'spc2' 74: 100 steps, 0.1 ps. 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 100 steps, 0.1 ps. 74: 74: Step 0: Run time exceeded 0.000 hours, will terminate the run within 2 steps 74: 74: Step 0: Run time exceeded 0.000 hours, will terminate the run within 2 steps 74: 74: Step 0: Run time exceeded 0.000 hours, will terminate the run within 2 steps 74: 74: Step 0: Run time exceeded 0.000 hours, will terminate the run within 2 steps 74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 74: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 74: 74: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 74: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 74: 74: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 74: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 74: 74: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 74: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 74: 74: 74: This is simulation 0 out of 4 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 1 MPI process 74: 74: This is simulation 2 out of 4 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 1 MPI process 74: 74: This is simulation 1 out of 4 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 1 MPI process 74: 74: This is simulation 3 out of 4 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 1 MPI process 74: Using 1 OpenMP thread 74: 74: Using 1 OpenMP thread 74: 74: Using 1 OpenMP thread 74: 74: Using 1 OpenMP thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 3 steps, 0.0 ps (continuing from step 1, 0.0 ps). 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 3 steps, 0.0 ps (continuing from step 1, 0.0 ps). 74: starting mdrun 'spc2' 74: 3 steps, 0.0 ps (continuing from step 1, 0.0 ps). 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 3 steps, 0.0 ps (continuing from step 1, 0.0 ps). 74: 74: Writing final coordinates. 74: 74: Writing final coordinates. 74: 74: Writing final coordinates. 74: 74: Writing final coordinates. 74: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (640 ms) 74: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1_input.mdp]: 74: You have set rlist larger than the interaction cut-off, but you also have 74: verlet-buffer-tolerance > 0. Will set rlist using 74: verlet-buffer-tolerance. 74: 74: Setting the LD random seed to -269362186 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: Generating 1-4 interactions: fudge = 0.5 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Setting gen_seed to -29395011 74: 74: Velocities were taken from a Maxwell distribution at 298 K 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 2 NOTEs 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1_input.mdp]: 74: You have set rlist larger than the interaction cut-off, but you also have 74: verlet-buffer-tolerance > 0. Will set rlist using 74: verlet-buffer-tolerance. 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 2 NOTEs 74: Setting the LD random seed to -470708305 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Setting gen_seed to 1056896991 74: 74: Velocities were taken from a Maxwell distribution at 278 K 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 74: 74: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 74: 74: This is simulation 0 out of 2 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 2 MPI processes 74: This is simulation 1 out of 2 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 2 MPI processes 74: Using 1 OpenMP thread per MPI process 74: 74: Using 1 OpenMP thread per MPI process 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 100 steps, 0.1 ps. 74: starting mdrun 'spc2' 74: 100 steps, 0.1 ps. 74: 74: Step 0: Run time exceeded 0.000 hours, will terminate the run within 2 steps 74: 74: Step 5: Run time exceeded 0.000 hours, will terminate the run within 2 steps 74: 74: 74: Dynamic load balancing report: 74: DLB was off during the run due to low measured imbalance. 74: Average load imbalance: 0.7%. 74: The balanceable part of the MD step is 10%, load imbalance is computed from this. 74: Part of the total run time spent waiting due to load imbalance: 0.1%. 74: 74: 74: NOTE: 48 % of the run time was spent communicating energies, 74: you might want to increase some nst* mdp options 74: 74: 74: Dynamic load balancing report: 74: DLB was off during the run due to low measured imbalance. 74: Average load imbalance: 6.7%. 74: The balanceable part of the MD step is 6%, load imbalance is computed from this. 74: Part of the total run time spent waiting due to load imbalance: 0.4%. 74: 74: 74: NOTE: 49 % of the run time was spent communicating energies, 74: you might want to increase some nst* mdp options 74: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 74: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 74: 74: 74: This is simulation 1 out of 2 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 2 MPI processes 74: Using 1 OpenMP thread per MPI process 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). 74: 74: Note: The initial step is not consistent across multi simulations, 74: but we are proceeding anyway! 74: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 74: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 74: 74: 74: This is simulation 0 out of 2 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 2 MPI processes 74: Using 1 OpenMP thread per MPI process 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 3 steps, 0.0 ps (continuing from step 1, 0.0 ps). 74: 74: Note: The initial step is not consistent across multi simulations, 74: but we are proceeding anyway! 74: 74: Writing final coordinates. 74: 74: NOTE: 49 % of the run time was spent communicating energies, 74: you might want to increase some nst* mdp options 74: 74: Writing final coordinates. 74: 74: NOTE: 49 % of the run time was spent communicating energies, 74: you might want to increase some nst* mdp options 74: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 (202 ms) 74: [----------] 2 tests from InNvt/MultiSimTerminationTest (884 ms total) 74: 74: [----------] Global test environment tear-down 74: [==========] 6 tests from 2 test suites ran. (1726 ms total) 74: [ PASSED ] 6 tests. 74/91 Test #74: MdrunMultiSimTests ........................... Passed 2.21 sec test 75 Start 75: MdrunMultiSimReplexTests 75: Test command: /usr/bin/mpiexec "-n" "4" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-multisim-replex-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunMultiSimReplexTests.xml" 75: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 75: Test timeout computed to be: 600 75: [==========] Running 5 tests from 2 test suites. 75: [----------] Global test environment set-up. 75: [----------] 4 tests from WithDifferentControlVariables/ReplicaExchangeEnsembleTest 75: [ RUN ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/0 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 75: You have set rlist larger than the interaction cut-off, but you also have 75: verlet-buffer-tolerance > 0. Will set rlist using 75: verlet-buffer-tolerance. 75: 75: Setting the LD random seed to -721732371 75: 75: Generated 3 of the 3 non-bonded parameter combinations 75: 75: Generated 3 of the 3 1-4 parameter combinations 75: Generating 1-4 interactions: fudge = 0.5 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Setting gen_seed to -872579587 75: 75: Velocities were taken from a Maxwell distribution at 298 K 75: Number of degrees of freedom in T-Coupling group System is 9.00 75: 75: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 75: You have set rlist larger than the interaction cut-off, but you also have 75: verlet-buffer-tolerance > 0. Will set rlist using 75: verlet-buffer-tolerance. 75: 75: Setting the LD random seed to 1055194815 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 75: You have set rlist larger than the interaction cut-off, but you also have 75: verlet-buffer-tolerance > 0. Will set rlist using 75: verlet-buffer-tolerance. 75: 75: Setting the LD random seed to -10813830 75: 75: Generated 3 of the 3 non-bonded parameter combinations 75: 75: Generating 1-4 interactions: fudge = 0.5 75: Generated 3 of the 3 1-4 parameter combinations 75: 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 75: You have set rlist larger than the interaction cut-off, but you also have 75: verlet-buffer-tolerance > 0. Will set rlist using 75: verlet-buffer-tolerance. 75: 75: Number of degrees of freedom in T-Coupling group System is 9.00 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: There were 2 NOTEs 75: Generating 1-4 interactions: fudge = 0.5 75: Number of degrees of freedom in T-Coupling group System is 9.00 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: There were 2 NOTEs 75: Generating 1-4 interactions: fudge = 0.5 75: Setting the LD random seed to -83903875 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Setting gen_seed to -705169665 75: 75: Velocities were taken from a Maxwell distribution at 288 K 75: 75: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Generated 3 of the 3 non-bonded parameter combinations 75: 75: Generated 3 of the 3 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Setting gen_seed to -66051 75: 75: Velocities were taken from a Maxwell distribution at 268 K 75: 75: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Generated 3 of the 3 non-bonded parameter combinations 75: 75: Generated 3 of the 3 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Setting gen_seed to 2146948799 75: 75: Velocities were taken from a Maxwell distribution at 278 K 75: 75: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Number of degrees of freedom in T-Coupling group System is 9.00 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: There were 2 NOTEs 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: There were 2 NOTEs 75: 75: This run will generate roughly 0 Mb of data 75: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 75: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 75: 75: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 75: 75: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 75: 75: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 75: 75: This is simulation 0 out of 4 running as a composite GROMACS 75: multi-simulation job. Setup for this simulation: 75: This is simulation 1 out of 4 running as a composite GROMACS 75: multi-simulation job. Setup for this simulation: 75: 75: Using 1 MPI process 75: 75: Using 1 MPI process 75: This is simulation 3 out of 4 running as a composite GROMACS 75: multi-simulation job. Setup for this simulation: 75: This is simulation 2 out of 4 running as a composite GROMACS 75: multi-simulation job. Setup for this simulation: 75: 75: Using 1 MPI process 75: 75: Using 1 MPI process 75: Using 1 OpenMP thread Using 1 OpenMP thread 75: 75: 75: 75: Using 1 OpenMP thread 75: 75: Using 1 OpenMP thread 75: 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'spc2' 75: 2 steps, 0.0 ps. 75: starting mdrun 'spc2' 75: 2 steps, 0.0 ps. 75: starting mdrun 'spc2' 75: 2 steps, 0.0 ps. 75: starting mdrun 'spc2' 75: 2 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: Writing final coordinates. 75: 75: Writing final coordinates. 75: 75: Writing final coordinates. 75: [ OK ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/0 (440 ms) 75: [ RUN ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/1 75: Setting the LD random seed to -209715521 75: Setting the LD random seed to -1744912905 75: 75: Generated 3 of the 3 non-bonded parameter combinations 75: 75: Generated 3 of the 3 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Setting gen_seed to -339805577 75: 75: Velocities were taken from a Maxwell distribution at 298 K 75: 75: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 75: You have set rlist larger than the interaction cut-off, but you also have 75: verlet-buffer-tolerance > 0. Will set rlist using 75: verlet-buffer-tolerance. 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: We recommend using the C-rescale barostat instead. 75: 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 75: You have set rlist larger than the interaction cut-off, but you also have 75: verlet-buffer-tolerance > 0. Will set rlist using 75: verlet-buffer-tolerance. 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: We recommend using the C-rescale barostat instead. 75: 75: Generating 1-4 interactions: fudge = 0.5 75: Number of degrees of freedom in T-Coupling group System is 9.00 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: There were 2 NOTEs 75: 75: There was 1 WARNING 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentCo 75: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 75: You have set rlist larger than the interaction cut-off, but you also have 75: verlet-buffer-tolerance > 0. Will set rlist using 75: verlet-buffer-tolerance. 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: We recommend using the C-rescale barostat instead. 75: 75: Generating 1-4 interactions: fudge = 0.5 75: Number of degrees of freedom in T-Coupling group System is 9.00 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: There were 2 NOTEs 75: 75: There was 1 WARNING 75: Setting the LD random seed to -536978225 75: 75: Generated 3 of the 3 non-bonded parameter combinations 75: 75: Generated 3 of the 3 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Setting gen_seed to -41953305 75: 75: Velocities were taken from a Maxwell distribution at 288 K 75: 75: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Generated 3 of the 3 non-bonded parameter combinations 75: 75: Generated 3 of the 3 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Setting gen_seed to -1260913793 75: 75: Velocities were taken from a Maxwell distribution at 268 K 75: 75: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Generating 1-4 interactions: fudge = 0.5 75: Number of degrees of freedom in T-Coupling group System is 9.00 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: There were 2 NOTEs 75: 75: There was 1 WARNING 75: ntrolVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 75: You have set rlist larger than the interaction cut-off, but you also have 75: verlet-buffer-tolerance > 0. Will set rlist using 75: verlet-buffer-tolerance. 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: We recommend using the C-rescale barostat instead. 75: 75: Setting the LD random seed to -1749631521 75: 75: Generated 3 of the 3 non-bonded parameter combinations 75: 75: Generated 3 of the 3 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: Generating 1-4 interactions: fudge = 0.5 75: 75: Setting gen_seed to 2040482497 75: 75: Velocities were taken from a Maxwell distribution at 278 K 75: 75: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 75: Number of degrees of freedom in T-Coupling group System is 9.00 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: There were 2 NOTEs 75: 75: There was 1 WARNING 75: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 75: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 75: 75: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 75: 75: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 75: 75: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 75: 75: This is simulation 0 out of 4 running as a composite GROMACS 75: multi-simulation job. Setup for this simulation: 75: 75: Using 1 MPI process 75: This is simulation 1 out of 4 running as a composite GROMACS 75: multi-simulation job. Setup for this simulation: 75: 75: Using 1 MPI process 75: This is simulation 2 out of 4 running as a composite GROMACS 75: multi-simulation job. Setup for this simulation: 75: 75: Using 1 MPI process 75: This is simulation 3 out of 4 running as a composite GROMACS 75: multi-simulation job. Setup for this simulation: 75: 75: Using 1 MPI process 75: Using 1 OpenMP thread 75: 75: Using 1 OpenMP thread 75: 75: Using 1 OpenMP thread Using 1 OpenMP thread 75: 75: 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'spc2' 75: 2 steps, 0.0 ps. 75: starting mdrun 'spc2' 75: 2 steps, 0.0 ps. 75: starting mdrun 'spc2' 75: 2 steps, 0.0 ps. 75: starting mdrun 'spc2' 75: 2 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: Writing final coordinates. 75: 75: Writing final coordinates. 75: 75: Writing final coordinates. 75: [ OK ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/1 (196 ms) 75: [ RUN ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/2 75: Setting the LD random seed to -566886852 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2_input.mdp]: 75: You have set rlist larger than the interaction cut-off, but you also have 75: verlet-buffer-tolerance > 0. Will set rlist using 75: verlet-buffer-tolerance. 75: 75: 75: Generated 3 of the 3 non-bonded parameter combinations 75: 75: Generated 3 of the 3 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Setting gen_seed to -1415063559 75: 75: Velocities were taken from a Maxwell distribution at 298 K 75: 75: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Setting the LD random seed to -177342491 75: 75: Generated 3 of the 3 non-bonded parameter combinations 75: 75: Generated 3 of the 3 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Setting gen_seed to 2104490471 75: 75: Velocities were taken from a Maxwell distribution at 278 K 75: 75: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Generating 1-4 interactions: fudge = 0.5 75: Number of degrees of freedom in T-Coupling group System is 9.00 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: There were 2 NOTEs 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2_input.mdp]: 75: You have set rlist larger than the interaction cut-off, but you also have 75: verlet-buffer-tolerance > 0. Will set rlist using 75: verlet-buffer-tolerance. 75: 75: Generating 1-4 interactions: fudge = 0.5 75: Number of degrees of freedom in T-Coupling group System is 9.00 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: There were 2 NOTEs 75: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 75: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 75: 75: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 75: 75: This is simulation 1 out of 2 running as a composite GROMACS 75: multi-simulation job. Setup for this simulation: 75: This is simulation 0 out of 2 running as a composite GROMACS 75: multi-simulation job. Setup for this simulation: 75: 75: Using 2 MPI processes 75: 75: Using 2 MPI processes 75: Using 1 OpenMP thread per MPI process 75: 75: Using 1 OpenMP thread per MPI process 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'spc2' 75: 2 steps, 0.0 ps. 75: starting mdrun 'spc2' 75: 2 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 1.1%. 75: The balanceable part of the MD step is 0%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.0%. 75: 75: 75: NOTE: 27 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 17.7%. 75: The balanceable part of the MD step is 0%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.0%. 75: 75: 75: NOTE: 36 % of the run time was spent in domain decomposition, 75: 0 % of the run time was spent in pair search, 75: you might want to increase nstlist (this has no effect on accuracy) 75: 75: NOTE: 27 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: 75: You have set rlist larger than the interaction cut-off, but you also have 75: verlet-buffer-tolerance > 0. Will set rlist using 75: verlet-buffer-tolerance. 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: We recommend using the C-rescale barostat instead. 75: 75: Generating 1-4 interactions: fudge = 0.5 75: Number of degrees of freedom in T-Coupling group System is 9.00 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: There were 2 NOTEs 75: 75: There was 1 WARNING 75: [ OK ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/2 (96 ms) 75: [ RUN ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/3 75: Setting the LD random seed to 519975634 75: 75: Generated 3 of the 3 non-bonded parameter combinations 75: 75: Generated 3 of the 3 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Setting gen_seed to -8524801 75: 75: Velocities were taken from a Maxwell distribution at 278 K 75: 75: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: 75: You have set rlist larger than the interaction cut-off, but you also have 75: verlet-buffer-tolerance > 0. Will set rlist using 75: verlet-buffer-tolerance. 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: We recommend using the C-rescale barostat instead. 75: 75: Setting the LD random seed to 1040185047 75: 75: Generated 3 of the 3 non-bonded parameter combinations 75: 75: Generated 3 of the 3 1-4 parameter combinations 75: 75: Generating 1-4 interactions: fudge = 0.5 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Setting gen_seed to -95947541 75: 75: Velocities were taken from a Maxwell distribution at 298 K 75: Number of degrees of freedom in T-Coupling group System is 9.00 75: 75: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: There were 2 NOTEs 75: 75: There was 1 WARNING 75: 75: This run will generate roughly 0 Mb of data 75: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 75: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 75: 75: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 75: 75: This is simulation 0 out of 2 running as a composite GROMACS 75: multi-simulation job. Setup for this simulation: 75: 75: Using 2 MPI processes 75: This is simulation 1 out of 2 running as a composite GROMACS 75: multi-simulation job. Setup for this simulation: 75: 75: Using 2 MPI processes 75: Using 1 OpenMP thread per MPI process 75: 75: Using 1 OpenMP thread per MPI process 75: 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'spc2' 75: starting mdrun 'spc2' 75: 2 steps, 0.0 ps. 75: 2 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 16.6%. 75: The balanceable part of the MD step is 9%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 1.5%. 75: 75: 75: NOTE: 49 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 18.5%. 75: The balanceable part of the MD step is 4%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.8%. 75: 75: 75: NOTE: 49 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: [ OK ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/3 (140 ms) 75: [----------] 4 tests from WithDifferentControlVariables/ReplicaExchangeEnsembleTest (900 ms total) 75: 75: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest 75: [ RUN ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 75: You have set rlist larger than the interaction cut-off, but you also have 75: verlet-buffer-tolerance > 0. Will set rlist using 75: verlet-buffer-tolerance. 75: 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 75: You have set rlist larger than the interaction cut-off, but you also have 75: verlet-buffer-tolerance > 0. Will set rlist using 75: verlet-buffer-tolerance. 75: 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 75: You have set rlist larger than the interaction cut-off, but you also have 75: verlet-buffer-tolerance > 0. Will set rlist using 75: verlet-buffer-tolerance. 75: 75: Generating 1-4 interactions: fudge = 0.5 75: Number of degrees of freedom in T-Coupling group System is 9.00 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: There were 2 NOTEs 75: Generating 1-4 interactions: fudge = 0.5 75: Number of degrees of freedom in T-Coupling group System is 9.00 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: There were 2 NOTEs 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 75: You have set rlist larger than the interaction cut-off, but you also have 75: verlet-buffer-tolerance > 0. Will set rlist using 75: verlet-buffer-tolerance. 75: 75: Setting the LD random seed to -144203778 75: 75: Generated 3 of the 3 non-bonded parameter combinations 75: 75: Generated 3 of the 3 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Setting gen_seed to -580403458 75: 75: Velocities were taken from a Maxwell distribution at 298 K 75: 75: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Setting the LD random seed to -268966408 75: Setting the LD random seed to -372703489 75: 75: Generated 3 of the 3 non-bonded parameter combinations 75: 75: Generated 3 of the 3 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Setting gen_seed to -2233866 75: 75: Velocities were taken from a Maxwell distribution at 288 K 75: 75: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Setting the LD random seed to -4227489 75: 75: Generated 3 of the 3 non-bonded parameter combinations 75: Generating 1-4 interactions: fudge = 0.5 75: Number of degrees of freedom in T-Coupling group System is 9.00 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: There were 2 NOTEs 75: 75: Generated 3 of the 3 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Setting gen_seed to -546441249 75: 75: Velocities were taken from a Maxwell distribution at 278 K 75: 75: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Generated 3 of the 3 non-bonded parameter combinations 75: 75: Generated 3 of the 3 1-4 parameter combinations 75: Generating 1-4 interactions: fudge = 0.5 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Setting gen_seed to -33571875 75: 75: Velocities were taken from a Maxwell distribution at 268 K 75: 75: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Number of degrees of freedom in T-Coupling group System is 9.00 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: There were 2 NOTEs 75: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 75: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_ReplicaExcReading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: hangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 75: 75: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 75: 75: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 75: 75: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 75: 75: This is simulation 0 out of 4 running as a composite GROMACS 75: multi-simulation job. Setup for this simulation: 75: 75: Using 1 MPI process 75: This is simulation 1 out of 4 running as a composite GROMACS 75: multi-simulation job. Setup for this simulation: 75: 75: Using 1 MPI process 75: This is simulation 3 out of 4 running as a composite GROMACS 75: multi-simulation job. Setup for this simulation: 75: 75: Using 1 MPI process 75: Using 1 OpenMP thread 75: 75: This is simulation 2 out of 4 running as a composite GROMACS 75: multi-simulation job. Setup for this simulation: 75: 75: Using 1 MPI process 75: Using 1 OpenMP thread 75: 75: Using 1 OpenMP thread 75: 75: Using 1 OpenMP thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'spc2' 75: 100 steps, 0.1 ps. 75: starting mdrun 'spc2' 75: 100 steps, 0.1 ps. 75: starting mdrun 'spc2' 75: 100 steps, 0.1 ps. 75: starting mdrun 'spc2' 75: 100 steps, 0.1 ps. 75: 75: Step 1: Run time exceeded 0.000 hours, will terminate the run within 400 steps 75: 75: Step 1: Run time exceeded 0.000 hours, will terminate the run within 400 steps 75: 75: Step 1: Run time exceeded 0.000 hours, will terminate the run within 400 steps 75: 75: Step 2: Run time exceeded 0.000 hours, will terminate the run within 400 steps 75: 75: Writing final coordinates. 75: 75: Writing final coordinates. 75: 75: Writing final coordinates. 75: 75: Writing final coordinates. 75: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 75: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 75: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 75: 75: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 75: Changing nstlist from 10 to 25, rlist from 0.737 to 0.812 75: 75: Overriding nsteps with value passed on the command line: 2 steps, 0.002 psOverriding nsteps with value passed on the command line: 2 steps, 0.002 ps 75: 75: Changing nstlist from 10 to 25, rlist from 0.737 to 0.812 75: 75: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 75: 75: 75: This is simulation 2 out of 4 running as a composite GROMACS 75: multi-simulation job. Setup for this simulation: 75: 75: Using 1 MPI process 75: 75: This is simulation 0 out of 4 running as a composite GROMACS 75: multi-simulation job. Setup for this simulation: 75: 75: Using 1 MPI process 75: 75: This is simulation 1 out of 4 running as a composite GROMACS 75: multi-simulation job. Setup for this simulation: 75: 75: Using 1 MPI process 75: 75: This is simulation 3 out of 4 running as a composite GROMACS 75: multi-simulation job. Setup for this simulation: 75: 75: Using 1 MPI process 75: Using 1 OpenMP thread Using 1 OpenMP thread 75: 75: 75: 75: Using 1 OpenMP thread Using 1 OpenMP thread 75: 75: 75: 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'spc2' 75: starting mdrun 'spc2' 75: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). 75: starting mdrun 'spc2' 75: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). 75: starting mdrun 'spc2' 75: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). 75: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). 75: 75: Writing final coordinates. 75: 75: Writing final coordinates. 75: 75: Writing final coordinates. 75: 75: Writing final coordinates. 75: [ OK ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (1709 ms) 75: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest (1729 ms total) 75: 75: [----------] Global test environment tear-down 75: [==========] 5 tests from 2 test suites ran. (2899 ms total) 75: [ PASSED ] 5 tests. 75/91 Test #75: MdrunMultiSimReplexTests ..................... Passed 3.38 sec test 76 Start 76: MdrunMultiSimReplexEquivalenceTests 76: Test command: /usr/bin/mpiexec "-n" "4" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-multisim-replex-equivalence-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunMultiSimReplexEquivalenceTests.xml" 76: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 76: Test timeout computed to be: 600 76: [==========] Running 10 tests from 2 test suites. 76: [----------] Global test environment set-up. 76: [----------] 8 tests from LF/ReplicaExchangeTest 76: [ RUN ] LF/ReplicaExchangeTest.Works/md_Vrescale_Crescale_4Ranks_1RanksPerSim_s 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 298 K 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 288 K 76: 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 2 NOTEs 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 2 NOTEs 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 278 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 2 NOTEs 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 268 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 2 NOTEs 76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: This is simulation 0 out of 4 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 1 MPI process 76: This is simulation 1 out of 4 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 1 MPI process 76: This is simulation 3 out of 4 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 1 MPI process 76: This is simulation 2 out of 4 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 1 MPI process 76: Using 1 OpenMP thread 76: 76: Using 1 OpenMP thread 76: 76: Using 1 OpenMP thread 76: 76: Using 1 OpenMP thread 76: 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Writing final coordinates. 76: 76: Writing final coordinates. 76: 76: Writing final coordinates. 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 trr version: GMX_trn_file (single precision) 76: 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: [ OK ] LF/ReplicaExchangeTest.Works/md_Vrescale_Crescale_4Ranks_1RanksPerSim_s (1020 ms) 76: [ RUN ] LF/ReplicaExchangeTest.Works/md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are generating velocities so I am assuming you are equilibrating a 76: system. You are using Parrinello-Rahman pressure coupling, but this can 76: be unstable for equilibration. If your system crashes, try equilibrating 76: first with Berendsen pressure coupling. If you are not equilibrating the 76: system, you can probably ignore this warning. 76: 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are generating velocities so I am assuming you are equilibrating a 76: system. You are using Parrinello-Rahman pressure coupling, but this can 76: be unstable for equilibration. If your system crashes, try equilibrating 76: first with Berendsen pressure coupling. If you are not equilibrating the 76: system, you can probably ignore this warning. 76: 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are generating velocities so I am assuming you are equilibrating a 76: system. You are using Parrinello-Rahman pressure coupling, but this can 76: be unstable for equilibration. If your system crashes, try equilibrating 76: first with Berendsen pressure coupling. If you are not equilibrating the 76: system, you can probably ignore this warning. 76: 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are generating velocities so I am assuming you are equilibrating a 76: system. You are using Parrinello-Rahman pressure coupling, but this can 76: be unstable for equilibration. If your system crashes, try equilibrating 76: first with Berendsen pressure coupling. If you are not equilibrating the 76: system, you can probably ignore this warning. 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: Generating 1-4 interactions: fudge = 0.5 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 298 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 2 NOTEs 76: 76: There was 1 WARNING 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 278 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 2 NOTEs 76: 76: There was 1 WARNING 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 268 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 2 NOTEs 76: 76: There was 1 WARNING 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 288 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 2 NOTEs 76: 76: There was 1 WARNING 76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchanReading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: geTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: This is simulation 1 out of 4 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 1 MPI process 76: This is simulation 2 out of 4 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 1 MPI process 76: This is simulation 0 out of 4 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: This is simulation 3 out of 4 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 1 MPI process 76: 76: Using 1 MPI process 76: Using 1 OpenMP thread 76: 76: Using 1 OpenMP thread 76: 76: Using 1 OpenMP thread Using 1 OpenMP thread 76: 76: 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Writing final coordinates. 76: 76: Writing final coordinates. 76: 76: Writing final coordinates. 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: [ OK ] LF/ReplicaExchangeTest.Works/md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s (630 ms) 76: [ RUN ] LF/ReplicaExchangeTest.Works/md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 76: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 76: 1 76: 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 76: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 76: 1 76: 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 76: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 76: 1 76: 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 76: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 76: 1 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 278 K 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 268 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 3 NOTEs 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 298 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 3 NOTEs 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 288 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchanReading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: geTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: This is simulation 0 out of 4 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: This is simulation 1 out of 4 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 1 MPI process 76: This is simulation 3 out of 4 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 1 MPI process 76: This is simulation 2 out of 4 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 1 MPI process 76: 76: Using 1 MPI process 76: Using 1 OpenMP thread 76: 76: Using 1 OpenMP thread 76: 76: Using 1 OpenMP thread 76: 76: Using 1 OpenMP thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Writing final coordinates. 76: 76: Writing final coordinates. 76: 76: Writing final coordinates. 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 76: 0.016 Last energy frame read 16 time 0.016 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time [ OK ] LF/ReplicaExchangeTest.Works/md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s (498 ms) 76: [ RUN ] LF/ReplicaExchangeTest.Works/md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 76: 1 76: 76: 76: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are generating velocities so I am assuming you are equilibrating a 76: system. You are using Parrinello-Rahman pressure coupling, but this can 76: be unstable for equilibration. If your system crashes, try equilibrating 76: first with Berendsen pressure coupling. If you are not equilibrating the 76: system, you can probably ignore this warning. 76: 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 76: 1 76: 76: 76: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are generating velocities so I am assuming you are equilibrating a 76: system. You are using Parrinello-Rahman pressure coupling, but this can 76: be unstable for equilibration. If your system crashes, try equilibrating 76: first with Berendsen pressure coupling. If you are not equilibrating the 76: system, you can probably ignore this warning. 76: 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 76: 1 76: 76: 76: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are generating velocities so I am assuming you are equilibrating a 76: system. You are using Parrinello-Rahman pressure coupling, but this can 76: be unstable for equilibration. If your system crashes, try equilibrating 76: first with Berendsen pressure coupling. If you are not equilibrating the 76: system, you can probably ignore this warning. 76: 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 76: 1 76: 76: 76: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are generating velocities so I am assuming you are equilibrating a 76: system. You are using Parrinello-Rahman pressure coupling, but this can 76: be unstable for equilibration. If your system crashes, try equilibrating 76: first with Berendsen pressure coupling. If you are not equilibrating the 76: system, you can probably ignore this warning. 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: Generating 1-4 interactions: fudge = 0.5 76: Generating 1-4 interactions: fudge = 0.5 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 298 K 76: 76: Velocities were taken from a Maxwell distribution at 288 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: 76: There was 1 WARNING 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 268 K 76: 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: 76: There was 1 WARNING 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 3 NOTEs 76: 76: There was 1 WARNING 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 278 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: 76: There was 1 WARNING 76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: This is simulation 2 out of 4 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 1 MPI process 76: This is simulation 0 out of 4 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 1 MPI process 76: This is simulation 3 out of 4 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 1 MPI process 76: This is simulation 1 out of 4 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 1 MPI process 76: Using 1 OpenMP thread 76: 76: Using 1 OpenMP thread 76: 76: Using 1 OpenMP thread 76: 76: Using 1 OpenMP thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: starting mdrun 'spc2' 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Writing final coordinates. 76: 76: Writing final coordinates. 76: 76: Writing final coordinates. 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: [ OK ] LF/ReplicaExchangeTest.Works/md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s (470 ms) 76: [ RUN ] LF/ReplicaExchangeTest.Works/md_Vrescale_Crescale_4Ranks_2RanksPerSim_s 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 298 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 2 NOTEs 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 278 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 2 NOTEs 76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: This is simulation 0 out of 2 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: This is simulation 1 out of 2 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 2 MPI processes 76: 76: Using 2 MPI processes 76: Using 1 OpenMP thread per MPI processUsing 1 OpenMP thread per MPI process 76: 76: 76: 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Writing final coordinates. 76: 76: 76: Dynamic load balancing report: 76: DLB was off during the run due to low measured imbalance. 76: Average load imbalance: 0.5%. 76: The balanceable part of the MD step is 44%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 0.2%. 76: 76: 76: 76: Dynamic load balancing report: 76: DLB was off during the run due to low measured imbalance. 76: Average load imbalance: 1.0%. 76: The balanceable part of the MD step is 40%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 0.4%. 76: 76: 76: NOTE: 5 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: [ OK ] LF/ReplicaExchangeTest.Works/md_Vrescale_Crescale_4Ranks_2RanksPerSim_s (348 ms) 76: [ RUN ] LF/ReplicaExchangeTest.Works/md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 76: You are generating velocities so I am assuming you are equilibrating a 76: system. You are using Parrinello-Rahman pressure coupling, but this can 76: be unstable for equilibration. If your system crashes, try equilibrating 76: first with Berendsen pressure coupling. If you are not equilibrating the 76: system, you can probably ignore this warning. 76: 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 76: You are generating velocities so I am assuming you are equilibrating a 76: system. You are using Parrinello-Rahman pressure coupling, but this can 76: be unstable for equilibration. If your system crashes, try equilibrating 76: first with Berendsen pressure coupling. If you are not equilibrating the 76: system, you can probably ignore this warning. 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 278 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 2 NOTEs 76: 76: There was 1 WARNING 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 298 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 2 NOTEs 76: 76: There was 1 WARNING 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: This is simulation 1 out of 2 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 2 MPI processes 76: This is simulation 0 out of 2 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 2 MPI processes 76: Using 1 OpenMP thread per MPI process 76: 76: Using 1 OpenMP thread per MPI process 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Writing final coordinates. 76: 76: 76: Dynamic load balancing report: 76: DLB was off during the run due to low measured imbalance. 76: Average load imbalance: 1.0%. 76: The balanceable part of the MD step is 1%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 0.0%. 76: 76: 76: 76: Dynamic load balancing report: 76: DLB was off during the run due to low measured imbalance. 76: Average load imbalance: 0.5%. 76: The balanceable part of the MD step is 2%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 0.0%. 76: 76: 76: NOTE: 28 % of the run time was spent in domain decomposition, 76: 0 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: NOTE: 12 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: [ OK ] LF/ReplicaExchangeTest.Works/md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s (659 ms) 76: [ RUN ] LF/ReplicaExchangeTest.Works/md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 76: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 76: 1 76: 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 76: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 76: 1 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 278 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 298 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: 76: This run will generate roughly 0 Mb of data 76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: This is simulation 0 out of 2 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 2 MPI processes 76: This is simulation 1 out of 2 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 2 MPI processes 76: Using 1 OpenMP thread per MPI process 76: 76: Using 1 OpenMP thread per MPI process 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Writing final coordinates. 76: 76: 76: Dynamic load balancing report: 76: DLB was off during the run due to low measured imbalance. 76: Average load imbalance: 1.4%. 76: The balanceable part of the MD step is 42%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 0.6%. 76: 76: 76: 76: Dynamic load balancing report: 76: DLB was off during the run due to low measured imbalance. 76: Average load imbalance: 1.0%. 76: The balanceable part of the MD step is 28%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 0.3%. 76: 76: 76: NOTE: 6 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: [ OK ] LF/ReplicaExchangeTest.Works/md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s (447 ms) 76: [ RUN ] LF/ReplicaExchangeTest.Works/md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 76: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 76: 1 76: 76: 76: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 76: You are generating velocities so I am assuming you are equilibrating a 76: system. You are using Parrinello-Rahman pressure coupling, but this can 76: be unstable for equilibration. If your system crashes, try equilibrating 76: first with Berendsen pressure coupling. If you are not equilibrating the 76: system, you can probably ignore this warning. 76: 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 76: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 76: 1 76: 76: 76: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 76: You are generating velocities so I am assuming you are equilibrating a 76: system. You are using Parrinello-Rahman pressure coupling, but this can 76: be unstable for equilibration. If your system crashes, try equilibrating 76: first with Berendsen pressure coupling. If you are not equilibrating the 76: system, you can probably ignore this warning. 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 278 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 3 NOTEs 76: 76: There was 1 WARNING 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 298 K 76: 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: 76: There was 1 WARNING 76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: This is simulation 0 out of 2 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 2 MPI processes 76: Using 1 OpenMP thread per MPI process 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: This is simulation 1 out of 2 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 2 MPI processes 76: Using 1 OpenMP thread per MPI process 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: 76: Dynamic load balancing report: 76: DLB was off during the run due to low measured imbalance. 76: Average load imbalance: 1.5%. 76: The balanceable part of the MD step is 45%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 0.7%. 76: 76: 76: Writing final coordinates. 76: 76: 76: Dynamic load balancing report: 76: DLB was off during the run due to low measured imbalance. 76: Average load imbalance: 1.7%. 76: The balanceable part of the MD step is 46%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 0.8%. 76: 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: [ OK ] LF/ReplicaExchangeTest.Works/md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s (515 ms) 76: [----------] 8 tests from LF/ReplicaExchangeTest (4660 ms total) 76: 76: [----------] 2 tests from VV/ReplicaExchangeTest 76: [ RUN ] VV/ReplicaExchangeTest.Works/mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 278 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 2 NOTEs 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 288 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 2 NOTEs 76: 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 268 K 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 298 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 2 NOTEs 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 2 NOTEs 76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: This is simulation 0 out of 4 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: This is simulation 2 out of 4 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 1 MPI process 76: 76: Using 1 MPI process 76: This is simulation 1 out of 4 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 1 MPI process 76: This is simulation 3 out of 4 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 1 MPI process 76: Using 1 OpenMP thread 76: 76: Using 1 OpenMP thread Using 1 OpenMP thread 76: 76: 76: 76: Using 1 OpenMP thread 76: 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Writing final coordinates. 76: 76: Writing final coordinates. 76: 76: Writing final coordinates. 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: [ OK ] VV/ReplicaExchangeTest.Works/mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s (836 ms) 76: [ RUN ] VV/ReplicaExchangeTest.Works/mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 278 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 2 NOTEs 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 298 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 2 NOTEs 76: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: This is simulation 0 out of 2 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 2 MPI processes 76: This is simulation 1 out of 2 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 2 MPI processes 76: Using 1 OpenMP thread per MPI process 76: 76: Using 1 OpenMP thread per MPI process 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: 76: Dynamic load balancing report: 76: DLB was off during the run due to low measured imbalance. 76: Average load imbalance: 5.1%. 76: The balanceable part of the MD step is 2%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 0.1%. 76: 76: 76: NOTE: 19 % of the run time was spent in domain decomposition, 76: 0 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Writing final coordinates. 76: 76: 76: Dynamic load balancing report: 76: DLB was turned on during the run due to measured imbalance. 76: Average load imbalance: 20.2%. 76: The balanceable part of the MD step is 11%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 2.3%. 76: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 76: 76: 76: NOTE: 9 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: [ OK ] VV/ReplicaExchangeTest.Works/mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s (729 ms) 76: [----------] 2 tests from VV/ReplicaExchangeTest (1588 ms total) 76: 76: [----------] Global test environment tear-down 76: [==========] 10 tests from 2 test suites ran. (6501 ms total) 76: [ PASSED ] 10 tests. 76/91 Test #76: MdrunMultiSimReplexEquivalenceTests .......... Passed 7.05 sec test 77 Start 77: MdrunMpi1RankPmeTests 77: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-mpi-pme-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunMpi1RankPmeTests.xml" 77: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 77: Test timeout computed to be: 600 77: [==========] Running 19 tests from 1 test suite. 77: [----------] Global test environment set-up. 77: [----------] 19 tests from ReproducesEnergies/PmeTest 77: Setting the LD random seed to -335806535 77: 77: Generated 8 of the 10 non-bonded parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'Methanol' 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group rest is 12.00 77: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 77: 77: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 77: 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 77: NVE simulation: will use the initial temperature of 1046.791 K for 77: determining the Verlet buffer size 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: Calculating fourier grid dimensions for X Y Z 77: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 77: 77: Estimate for the relative computational load of the PME mesh part: 1.00 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 77: The optimal PME mesh load for parallel simulations is below 0.5 77: and for highly parallel simulations between 0.25 and 0.33, 77: for higher performance, increase the cut-off and the PME grid spacing. 77: 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: There were 2 NOTEs 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 77: For a correct single-point energy evaluation with nsteps = 0, use 77: continuation = yes to avoid constraining the input coordinates. 77: 77: Setting the LD random seed to 939386511 77: 77: Generated 8 of the 10 non-bonded parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'Methanol' 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Searching the wall atom type(s) 77: Number of degrees of freedom in T-Coupling group rest is 13.00 77: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 77: 77: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 77: NVE simulation: will use the initial temperature of 966.268 K for 77: determining the Verlet buffer size 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: Calculating fourier grid dimensions for X Y Z 77: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 77: The optimal PME mesh load for parallel simulations is below 0.5 77: and for highly parallel simulations between 0.25 and 0.33, 77: for higher performance, increase the cut-off and the PME grid spacing. 77: 77: 77: 77: Estimate for the relative computational load of the PME mesh part: 1.00 77: 77: This run will generate roughly 0 Mb of data 77: 77: There were 3 NOTEs 77: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu 77: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI process 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc-and-methanol' 77: 20 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.099 0.049 199.8 77: (ns/day) (hour/ns) 77: Performance: 36.725 0.654 77: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_0_pme_cpu.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI process 77: Using 2 OpenMP threads 77: 77: [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu (361 ms) 77: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc-and-methanol' 77: 20 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.089 0.045 199.8 77: (ns/day) (hour/ns) 77: Performance: 40.764 0.589 77: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_0_pme_auto.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto (74 ms) 77: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 77: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 77: Test is being skipped because: 77: it targets GPU execution, but no compatible devices were detected 77: PME GPU does not support: 77: Non-GPU build of GROMACS. 77: 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 77: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 77: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 77: Test is being skipped because: 77: it targets GPU execution, but no compatible devices were detected 77: PME GPU does not support: 77: Non-GPU build of GROMACS. 77: 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 77: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto 77: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 77: Test is being skipped because: 77: it targets GPU execution, but no compatible devices were detected 77: PME GPU does not support: 77: Non-GPU build of GROMACS. 77: 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto (0 ms) 77: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu 77: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI process 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc-and-methanol' 77: 0 steps, 0.0 ps. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.002 0.001 192.0 77: (ns/day) (hour/ns) 77: Performance: 75.450 0.318 77: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_R[ OK ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu (1092 ms) 77: uns_with_walls_mdrun_notunepme_npme_0_pme_cpu.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 77: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 77: Test is being skipped because: 77: it targets GPU execution, but no compatible devices were detected 77: PME GPU does not support: 77: Non-GPU build of GROMACS. 77: 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 77: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 77: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 77: Test is being skipped because: 77: it targets GPU execution, but no compatible devices were detected 77: PME GPU does not support: 77: Non-GPU build of GROMACS. 77: 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 77: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu 77: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 77: Test is being skipped because: 77: it targets using PME rank(s) but the simulation is using only one rank 77: 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu (0 ms) 77: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto 77: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 77: Test is being skipped because: 77: it targets using PME rank(s) but the simulation is using only one rank 77: 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto (0 ms) 77: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 77: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 77: Test is being skipped because: 77: it targets using PME rank(s) but the simulation is using only one rank 77: it targets GPU execution, but no compatible devices were detected 77: PME GPU does not support: 77: Non-GPU build of GROMACS. 77: 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu (0 ms) 77: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 77: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 77: Test is being skipped because: 77: it targets using PME rank(s) but the simulation is using only one rank 77: it targets GPU execution, but no compatible devices were detected 77: PME GPU does not support: 77: Non-GPU build of GROMACS. 77: 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu (0 ms) 77: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto 77: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 77: Test is being skipped because: 77: it targets using PME rank(s) but the simulation is using only one rank 77: it targets GPU execution, but no compatible devices were detected 77: PME GPU does not support: 77: Non-GPU build of GROMACS. 77: 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto (0 ms) 77: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu 77: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 77: Test is being skipped because: 77: it targets using PME rank(s) but the simulation is using only one rank 77: 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu (0 ms) 77: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 77: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 77: Test is being skipped because: 77: it targets using PME rank(s) but the simulation is using only one rank 77: it targets GPU execution, but no compatible devices were detected 77: PME GPU does not support: 77: Non-GPU build of GROMACS. 77: 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu (0 ms) 77: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 77: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 77: Test is being skipped because: 77: it targets using PME rank(s) but the simulation is using only one rank 77: it targets GPU execution, but no compatible devices were detected 77: PME GPU does not support: 77: Non-GPU build of GROMACS. 77: 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu (0 ms) 77: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu 77: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI process 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc-and-methanol' 77: 20 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.138 0.069 199.9 77: (ns/day) (hour/ns) 77: Performance: 26.251 0.914 77: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_tunepme_npme_0_pme_cpu.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu (77 ms) 77: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu 77: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 77: Test is being skipped because: 77: it targets GPU execution, but no compatible devices were detected 77: PME GPU does not support: 77: Non-GPU build of GROMACS. 77: 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 77: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu 77: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 77: Test is being skipped because: 77: it targets GPU execution, but no compatible devices were detected 77: PME GPU does not support: 77: Non-GPU build of GROMACS. 77: 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 77: [----------] 19 tests from ReproducesEnergies/PmeTest (1618 ms total) 77: 77: [----------] Global test environment tear-down 77: [==========] 19 tests from 1 test suite ran. (1650 ms total) 77: [ PASSED ] 4 tests. 77: [ SKIPPED ] 15 tests, listed below: 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu 77/91 Test #77: MdrunMpi1RankPmeTests ........................ Passed 2.10 sec test 78 Start 78: MdrunMpi2RankPmeTests 78: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-mpi-pme-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunMpi2RankPmeTests.xml" 78: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 78: Test timeout computed to be: 600 78: [==========] Running 19 tests from 1 test suite. 78: [----------] Global test environment set-up. 78: [----------] 19 tests from ReproducesEnergies/PmeTest 78: Setting the LD random seed to -100950273 78: 78: Generated 8 of the 10 non-bonded parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'Methanol' 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 78: 78: Estimate for the relative computational load of the PME mesh part: 1.00 78: 78: This run will generate roughly 0 Mb of data 78: Setting the LD random seed to -429920897 78: Number of degrees of freedom in T-Coupling group rest is 12.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 78: NVE simulation: will use the initial temperature of 1046.791 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 78: For a correct single-point energy evaluation with nsteps = 0, use 78: continuation = yes to avoid constraining the input coordinates. 78: 78: 78: Generated 8 of the 10 non-bonded parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'Methanol' 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Searching the wall atom type(s) 78: 78: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 78: 78: Estimate for the relative computational load of the PME mesh part: 1.00 78: 78: This run will generate roughly 0 Mb of data 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu 78: Number of degrees of freedom in T-Coupling group rest is 13.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 78: NVE simulation: will use the initial temperature of 966.268 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: There were 3 NOTEs 78: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI processes 78: Using 2 OpenMP threads per MPI process 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc-and-methanol' 78: 20 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: 78: Dynamic load balancing report: 78: DLB was turned on during the run due to measured imbalance. 78: Average load imbalance: 95.2%. 78: The balanceable part of the MD step is 6%, load imbalance is computed from this. 78: Part of the total run time spent waiting due to load imbalance: 5.7%. 78: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 78: 78: NOTE: 5.7 % of the available CPU time was lost due to load imbalance 78: in the domain decomposition. 78: You can consider manually changing the decomposition (option -dd); 78: e.g. by using fewer domains along the box dimension in which there is 78: considerable inhomogeneity in the simulated system. 78: 78: NOTE: 15 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: 78: Core t (s) Wall t (s) (%) 78: Time: 1.224 0.306 399.9 78: (ns/day) (hour/ns) 78: Performance: 5.928 4.048 78: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_0_pme_cpu.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI processes 78: Using 2 OpenMP threads per MPI process 78: 78: [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu (867 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc-and-methanol' 78: 20 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: 78: Dynamic load balancing report: 78: DLB was turned on during the run due to measured imbalance. 78: Average load imbalance: 92.5%. 78: The balanceable part of the MD step is 8%, load imbalance is computed from this. 78: Part of the total run time spent waiting due to load imbalance: 7.0%. 78: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 78: 78: NOTE: 7.0 % of the available CPU time was lost due to load imbalance 78: in the domain decomposition. 78: You can consider manually changing the decomposition (option -dd); 78: e.g. by using fewer domains along the box dimension in which there is 78: considerable inhomogeneity in the simulated system. 78: 78: NOTE: 13 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.625 0.156 399.9 78: (ns/day) (hour/ns) 78: Performance: 11.600 2.069 78: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_0_pme_auto.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto (170 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu (2 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu 78: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI processes 78: Using 2 OpenMP threads per MPI process 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc-and-methanol' 78: 0 steps, 0.0 ps. 78: 78: NOTE: 24 % of the run time was spent in domain decomposition, 78: 4 % of the run time was spent in pair search, 78: you might want to increase nstlist (this has no effect on accuracy) 78: 78: Core t (s) Wall t (s) (%) 78: Time: 1.552 0.396 391.8 78: (ns/day) (hour/ns) 78: Performance: 0.218 110.032 78: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls_mdrun_notunepme_npme_0_pme_cpu.edr as single precision energy file 78: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI processes 78: Using 2 OpenMP threads per MPI process 78: 78: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu (1662 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc-and-methanol' 78: 20 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 2.431 0.613 396.4 78: (ns/day) (hour/ns) 78: Performance: 2.958 8.113 78: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_1_pme_cpu.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI processes 78: Using 2 OpenMP threads per MPI process 78: 78: [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu (976 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc-and-methanol' 78: 20 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.170 0.043 398.9 78: (ns/day) (hour/ns) 78: Performance: 42.478 0.565 78: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_1_pme_auto.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI processes 78: Using 2 OpenMP threads per MPI process 78: 78: [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto (127 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc-and-methanol' 78: 0 steps, 0.0 ps. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.192 0.048 396.7 78: (ns/day) (hour/ns) 78: Performance: 1.785 13.446 78: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls_mdrun_notunepme_npme_1_pme_cpu.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu (584 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu 78: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI processes 78: Using 2 OpenMP threads per MPI process 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc-and-methanol' 78: 20 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: 78: Dynamic load balancing report: 78: DLB was turned on during the run due to measured imbalance. 78: Average load imbalance: 46.3%. 78: The balanceable part of the MD step is 11%, load imbalance is computed from this. 78: Part of the total run time spent waiting due to load imbalance: 5.3%. 78: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 78: 78: NOTE: 5.3 % of the available CPU time was lost due to load imbalance 78: in the domain decomposition. 78: You can consider manually changing the decomposition (option -dd); 78: e.g. by using fewer domains along the box dimension in which there is 78: considerable inhomogeneity in the simulated system. 78: 78: NOTE: 11 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: 78: Core t (s) Wall t (s) (%) 78: Time: 1.865 0.466 399.9 78: (ns/day) (hour/ns) 78: Performance: 3.891 6.169 78: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_tunepme_npme_0_pme_cpu.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu (502 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 78: [----------] 19 tests from ReproducesEnergies/PmeTest (4904 ms total) 78: 78: [----------] Global test environment tear-down 78: [==========] 19 tests from 1 test suite ran. (4982 ms total) 78: [ PASSED ] 7 tests. 78: [ SKIPPED ] 12 tests, listed below: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu 78/91 Test #78: MdrunMpi2RankPmeTests ........................ Passed 5.46 sec test 79 Start 79: MdrunCoordinationBasicTests1Rank 79: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-coordination-basic-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunCoordinationBasicTests1Rank.xml" 79: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 79: Test timeout computed to be: 1920 79: [==========] Running 1 test from 1 test suite. 79: [----------] Global test environment set-up. 79: [----------] 1 test from BasicPropagators/PeriodicActionsTest 79: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.024 0.024 99.9 79: (ns/day) (hour/ns) 79: Performance: 60.945 0.394 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.012 0.012 99.7 79: (ns/day) (hour/ns) 79: Performance: 124.693 0.192 79: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: COM removal frequency is set to (1). 79: Other settings require a global communication frequency of 4. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 4. 79: 79: 79: There were 5 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.011 99.7 79: (ns/day) (hour/ns) 79: Performance: 139.715 0.172 79: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: COM removal frequency is set to (1). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.010 99.7 79: (ns/day) (hour/ns) 79: Performance: 148.102 0.162 79: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: COM removal frequency is set to (1). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.010 99.6 79: (ns/day) (hour/ns) 79: Performance: 149.609 0.160 79: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: COM removal frequency is set to (1). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 4 NOTEs 79: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.011 0.011 99.7 79: (ns/day) (hour/ns) 79: Performance: 133.280 0.180 79: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 79: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (106 ms) 79: [----------] 1 test from BasicPropagators/PeriodicActionsTest (106 ms total) 79: 79: [----------] Global test environment tear-down 79: [==========] 1 test from 1 test suite ran. (148 ms total) 79: [ PASSED ] 1 test. 79/91 Test #79: MdrunCoordinationBasicTests1Rank ............. Passed 0.61 sec test 80 Start 80: MdrunCoordinationBasicTests2Ranks 80: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-coordination-basic-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunCoordinationBasicTests2Ranks.xml" 80: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 80: Test timeout computed to be: 1920 80: [==========] Running 1 test from 1 test suite. 80: [----------] Global test environment set-up. 80: [----------] 1 test from BasicPropagators/PeriodicActionsTest 80: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI processes 80: Using 1 OpenMP thread per MPI process 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 33.0%. 80: The balanceable part of the MD step is 53%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 17.5%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: NOTE: 17.5 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: You can consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 10 % of the run time was spent in domain decomposition, 80: 0 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 46 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.690 0.345 200.0 80: (ns/day) (hour/ns) 80: Performance: 4.258 5.636 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI processes 80: Using 1 OpenMP thread per MPI process 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 2.2%. 80: The balanceable part of the MD step is 51%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.1%. 80: 80: 80: NOTE: 62 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.019 0.009 199.3 80: (ns/day) (hour/ns) 80: Performance: 156.611 0.153 80: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: COM removal frequency is set to (1). 80: Other settings require a global communication frequency of 4. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 4. 80: 80: 80: There were 5 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI processes 80: Using 1 OpenMP thread per MPI process 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 2.0%. 80: The balanceable part of the MD step is 46%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.9%. 80: 80: 80: NOTE: 56 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.030 0.015 199.4 80: (ns/day) (hour/ns) 80: Performance: 97.184 0.247 80: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActOpened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: ionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: COM removal frequency is set to (1). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI processes 80: Using 1 OpenMP thread per MPI process 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 3.1%. 80: The balanceable part of the MD step is 43%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.3%. 80: 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.024 0.012 199.3 80: (ns/day) (hour/ns) 80: Performance: 122.864 0.195 80: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: COM removal frequency is set to (1). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI processes 80: Using 1 OpenMP thread per MPI process 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 3.0%. 80: The balanceable part of the MD step is 42%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.3%. 80: 80: 80: NOTE: 54 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.037 0.019 199.6 80: (ns/day) (hour/ns) 80: Performance: 78.204 0.307 80: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: COM removal frequency is set to (1). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI processes 80: Using 1 OpenMP thread per MPI process 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 4.0%. 80: The balanceable part of the MD step is 44%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.8%. 80: 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.021 0.010 199.3 80: (ns/day) (hour/ns) 80: Performance: 142.638 0.168 80: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 80: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (683 ms) 80: [----------] 1 test from BasicPropagators/PeriodicActionsTest (683 ms total) 80: 80: [----------] Global test environment tear-down 80: [==========] 1 test from 1 test suite ran. (767 ms total) 80: [ PASSED ] 1 test. 80/91 Test #80: MdrunCoordinationBasicTests2Ranks ............ Passed 1.26 sec test 81 Start 81: MdrunCoordinationCouplingTests1Rank 81: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-coordination-coupling-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunCoordinationCouplingTests1Rank.xml" 81: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 81: Test timeout computed to be: 1920 81: [==========] Running 25 tests from 1 test suite. 81: [----------] Global test environment set-up. 81: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.014 0.014 99.8 81: (ns/day) (hour/ns) 81: Performance: 104.553 0.230 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.008 0.008 99.6 81: (ns/day) (hour/ns) 81: Performance: 194.684 0.123 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 4. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 4. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.010 0.010 99.7 81: (ns/day) (hour/ns) 81: Performance: 147.598 0.163 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.017 0.017 99.7 81: (ns/day) (hour/ns) 81: Performance: 86.953 0.276 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.014 0.014 99.7 81: (ns/day) (hour/ns) 81: Performance: 104.671 0.229 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.016 0.016 99.7 81: (ns/day) (hour/ns) 81: Performance: 91.566 0.262 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (119 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.015 0.015 99.8 81: (ns/day) (hour/ns) 81: Performance: 97.489 0.246 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.013 0.013 99.7 81: (ns/day) (hour/ns) 81: Performance: 111.118 0.216 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: NOTE: 14 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.012 0.012 99.7 81: (ns/day) (hour/ns) 81: Performance: 119.470 0.201 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.021 0.021 99.8 81: (ns/day) (hour/ns) 81: Performance: 70.221 0.342 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.014 0.014 99.7 81: (ns/day) (hour/ns) 81: Performance: 107.806 0.223 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.020 0.020 99.9 81: (ns/day) (hour/ns) 81: Performance: 73.336 0.327 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (129 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.017 0.017 99.9 81: (ns/day) (hour/ns) 81: Performance: 87.311 0.275 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.014 0.014 99.7 81: (ns/day) (hour/ns) 81: Performance: 101.434 0.237 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.022 0.022 99.9 81: (ns/day) (hour/ns) 81: Performance: 67.576 0.355 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.212 0.212 100.0 81: (ns/day) (hour/ns) 81: Performance: 6.917 3.470 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.068 0.069 99.9 81: (ns/day) (hour/ns) 81: Performance: 21.435 1.120 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.045 0.045 99.9 81: (ns/day) (hour/ns) 81: Performance: 32.686 0.734 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (601 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.015 0.015 99.8 81: (ns/day) (hour/ns) 81: Performance: 96.021 0.250 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.014 0.014 99.8 81: (ns/day) (hour/ns) 81: Performance: 101.317 0.237 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.021 0.021 99.9 81: (ns/day) (hour/ns) 81: Performance: 69.827 0.344 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.024 0.024 99.8 81: (ns/day) (hour/ns) 81: Performance: 61.427 0.391 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.022 0.022 99.8 81: (ns/day) (hour/ns) 81: Performance: 65.416 0.367 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.030 0.031 99.9 81: (ns/day) (hour/ns) 81: Performance: 48.150 0.498 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (178 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.017 0.017 99.8 81: (ns/day) (hour/ns) 81: Performance: 85.464 0.281 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.011 0.011 99.4 81: (ns/day) (hour/ns) 81: Performance: 131.236 0.183 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.012 0.012 99.8 81: (ns/day) (hour/ns) 81: Performance: 120.611 0.199 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.023 0.023 99.8 81: (ns/day) (hour/ns) 81: Performance: 64.728 0.371 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.028 0.028 99.8 81: (ns/day) (hour/ns) 81: Performance: 52.850 0.454 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.022 0.022 99.8 81: (ns/day) (hour/ns) 81: Performance: 65.446 0.367 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (171 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.028 0.028 99.9 81: (ns/day) (hour/ns) 81: Performance: 52.200 0.460 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.057 0.057 99.9 81: (ns/day) (hour/ns) 81: Performance: 25.770 0.931 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.028 0.028 99.8 81: (ns/day) (hour/ns) 81: Performance: 52.922 0.453 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.018 0.018 99.8 81: (ns/day) (hour/ns) 81: Performance: 79.577 0.302 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.022 0.022 99.9 81: (ns/day) (hour/ns) 81: Performance: 66.323 0.362 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.020 0.020 99.9 81: (ns/day) (hour/ns) 81: Performance: 74.705 0.321 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (233 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.020 0.020 99.8 81: (ns/day) (hour/ns) 81: Performance: 72.862 0.329 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.015 0.015 99.6 81: (ns/day) (hour/ns) 81: Performance: 97.866 0.245 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.028 0.028 99.9 81: (ns/day) (hour/ns) 81: Performance: 51.982 0.462 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.027 0.027 99.9 81: (ns/day) (hour/ns) 81: Performance: 55.253 0.434 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.038 0.038 99.9 81: (ns/day) (hour/ns) 81: Performance: 38.175 0.629 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.017 0.017 99.8 81: (ns/day) (hour/ns) 81: Performance: 84.771 0.283 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (200 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.028 0.028 99.8 81: (ns/day) (hour/ns) 81: Performance: 52.348 0.458 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.017 0.017 99.8 81: (ns/day) (hour/ns) 81: Performance: 86.226 0.278 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.016 0.016 99.8 81: (ns/day) (hour/ns) 81: Performance: 90.641 0.265 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.016 0.016 99.8 81: (ns/day) (hour/ns) 81: Performance: 90.435 0.265 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.013 0.013 99.8 81: (ns/day) (hour/ns) 81: Performance: 116.137 0.207 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.021 0.021 99.8 81: (ns/day) (hour/ns) 81: Performance: 70.631 0.340 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (176 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.021 0.021 99.8 81: (ns/day) (hour/ns) 81: Performance: 68.672 0.349 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 3 NOTEs 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.011 0.011 99.7 81: (ns/day) (hour/ns) 81: Performance: 134.728 0.178 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: ionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActGenerated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.015 0.015 99.8 81: (ns/day) (hour/ns) 81: Performance: 94.888 0.253 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.026 0.026 99.8 81: (ns/day) (hour/ns) 81: Performance: 56.514 0.425 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.018 0.018 99.8 81: (ns/day) (hour/ns) 81: Performance: 82.769 0.290 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.023 0.023 99.8 81: (ns/day) (hour/ns) 81: Performance: 63.656 0.377 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (171 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.027 0.027 99.9 81: (ns/day) (hour/ns) 81: Performance: 54.889 0.437 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.007 0.007 99.6 81: (ns/day) (hour/ns) 81: Performance: 199.050 0.121 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.029 0.029 99.8 81: (ns/day) (hour/ns) 81: Performance: 50.550 0.475 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.025 0.025 99.8 81: (ns/day) (hour/ns) 81: Performance: 59.140 0.406 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.022 0.022 99.8 81: (ns/day) (hour/ns) 81: Performance: 67.891 0.354 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.021 0.021 99.8 81: (ns/day) (hour/ns) 81: Performance: 70.802 0.339 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (186 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.019 0.020 99.8 81: (ns/day) (hour/ns) 81: Performance: 75.256 0.319 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.011 0.011 99.8 81: (ns/day) (hour/ns) 81: Performance: 137.559 0.174 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.019 0.019 99.9 81: (ns/day) (hour/ns) 81: Performance: 76.961 0.312 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 3 NOTEs 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.021 0.021 99.8 81: (ns/day) (hour/ns) 81: Performance: 70.703 0.339 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 3 NOTEs 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.023 0.024 99.9 81: (ns/day) (hour/ns) 81: Performance: 62.419 0.384 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 3 NOTEs 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.027 0.027 99.8 81: (ns/day) (hour/ns) 81: Performance: 54.479 0.441 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (174 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.022 0.022 99.8 81: (ns/day) (hour/ns) 81: Performance: 67.454 0.356 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.013 0.013 99.8 81: (ns/day) (hour/ns) 81: Performance: 116.550 0.206 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.016 0.016 99.8 81: (ns/day) (hour/ns) 81: Performance: 92.307 0.260 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 3 NOTEs 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.024 0.024 99.9 81: (ns/day) (hour/ns) 81: Performance: 60.650 0.396 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.027 0.027 99.8 81: (ns/day) (hour/ns) 81: Performance: 54.238 0.442 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 3 NOTEs 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.024 0.024 99.9 81: (ns/day) (hour/ns) 81: Performance: 62.306 0.385 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (181 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.026 0.026 99.9 81: (ns/day) (hour/ns) 81: Performance: 55.696 0.431 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.013 0.013 99.8 81: (ns/day) (hour/ns) 81: Performance: 116.229 0.206 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 4. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 4. 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.007 0.007 99.7 81: (ns/day) (hour/ns) 81: Performance: 198.198 0.121 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.031 0.031 99.9 81: (ns/day) (hour/ns) 81: Performance: 47.924 0.501 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.023 0.023 99.9 81: (ns/day) (hour/ns) 81: Performance: 64.462 0.372 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.030 0.030 99.9 81: (ns/day) (hour/ns) 81: Performance: 48.365 0.496 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (170 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.018 0.018 99.9 81: (ns/day) (hour/ns) 81: Performance: 80.340 0.299 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.008 0.008 99.8 81: (ns/day) (hour/ns) 81: Performance: 188.075 0.128 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.022 0.022 99.9 81: (ns/day) (hour/ns) 81: Performance: 65.801 0.365 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.023 0.024 99.9 81: (ns/day) (hour/ns) 81: Performance: 62.490 0.384 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.025 0.025 99.9 81: (ns/day) (hour/ns) 81: Performance: 59.255 0.405 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.030 0.030 99.9 81: (ns/day) (hour/ns) 81: Performance: 49.384 0.486 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (170 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.020 0.020 99.9 81: (ns/day) (hour/ns) 81: Performance: 75.137 0.319 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.007 0.007 99.7 81: (ns/day) (hour/ns) 81: Performance: 211.755 0.113 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.014 0.014 99.7 81: (ns/day) (hour/ns) 81: Performance: 105.810 0.227 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.024 0.024 99.8 81: (ns/day) (hour/ns) 81: Performance: 61.101 0.393 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.023 0.023 99.9 81: (ns/day) (hour/ns) 81: Performance: 63.973 0.375 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.029 0.029 99.9 81: (ns/day) (hour/ns) 81: Performance: 51.160 0.469 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (174 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.025 0.025 99.8 81: (ns/day) (hour/ns) 81: Performance: 58.561 0.410 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.008 0.008 99.7 81: (ns/day) (hour/ns) 81: Performance: 191.364 0.125 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.007 0.007 99.7 81: (ns/day) (hour/ns) 81: Performance: 210.281 0.114 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.023 0.024 99.9 81: (ns/day) (hour/ns) 81: Performance: 62.452 0.384 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.022 0.022 99.9 81: (ns/day) (hour/ns) 81: Performance: 68.034 0.353 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.024 0.024 99.9 81: (ns/day) (hour/ns) 81: Performance: 61.657 0.389 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (173 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.030 0.030 99.8 81: (ns/day) (hour/ns) 81: Performance: 48.281 0.497 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.020 0.020 99.8 81: (ns/day) (hour/ns) 81: Performance: 74.497 0.322 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 4. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 4. 81: 81: 81: There were 4 NOTEs 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.016 0.016 99.8 81: (ns/day) (hour/ns) 81: Performance: 92.367 0.260 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.039 0.039 99.9 81: (ns/day) (hour/ns) 81: Performance: 37.267 0.644 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupli 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: ng_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.036 0.036 99.9 81: (ns/day) (hour/ns) 81: Performance: 41.158 0.583 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.024 0.024 99.9 81: (ns/day) (hour/ns) 81: Performance: 62.016 0.387 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (231 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: 81: This run will generate roughly 0 Mb of data 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.022 0.022 99.9 81: (ns/day) (hour/ns) 81: Performance: 65.979 0.364 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.019 0.019 99.8 81: (ns/day) (hour/ns) 81: Performance: 76.961 0.312 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.025 0.025 99.9 81: (ns/day) (hour/ns) 81: Performance: 59.063 0.406 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.043 0.043 99.9 81: (ns/day) (hour/ns) 81: Performance: 34.386 0.698 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupli 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: ng_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: 81: This run will generate roughly 0 Mb of data 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.031 0.031 99.9 81: (ns/day) (hour/ns) 81: Performance: 47.646 0.504 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.024 0.024 99.9 81: (ns/day) (hour/ns) 81: Performance: 60.275 0.398 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (201 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.027 0.027 99.9 81: (ns/day) (hour/ns) 81: Performance: 54.299 0.442 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.021 0.021 99.8 81: (ns/day) (hour/ns) 81: Performance: 69.788 0.344 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.024 0.024 99.9 81: (ns/day) (hour/ns) 81: Performance: 61.069 0.393 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.034 0.034 99.9 81: (ns/day) (hour/ns) 81: Performance: 43.496 0.552 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.033 0.033 99.8 81: (ns/day) (hour/ns) 81: Performance: 44.548 0.539 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.031 0.032 99.8 81: (ns/day) (hour/ns) 81: Performance: 46.605 0.515 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (196 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.017 0.017 99.8 81: (ns/day) (hour/ns) 81: Performance: 85.867 0.280 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.016 0.016 99.8 81: (ns/day) (hour/ns) 81: Performance: 92.218 0.260 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.013 0.013 99.8 81: (ns/day) (hour/ns) 81: Performance: 115.679 0.207 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.141 0.141 100.0 81: (ns/day) (hour/ns) 81: Performance: 10.392 2.309 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 3 NOTEs 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.029 0.029 99.8 81: (ns/day) (hour/ns) 81: Performance: 50.801 0.472 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.028 0.028 99.9 81: (ns/day) (hour/ns) 81: Performance: 53.115 0.452 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (310 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.018 0.018 99.8 81: (ns/day) (hour/ns) 81: Performance: 83.194 0.288 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.020 0.020 99.8 81: (ns/day) (hour/ns) 81: Performance: 73.157 0.328 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.028 0.028 99.8 81: (ns/day) (hour/ns) 81: Performance: 52.676 0.456 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.029 0.029 99.2 81: (ns/day) (hour/ns) 81: Performance: 50.119 0.479 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.036 0.036 99.9 81: (ns/day) (hour/ns) 81: Performance: 41.211 0.582 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.029 0.029 99.9 81: (ns/day) (hour/ns) 81: Performance: 51.459 0.466 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (209 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.025 0.025 99.7 81: (ns/day) (hour/ns) 81: Performance: 58.471 0.410 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.331 0.331 100.0 81: (ns/day) (hour/ns) 81: Performance: 4.441 5.404 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: There were 2 NOTEs 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.896 0.896 100.0 81: (ns/day) (hour/ns) 81: Performance: 1.639 14.643 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.840 0.840 100.0 81: (ns/day) (hour/ns) 81: Performance: 1.749 13.723 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.967 0.967 100.0 81: (ns/day) (hour/ns) 81: Performance: 1.518 15.806 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.684 0.684 100.0 81: (ns/day) (hour/ns) 81: Performance: 2.148 11.175 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (3903 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.682 0.682 100.0 81: (ns/day) (hour/ns) 81: Performance: 2.154 11.140 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: 81: There were 2 NOTEs 81: This run will generate roughly 0 Mb of data 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.010 0.010 99.7 81: (ns/day) (hour/ns) 81: Performance: 140.243 0.171 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 3 NOTEs 81: 81: This run will generate roughly 0 Mb of data 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.009 0.009 99.7 81: (ns/day) (hour/ns) 81: Performance: 155.112 0.155 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.014 0.014 99.6 81: (ns/day) (hour/ns) 81: Performance: 101.516 0.236 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.024 0.024 99.8 81: (ns/day) (hour/ns) 81: Performance: 61.371 0.391 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.019 0.019 99.7 81: (ns/day) (hour/ns) 81: Performance: 77.781 0.309 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (831 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: for current Trotter decomposition methods with vv, nsttcouple and 81: nstpcouple must be equal. Both have been reset to 81: min(nsttcouple,nstpcouple) = 2 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.021 0.022 99.7 81: (ns/day) (hour/ns) 81: Performance: 68.277 0.352 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: for current Trotter decomposition methods with vv, nsttcouple and 81: nstpcouple must be equal. Both have been reset to 81: min(nsttcouple,nstpcouple) = 2 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.107 0.107 99.9 81: (ns/day) (hour/ns) 81: Performance: 13.717 1.750 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: for current Trotter decomposition methods with vv, nsttcouple and 81: nstpcouple must be equal. Both have been reset to 81: min(nsttcouple,nstpcouple) = 2 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.020 0.021 99.8 81: (ns/day) (hour/ns) 81: Performance: 71.534 0.336 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: for current Trotter decomposition methods with vv, nsttcouple and 81: nstpcouple must be equal. Both have been reset to 81: min(nsttcouple,nstpcouple) = 2 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.026 0.026 99.8 81: (ns/day) (hour/ns) 81: Performance: 57.221 0.419 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: for current Trotter decomposition methods with vv, nsttcouple and 81: nstpcouple must be equal. Both have been reset to 81: min(nsttcouple,nstpcouple) = 2 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.028 0.028 99.9 81: (ns/day) (hour/ns) 81: Performance: 52.449 0.458 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: for current Trotter decomposition methods with vv, nsttcouple and 81: nstpcouple must be equal. Both have been reset to 81: min(nsttcouple,nstpcouple) = 2 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.032 0.032 99.8 81: (ns/day) (hour/ns) 81: Performance: 46.166 0.520 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (298 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.013 0.013 99.9 81: (ns/day) (hour/ns) 81: Performance: 112.035 0.214 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.021 0.021 99.9 81: (ns/day) (hour/ns) 81: Performance: 68.445 0.351 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.024 0.024 99.6 81: (ns/day) (hour/ns) 81: Performance: 61.217 0.392 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.027 0.028 99.9 81: (ns/day) (hour/ns) 81: Performance: 53.389 0.450 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.027 0.027 99.9 81: (ns/day) (hour/ns) 81: Performance: 54.008 0.444 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.063 0.063 99.9 81: (ns/day) (hour/ns) 81: Performance: 23.404 1.025 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (242 ms) 81: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (9642 ms total) 81: 81: [----------] Global test environment tear-down 81: [==========] 25 tests from 1 test suite ran. (9678 ms total) 81: [ PASSED ] 25 tests. 81/91 Test #81: MdrunCoordinationCouplingTests1Rank .......... Passed 10.15 sec test 82 Start 82: MdrunCoordinationCouplingTests2Ranks 82: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-coordination-coupling-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunCoordinationCouplingTests2Ranks.xml" 82: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 82: Test timeout computed to be: 1920 82: [==========] Running 25 tests from 1 test suite. 82: [----------] Global test environment set-up. 82: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: 82: There were 3 NOTEs 82: This run will generate roughly 0 Mb of data 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was turned on during the run due to measured imbalance. 82: Average load imbalance: 6.0%. 82: The balanceable part of the MD step is 50%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 3.0%. 82: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 82: 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.058 0.029 199.6 82: (ns/day) (hour/ns) 82: Performance: 50.748 0.473 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 2.4%. 82: The balanceable part of the MD step is 49%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.2%. 82: 82: 82: NOTE: 48 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.014 0.007 199.1 82: (ns/day) (hour/ns) 82: Performance: 206.437 0.116 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 4. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 4. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 4.1%. 82: The balanceable part of the MD step is 40%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.6%. 82: 82: 82: NOTE: 62 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.062 0.035 176.8 82: (ns/day) (hour/ns) 82: Performance: 41.845 0.574 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 6.9%. 82: The balanceable part of the MD step is 23%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.6%. 82: 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.036 0.018 199.3 82: (ns/day) (hour/ns) 82: Performance: 81.326 0.295 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: 82: This run will generate roughly 0 Mb of data 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.9%. 82: The balanceable part of the MD step is 36%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.7%. 82: 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.033 0.017 199.1 82: (ns/day) (hour/ns) 82: Performance: 87.673 0.274 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 2.8%. 82: The balanceable part of the MD step is 34%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.0%. 82: 82: 82: NOTE: 50 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.054 0.027 199.4 82: (ns/day) (hour/ns) 82: Performance: 54.716 0.439 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (213 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 68. 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.7%. 82: The balanceable part of the MD step is 42%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.3%. 82: 82: 82: NOTE: 61 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.056 0.034 165.5 82: (ns/day) (hour/ns) 82: Performance: 43.036 0.558 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.4%. 82: The balanceable part of the MD step is 46%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.6%. 82: 82: 82: NOTE: 50 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.031 0.016 199.0 82: (ns/day) (hour/ns) 82: Performance: 93.376 0.257 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 2.0%. 82: The balanceable part of the MD step is 42%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.8%. 82: 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE: 48 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.017 0.008 198.6 82: (ns/day) (hour/ns) 82: Performance: 174.965 0.137 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.5%. 82: The balanceable part of the MD step is 42%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.6%. 82: 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.020 0.010 198.8 82: (ns/day) (hour/ns) 82: Performance: 143.619 0.167 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.9%. 82: The balanceable part of the MD step is 40%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.8%. 82: 82: 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.026 0.013 199.0 82: (ns/day) (hour/ns) 82: Performance: 112.260 0.214 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 2.4%. 82: The balanceable part of the MD step is 25%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.6%. 82: 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.045 0.023 199.5 82: (ns/day) (hour/ns) 82: Performance: 65.018 0.369 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (175 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.4%. 82: The balanceable part of the MD step is 46%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.2%. 82: 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.023 0.012 198.6 82: (ns/day) (hour/ns) 82: Performance: 127.180 0.189 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was turned on during the run due to measured imbalance. 82: Average load imbalance: 8.8%. 82: The balanceable part of the MD step is 43%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 3.8%. 82: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 82: 82: 82: NOTE: 48 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.018 0.009 198.0 82: (ns/day) (hour/ns) 82: Performance: 165.563 0.145 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 82: Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.2%. 82: The balanceable part of the MD step is 43%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.5%. 82: 82: 82: NOTE: 58 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.039 0.019 199.4 82: (ns/day) (hour/ns) 82: Performance: 75.799 0.317 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 82: Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 82: Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 0 time 0.000 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 0 time 0.000 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Last energy frame read 4 time 0.016 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.6%. 82: The balanceable part of the MD step is 40%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.6%. 82: 82: 82: NOTE: 51 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.030 0.015 199.2 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 82: (ns/day) (hour/ns) 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 82: Performance: 97.666 0.246 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.3%. 82: The balanceable part of the MD step is 41%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.5%. 82: 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.035 0.018 199.4 82: (ns/day) (hour/ns) 82: Performance: 82.874 0.290 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 3.1%. 82: The balanceable part of the MD step is 41%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.3%. 82: 82: 82: NOTE: 50 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.044 0.022 199.5 82: (ns/day) (hour/ns) 82: Performance: 66.707 0.360 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (187 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.8%. 82: The balanceable part of the MD step is 50%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.4%. 82: 82: 82: NOTE: 56 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.046 0.023 199.5 82: (ns/day) (hour/ns) 82: Performance: 63.429 0.378 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 2.8%. 82: The balanceable part of the MD step is 46%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.3%. 82: 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.030 0.015 199.3 82: (ns/day) (hour/ns) 82: Performance: 97.747 0.246 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriOpened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 82: odicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 2.0%. 82: The balanceable part of the MD step is 39%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.8%. 82: 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.020 0.010 199.1 82: (ns/day) (hour/ns) 82: Performance: 148.940 0.161 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 0 time 0.000 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 2.0%. 82: The balanceable part of the MD step is 41%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.8%. 82: 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.038 0.019 199.5 82: (ns/day) (hour/ns) 82: Performance: 76.955 0.312 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 2.3%. 82: The balanceable part of the MD step is 42%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.0%. 82: 82: 82: NOTE: 50 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.037 0.019 199.4 82: (ns/day) (hour/ns) 82: Performance: 78.311 0.306 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 2.0%. 82: The balanceable part of the MD step is 30%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.6%. 82: 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.024 0.012 199.2 82: (ns/day) (hour/ns) 82: Performance: 122.283 0.196 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (177 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: 82: There were 2 NOTEs 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 48 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.024 0.012 199.2 82: (ns/day) (hour/ns) 82: Performance: 121.779 0.197 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.027 0.014 199.1 82: (ns/day) (hour/ns) 82: Performance: 107.838 0.223 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.025 0.012 198.8 82: (ns/day) (hour/ns) 82: Performance: 118.915 0.202 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 50 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.037 0.018 199.4 82: (ns/day) (hour/ns) 82: Performance: 79.401 0.302 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 50 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.036 0.018 199.3 82: (ns/day) (hour/ns) 82: Performance: 82.440 0.291 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 46 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.035 0.018 199.3 82: (ns/day) (hour/ns) 82: Performance: 82.983 0.289 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (136 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 48 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.025 0.013 199.0 82: (ns/day) (hour/ns) 82: Performance: 114.657 0.209 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 NOTE: 61 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.022 0.011 199.1 82: (ns/day) (hour/ns) 82: Performance: 131.971 0.182 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 52 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.037 0.019 199.5 82: (ns/day) (hour/ns) 82: Performance: 79.120 0.303 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.034 0.017 199.5 82: (ns/day) (hour/ns) 82: Performance: 86.150 0.279 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 60 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.030 0.015 197.9 82: (ns/day) (hour/ns) 82: Performance: 96.440 0.249 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: This run will generate roughly 0 Mb of data 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.035 0.017 199.2 82: (ns/day) (hour/ns) 82: Performance: 84.719 0.283 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (178 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.030 0.015 199.2 82: (ns/day) (hour/ns) 82: Performance: 98.882 0.243 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: NOTE: 35 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.024 0.012 198.1 82: (ns/day) (hour/ns) 82: Performance: 120.014 0.200 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 82: Reading energy frame 1 time 0.001 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 82: Reading energy frame 1 time 0.001 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 51 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.034 0.017 199.3 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 82: (ns/day) (hour/ns) 82: Performance: 86.160 0.279 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 82: Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 82: Reading energy frame 9 time 0.009 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 10 time 0.010 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 11 time 0.011 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 24 % of the run time was spent in domain decomposition, 82: 0 % of the run time was spent in pair search, 82: you might want to increase nstlist (this has no effect on accuracy) 82: 82: NOTE: 44 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.058 0.029 199.6 82: (ns/day) (hour/ns) 82: Performance: 50.284 0.477 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriOpened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 82: odicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.033 0.017 199.4 82: (ns/day) (hour/ns) 82: Performance: 88.996 0.270 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 47 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.051 0.026 199.2 82: (ns/day) (hour/ns) 82: Performance: 56.978 0.421 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (214 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 48 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.024 0.012 199.0 82: (ns/day) (hour/ns) 82: Performance: 123.507 0.194 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.030 0.015 199.1 82: (ns/day) (hour/ns) 82: Performance: 95.998 0.250 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriOpened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 odicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 82: Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 0 time 0.000 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 0 time 0.000 Reading energy frame 7 time 0.007 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 7 time 0.007 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 7 time 0.007 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 50 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.047 0.024 199.5 82: (ns/day) (hour/ns) 82: Performance: 61.741 0.389 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 62 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.038 0.019 199.3 82: (ns/day) (hour/ns) 82: Performance: 77.640 0.309 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.032 0.016 199.6 82: (ns/day) (hour/ns) 82: Performance: 91.701 0.262 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.032 0.016 199.5 82: (ns/day) (hour/ns) 82: Performance: 90.571 0.265 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (224 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 50 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.034 0.017 199.2 82: (ns/day) (hour/ns) 82: Performance: 86.492 0.277 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 61 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.051 0.033 152.1 82: (ns/day) (hour/ns) 82: Performance: 44.127 0.544 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 69 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.028 0.014 199.3 82: (ns/day) (hour/ns) 82: Performance: 104.988 0.229 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.032 0.016 199.5 82: (ns/day) (hour/ns) 82: Performance: 91.958 0.261 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 63 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.050 0.033 151.6 82: (ns/day) (hour/ns) 82: Performance: 44.584 0.538 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.026 0.013 198.8 82: (ns/day) (hour/ns) 82: Performance: 112.001 0.214 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (264 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 48 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.022 0.011 197.9 82: (ns/day) (hour/ns) 82: Performance: 134.092 0.179 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 48 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.014 0.007 197.7 82: (ns/day) (hour/ns) 82: Performance: 203.882 0.118 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.015 0.007 199.1 82: (ns/day) (hour/ns) 82: Performance: 196.922 0.122 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.030 0.015 199.2 82: (ns/day) (hour/ns) 82: Performance: 98.665 0.243 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.031 0.015 199.2 82: (ns/day) (hour/ns) 82: Performance: 95.213 0.252 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.032 0.016 199.2 82: (ns/day) (hour/ns) 82: Performance: 92.832 0.259 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (114 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.023 0.011 199.2 82: (ns/day) (hour/ns) 82: Performance: 130.050 0.185 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.029 0.015 199.5 82: (ns/day) (hour/ns) 82: Performance: 101.048 0.238 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.017 0.009 198.9 82: (ns/day) (hour/ns) 82: Performance: 170.843 0.140 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.021 0.011 199.2 82: (ns/day) (hour/ns) 82: Performance: 136.236 0.176 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.022 0.011 199.3 82: (ns/day) (hour/ns) 82: Performance: 131.807 0.182 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriOpened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 82: odicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: NOTE: 50 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.050 0.025 199.5 82: (ns/day) (hour/ns) 82: Performance: 58.737 0.409 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (145 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 56 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.047 0.024 199.5 82: (ns/day) (hour/ns) 82: Performance: 61.730 0.389 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 48 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.016 0.008 199.2 82: (ns/day) (hour/ns) 82: Performance: 183.832 0.131 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 54 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.017 0.009 198.9 82: (ns/day) (hour/ns) 82: Performance: 168.364 0.143 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_Peri 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: odicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 82: Generated 1 of the 1 non-bonded parameter combinations 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.040 0.020 199.5 82: (ns/day) (hour/ns) 82: Performance: 73.506 0.327 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 50 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.046 0.023 199.5 82: (ns/day) (hour/ns) 82: Performance: 64.286 0.373 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 50 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.044 0.022 199.7 82: (ns/day) (hour/ns) 82: Performance: 66.957 0.358 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (176 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 55 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.047 0.024 199.5 82: (ns/day) (hour/ns) 82: Performance: 62.394 0.385 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 60 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.050 0.031 161.5 82: (ns/day) (hour/ns) 82: Performance: 47.381 0.507 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 82: Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 82: Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 0 time 0.000 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 0 time 0.000 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Last energy frame read 16 time 0.016 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 4. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 4. 82: 82: 82: There were 3 NOTEs 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 53 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.062 0.031 199.7 82: (ns/day) (hour/ns) 82: Performance: 47.505 0.505 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 48 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.037 0.023 164.6 82: (ns/day) (hour/ns) 82: Performance: 64.570 0.372 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 53 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.038 0.019 199.6 82: (ns/day) (hour/ns) 82: Performance: 77.781 0.309 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriOpened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 82: odicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.032 0.016 199.4 82: (ns/day) (hour/ns) 82: Performance: 92.069 0.261 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriOpened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 82: odicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (243 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.045 0.023 199.4 82: (ns/day) (hour/ns) 82: Performance: 65.265 0.368 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 50 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.023 0.011 199.0 82: (ns/day) (hour/ns) 82: Performance: 128.347 0.187 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 66 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.044 0.025 172.0 82: (ns/day) (hour/ns) 82: Performance: 57.737 0.416 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.036 0.018 199.6 82: (ns/day) (hour/ns) 82: Performance: 80.605 0.298 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.033 0.016 199.5 82: (ns/day) (hour/ns) 82: Performance: 89.669 0.268 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.037 0.018 199.6 82: (ns/day) (hour/ns) 82: Performance: 79.773 0.301 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (176 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: NOTE: 54 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.045 0.032 138.5 82: (ns/day) (hour/ns) 82: Performance: 45.259 0.530 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 35 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.030 0.015 199.3 82: (ns/day) (hour/ns) 82: Performance: 98.126 0.245 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriOpened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: odicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 56 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.047 0.024 199.5 82: (ns/day) (hour/ns) 82: Performance: 61.978 0.387 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 61 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.048 0.030 161.0 82: (ns/day) (hour/ns) 82: Performance: 49.077 0.489 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 63 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.058 0.031 186.6 82: (ns/day) (hour/ns) 82: Performance: 47.572 0.505 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriOpened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 82: odicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 56 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.046 0.032 143.2 82: (ns/day) (hour/ns) 82: Performance: 45.257 0.530 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (228 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.034 0.017 199.4 82: (ns/day) (hour/ns) 82: Performance: 85.939 0.279 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.027 0.014 199.1 82: (ns/day) (hour/ns) 82: Performance: 107.830 0.223 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.029 0.015 198.7 82: (ns/day) (hour/ns) 82: Performance: 100.484 0.239 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 0 time 0.000 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 82: 82: NOTE: 67 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.057 0.044 128.1 82: (ns/day) (hour/ns) 82: Performance: 33.063 0.726 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.035 0.017 199.4 82: (ns/day) (hour/ns) 82: Performance: 84.874 0.283 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 52 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.037 0.018 199.1 82: (ns/day) (hour/ns) 82: Performance: 80.033 0.300 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (273 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.8%. 82: The balanceable part of the MD step is 60%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.1%. 82: 82: 82: NOTE: 51 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.038 0.023 166.5 82: (ns/day) (hour/ns) 82: Performance: 64.551 0.372 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.8%. 82: The balanceable part of the MD step is 53%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.4%. 82: 82: 82: NOTE: 47 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.028 0.014 195.9 82: (ns/day) (hour/ns) 82: Performance: 103.283 0.232 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 4. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 4. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/rOpened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 eproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.6%. 82: The balanceable part of the MD step is 54%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.9%. 82: 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.071 0.036 198.7 82: (ns/day) (hour/ns) 82: Performance: 41.267 0.582 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupliGenerated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: ng_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.3%. 82: The balanceable part of the MD step is 45%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.6%. 82: 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.040 0.020 198.1 82: (ns/day) (hour/ns) 82: Performance: 72.897 0.329 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupliGenerated 1 of the 1 non-bonded parameter combinations 82: ng_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.3%. 82: The balanceable part of the MD step is 45%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.1%. 82: 82: 82: NOTE: 48 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.031 0.016 197.0 82: (ns/day) (hour/ns) 82: Performance: 92.520 0.259 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcGenerated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: energy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.7%. 82: The balanceable part of the MD step is 46%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.8%. 82: 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.044 0.022 198.4 82: (ns/day) (hour/ns) 82: Performance: 66.547 0.361 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (230 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.6%. 82: The balanceable part of the MD step is 59%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.3%. 82: 82: 82: NOTE: 48 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.042 0.021 198.7 82: (ns/day) (hour/ns) 82: Performance: 69.855 0.344 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.1%. 82: The balanceable part of the MD step is 57%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.6%. 82: 82: 82: NOTE: 48 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.027 0.014 196.7 82: (ns/day) (hour/ns) 82: Performance: 107.092 0.224 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriOpened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 odicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.1%. 82: The balanceable part of the MD step is 52%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.6%. 82: 82: 82: NOTE: 48 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.034 0.017 195.8 82: (ns/day) (hour/ns) 82: Performance: 84.510 0.284 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 3.0%. 82: The balanceable part of the MD step is 52%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.5%. 82: 82: 82: NOTE: 48 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.035 0.018 195.9 82: (ns/day) (hour/ns) 82: Performance: 81.415 0.295 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was turned on during the run due to measured imbalance. 82: Average load imbalance: 4.5%. 82: The balanceable part of the MD step is 50%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 2.2%. 82: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 82: 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.055 0.028 197.7 82: (ns/day) (hour/ns) 82: Performance: 52.431 0.458 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 2.0%. 82: The balanceable part of the MD step is 50%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.0%. 82: 82: 82: NOTE: 48 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.038 0.019 198.4 82: (ns/day) (hour/ns) 82: Performance: 75.954 0.316 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (181 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.5%. 82: The balanceable part of the MD step is 58%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.9%. 82: 82: 82: NOTE: 47 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.033 0.017 198.1 82: (ns/day) (hour/ns) 82: Performance: 87.240 0.275 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.2%. 82: The balanceable part of the MD step is 54%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.7%. 82: 82: 82: NOTE: 48 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.043 0.022 197.8 82: (ns/day) (hour/ns) 82: Performance: 68.306 0.351 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was turned on during the run due to measured imbalance. 82: Average load imbalance: 4.2%. 82: The balanceable part of the MD step is 50%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 2.1%. 82: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 82: 82: 82: NOTE: 48 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.025 0.013 196.0 82: (ns/day) (hour/ns) 82: Performance: 116.772 0.206 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was turned on during the run due to measured imbalance. 82: Average load imbalance: 4.1%. 82: The balanceable part of the MD step is 50%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 2.1%. 82: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 82: 82: 82: NOTE: 49 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.050 0.025 198.4 82: (ns/day) (hour/ns) 82: Performance: 57.976 0.414 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was turned on during the run due to measured imbalance. 82: Average load imbalance: 5.2%. 82: The balanceable part of the MD step is 48%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 2.5%. 82: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 82: 82: 82: NOTE: 48 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.029 0.015 196.2 82: (ns/day) (hour/ns) 82: Performance: 98.871 0.243 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 82: 82: 82: Dynamic load balancing report: 82: DLB was turned on during the run due to measured imbalance. 82: Average load imbalance: 4.3%. 82: The balanceable part of the MD step is 50%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 2.1%. 82: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 82: 82: 82: NOTE: 48 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.029 0.015 197.8 82: (ns/day) (hour/ns) 82: Performance: 100.434 0.239 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (173 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.054 0.028 197.0 82: (ns/day) (hour/ns) 82: Performance: 53.201 0.451 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 25 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.033 0.017 195.7 82: (ns/day) (hour/ns) 82: Performance: 87.541 0.274 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.015 0.008 195.3 82: (ns/day) (hour/ns) 82: Performance: 187.526 0.128 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 29 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.100 0.051 197.6 82: (ns/day) (hour/ns) 82: Performance: 28.881 0.831 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.054 0.027 198.7 82: (ns/day) (hour/ns) 82: Performance: 54.451 0.441 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.038 0.019 198.2 82: (ns/day) (hour/ns) 82: Performance: 76.824 0.312 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriOpened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 82: odicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (196 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.926 0.463 199.9 82: (ns/day) (hour/ns) 82: Performance: 3.170 7.572 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.043 0.022 198.6 82: (ns/day) (hour/ns) 82: Performance: 67.104 0.358 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 82: Generated 1 of the 1 non-bonded parameter combinations 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.040 0.020 199.0 82: (ns/day) (hour/ns) 82: Performance: 72.864 0.329 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.026 0.013 198.6 82: (ns/day) (hour/ns) 82: Performance: 112.372 0.214 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.027 0.013 198.5 82: (ns/day) (hour/ns) 82: Performance: 109.876 0.218 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 11 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.039 0.020 199.0 82: (ns/day) (hour/ns) 82: Performance: 75.190 0.319 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (625 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.042 0.021 197.8 82: (ns/day) (hour/ns) 82: Performance: 69.395 0.346 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.050 0.025 198.7 82: (ns/day) (hour/ns) 82: Performance: 58.946 0.407 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_Peri Core t (s) Wall t (s) (%) 82: Time: 0.027 0.014 196.5 82: (ns/day) (hour/ns) 82: Performance: 106.068 0.226 82: odicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 82: Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 82: Reading energy frame 2 time 0.008 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.047 0.023 198.9 82: (ns/day) (hour/ns) 82: Performance: 62.595 0.383 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.055 0.028 198.8 82: (ns/day) (hour/ns) 82: Performance: 53.184 0.451 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.039 0.020 198.7 82: (ns/day) (hour/ns) 82: Performance: 74.460 0.322 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (236 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.040 0.020 198.9 82: (ns/day) (hour/ns) 82: Performance: 72.299 0.332 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.034 0.017 198.6 82: (ns/day) (hour/ns) 82: Performance: 85.877 0.279 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 82: Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.029 0.014 198.4 82: (ns/day) (hour/ns) 82: Performance: 101.336 0.237 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 82: Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.039 0.020 198.6 82: (ns/day) (hour/ns) 82: Performance: 75.100 0.320 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriOpened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 82: odicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.087 0.044 199.4 82: (ns/day) (hour/ns) 82: Performance: 33.622 0.714 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.044 0.022 198.4 82: (ns/day) (hour/ns) 82: Performance: 66.195 0.363 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriOpened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 82: odicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (192 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: for current Trotter decomposition methods with vv, nsttcouple and 82: nstpcouple must be equal. Both have been reset to 82: min(nsttcouple,nstpcouple) = 2 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 13 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.065 0.033 199.0 82: (ns/day) (hour/ns) 82: Performance: 44.934 0.534 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: for current Trotter decomposition methods with vv, nsttcouple and 82: nstpcouple must be equal. Both have been reset to 82: min(nsttcouple,nstpcouple) = 2 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.039 0.020 198.1 82: (ns/day) (hour/ns) 82: Performance: 75.254 0.319 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: for current Trotter decomposition methods with vv, nsttcouple and 82: nstpcouple must be equal. Both have been reset to 82: min(nsttcouple,nstpcouple) = 2 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.492 0.246 199.9 82: (ns/day) (hour/ns) 82: Performance: 5.961 4.026 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: for current Trotter decomposition methods with vv, nsttcouple and 82: nstpcouple must be equal. Both have been reset to 82: min(nsttcouple,nstpcouple) = 2 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 82: Core t (s) Wall t (s) (%) 82: Time: 0.031 0.015 197.4 82: (ns/day) (hour/ns) 82: Performance: 94.852 0.253 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: for current Trotter decomposition methods with vv, nsttcouple and 82: nstpcouple must be equal. Both have been reset to 82: min(nsttcouple,nstpcouple) = 2 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 82: 82: NOTE: 35 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.091 0.053 170.4 82: (ns/day) (hour/ns) 82: Performance: 27.459 0.874 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: for current Trotter decomposition methods with vv, nsttcouple and 82: nstpcouple must be equal. Both have been reset to 82: min(nsttcouple,nstpcouple) = 2 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.073 0.036 199.4 82: (ns/day) (hour/ns) 82: Performance: 40.243 0.596 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (675 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.030 0.015 198.7 82: (ns/day) (hour/ns) 82: Performance: 98.418 0.244 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.030 0.015 198.8 82: (ns/day) (hour/ns) 82: Performance: 98.399 0.244 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.023 0.012 198.2 82: (ns/day) (hour/ns) 82: Performance: 127.190 0.189 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_Peri Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 odicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 82: Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.040 0.020 199.1 82: (ns/day) (hour/ns) 82: Performance: 73.010 0.329 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.035 0.018 198.3 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 82: (ns/day) (hour/ns) 82: Performance: 82.498 0.291 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.031 0.016 198.8 82: (ns/day) (hour/ns) 82: Performance: 93.601 0.256 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (148 ms) 82: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (5932 ms total) 82: 82: [----------] Global test environment tear-down 82: [==========] 25 tests from 1 test suite ran. (5986 ms total) 82: [ PASSED ] 25 tests. 82/91 Test #82: MdrunCoordinationCouplingTests2Ranks ......... Passed 6.49 sec test 83 Start 83: MdrunCoordinationConstraintsTests1Rank 83: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-coordination-constraints-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunCoordinationConstraintsTests1Rank.xml" 83: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 83: Test timeout computed to be: 1920 83: [==========] Running 13 tests from 1 test suite. 83: [----------] Global test environment set-up. 83: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 83: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.026 0.026 99.8 83: (ns/day) (hour/ns) 83: Performance: 56.057 0.428 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.015 0.015 99.7 83: (ns/day) (hour/ns) 83: Performance: 97.028 0.247 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 4. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 4. 83: 83: 83: There were 5 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.012 0.012 99.7 83: (ns/day) (hour/ns) 83: Performance: 123.918 0.194 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 5 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.024 0.024 99.9 83: (ns/day) (hour/ns) 83: Performance: 60.173 0.399 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 5 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.016 0.016 99.5 83: (ns/day) (hour/ns) 83: Performance: 93.491 0.257 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 5 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.018 0.018 99.8 83: (ns/day) (hour/ns) 83: Performance: 80.273 0.299 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1640 ms) 83: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 4 NOTEs 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.023 0.023 99.8 83: (ns/day) (hour/ns) 83: Performance: 63.218 0.380 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 4 NOTEs 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.014 0.014 99.8 83: (ns/day) (hour/ns) 83: Performance: 103.996 0.231 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.014 0.014 99.6 83: (ns/day) (hour/ns) 83: Performance: 106.162 0.226 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.019 0.020 99.8 83: (ns/day) (hour/ns) 83: Performance: 75.245 0.319 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.026 0.026 99.8 83: (ns/day) (hour/ns) 83: Performance: 55.667 0.431 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.018 0.018 99.8 83: (ns/day) (hour/ns) 83: Performance: 82.629 0.290 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 83: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (1691 ms) 83: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: You are using a plain Coulomb cut-off, which might p 83: roduce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 4 NOTEs 83: This run will generate roughly 0 Mb of data 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.024 0.024 99.8 83: (ns/day) (hour/ns) 83: Performance: 60.895 0.394 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 4 NOTEs 83: 83: This run will generate roughly 0 Mb of data 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.034 0.034 99.9 83: (ns/day) (hour/ns) 83: Performance: 43.773 0.548 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 4 NOTEs 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.014 0.014 99.8 83: (ns/day) (hour/ns) 83: Performance: 106.239 0.226 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.032 0.032 99.9 83: (ns/day) (hour/ns) 83: Performance: 45.916 0.523 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 4 NOTEs 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.016 0.016 99.7 83: (ns/day) (hour/ns) 83: Performance: 90.542 0.265 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.013 0.013 99.8 83: (ns/day) (hour/ns) 83: Performance: 109.678 0.219 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 83: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (2267 ms) 83: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.013 0.013 99.8 83: (ns/day) (hour/ns) 83: Performance: 115.220 0.208 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.012 0.012 99.6 83: (ns/day) (hour/ns) 83: Performance: 121.520 0.197 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.012 0.013 99.7 83: (ns/day) (hour/ns) 83: Performance: 117.231 0.205 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.012 0.012 99.7 83: (ns/day) (hour/ns) 83: Performance: 121.528 0.197 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.015 0.015 99.7 83: (ns/day) (hour/ns) 83: Performance: 97.806 0.245 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.024 0.024 99.8 83: (ns/day) (hour/ns) 83: Performance: 61.232 0.392 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 83: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (2159 ms) 83: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.016 0.016 99.8 83: (ns/day) (hour/ns) 83: Performance: 92.201 0.260 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.013 0.013 99.8 83: (ns/day) (hour/ns) 83: Performance: 113.094 0.212 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.009 0.009 99.6 83: (ns/day) (hour/ns) 83: Performance: 170.004 0.141 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.015 0.015 99.8 83: (ns/day) (hour/ns) 83: Performance: 99.631 0.241 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.016 0.016 99.7 83: (ns/day) (hour/ns) 83: Performance: 90.863 0.264 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 3 NOTEs 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.017 0.017 99.8 83: (ns/day) (hour/ns) 83: Performance: 83.979 0.286 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 83: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (2225 ms) 83: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.016 0.016 99.8 83: (ns/day) (hour/ns) 83: Performance: 93.159 0.258 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.020 0.020 99.7 83: (ns/day) (hour/ns) 83: Performance: 73.138 0.328 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.024 0.025 99.8 83: (ns/day) (hour/ns) 83: Performance: 59.903 0.401 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.012 0.012 99.7 83: (ns/day) (hour/ns) 83: Performance: 118.637 0.202 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 3 NOTEs 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.020 0.020 99.7 83: (ns/day) (hour/ns) 83: Performance: 71.756 0.334 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 3 NOTEs 83: 83: This run will generate roughly 0 Mb of data 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.020 0.020 99.8 83: (ns/day) (hour/ns) 83: Performance: 73.192 0.328 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 83: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (2206 ms) 83: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 3 NOTEs 83: 83: This run will generate roughly 0 Mb of data 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.018 0.018 99.8 83: (ns/day) (hour/ns) 83: Performance: 82.271 0.292 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.011 0.011 99.8 83: (ns/day) (hour/ns) 83: Performance: 135.591 0.177 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 4. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 4. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.011 0.011 99.7 83: (ns/day) (hour/ns) 83: Performance: 138.705 0.173 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.036 0.036 99.9 83: (ns/day) (hour/ns) 83: Performance: 40.828 0.588 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.017 0.017 99.6 83: (ns/day) (hour/ns) 83: Performance: 85.025 0.282 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.015 0.016 99.8 83: (ns/day) (hour/ns) 83: Performance: 94.640 0.254 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 83: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (1877 ms) 83: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.016 0.016 99.8 83: (ns/day) (hour/ns) 83: Performance: 94.405 0.254 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 3 NOTEs 83: This run will generate roughly 0 Mb of data 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.019 0.019 99.8 83: (ns/day) (hour/ns) 83: Performance: 75.457 0.318 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.018 0.018 99.8 83: (ns/day) (hour/ns) 83: Performance: 80.045 0.300 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.020 0.020 99.9 83: (ns/day) (hour/ns) 83: Performance: 74.594 0.322 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: There were 3 NOTEs 83: 83: This run will generate roughly 0 Mb of data 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.019 0.019 99.7 83: (ns/day) (hour/ns) 83: Performance: 78.397 0.306 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.015 0.015 99.8 83: (ns/day) (hour/ns) 83: Performance: 99.906 0.240 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 83: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (1856 ms) 83: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.017 0.017 99.8 83: (ns/day) (hour/ns) 83: Performance: 87.635 0.274 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.014 0.014 99.8 83: (ns/day) (hour/ns) 83: Performance: 101.508 0.236 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.015 0.015 99.8 83: (ns/day) (hour/ns) 83: Performance: 96.968 0.248 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.018 0.018 99.8 83: (ns/day) (hour/ns) 83: Performance: 79.795 0.301 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstr 83: aints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 3 NOTEs 83: This run will generate roughly 0 Mb of data 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.014 0.014 99.7 83: (ns/day) (hour/ns) 83: Performance: 101.389 0.237 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.019 0.019 99.8 83: (ns/day) (hour/ns) 83: Performance: 75.817 0.317 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 83: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (1448 ms) 83: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.019 0.019 99.9 83: (ns/day) (hour/ns) 83: Performance: 76.726 0.313 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 4 NOTEs 83: 83: This run will generate roughly 0 Mb of data 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.020 0.020 99.8 83: (ns/day) (hour/ns) 83: Performance: 75.077 0.320 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 4. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 4. 83: 83: 83: There were 5 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.017 0.017 99.9 83: (ns/day) (hour/ns) 83: Performance: 87.378 0.275 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 5 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.484 0.484 100.0 83: (ns/day) (hour/ns) 83: Performance: 3.034 7.910 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 5 NOTEs 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.022 0.022 99.9 83: (ns/day) (hour/ns) 83: Performance: 67.694 0.355 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 5 NOTEs 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.030 0.030 99.9 83: (ns/day) (hour/ns) 83: Performance: 49.442 0.485 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 83: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (2475 ms) 83: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 4 NOTEs 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.037 0.037 99.9 83: (ns/day) (hour/ns) 83: Performance: 40.053 0.599 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.032 0.032 99.9 83: (ns/day) (hour/ns) 83: Performance: 45.305 0.530 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.017 0.017 99.8 83: (ns/day) (hour/ns) 83: Performance: 84.065 0.285 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.026 0.026 99.9 83: (ns/day) (hour/ns) 83: Performance: 56.140 0.428 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 4 NOTEs 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.021 0.021 99.8 83: (ns/day) (hour/ns) 83: Performance: 69.307 0.346 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.021 0.021 99.9 83: (ns/day) (hour/ns) 83: Performance: 69.273 0.346 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 83: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (2216 ms) 83: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.021 0.021 99.9 83: (ns/day) (hour/ns) 83: Performance: 69.872 0.343 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.016 0.016 99.7 83: (ns/day) (hour/ns) 83: Performance: 89.788 0.267 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 4 NOTEs 83: 83: This run will generate roughly 0 Mb of data 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.016 0.017 99.8 83: (ns/day) (hour/ns) 83: Performance: 88.953 0.270 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.016 0.016 99.7 83: (ns/day) (hour/ns) 83: Performance: 94.359 0.254 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.021 0.021 99.6 83: (ns/day) (hour/ns) 83: Performance: 69.240 0.347 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.017 0.017 99.7 83: (ns/day) (hour/ns) 83: Performance: 86.197 0.278 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 83: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (2116 ms) 83: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.028 0.028 99.9 83: (ns/day) (hour/ns) 83: Performance: 52.537 0.457 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 3 NOTEs 83: 83: This run will generate roughly 0 Mb of data 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.017 0.018 99.7 83: (ns/day) (hour/ns) 83: Performance: 83.862 0.286 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 3 NOTEs 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.019 0.019 99.7 83: (ns/day) (hour/ns) 83: Performance: 78.234 0.307 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.028 0.028 99.8 83: (ns/day) (hour/ns) 83: Performance: 52.512 0.457 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.024 0.024 99.7 83: (ns/day) (hour/ns) 83: Performance: 60.330 0.398 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 3 NOTEs 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.025 0.025 99.8 83: (ns/day) (hour/ns) 83: Performance: 58.292 0.412 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 83: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (1947 ms) 83: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (26127 ms total) 83: 83: [----------] Global test environment tear-down 83: [==========] 13 tests from 1 test suite ran. (26154 ms total) 83: [ PASSED ] 13 tests. 83/91 Test #83: MdrunCoordinationConstraintsTests1Rank ....... Passed 26.61 sec test 84 Start 84: MdrunCoordinationConstraintsTests2Ranks 84: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-coordination-constraints-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunCoordinationConstraintsTests2Ranks.xml" 84: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 84: Test timeout computed to be: 1920 84: [==========] Running 13 tests from 1 test suite. 84: [----------] Global test environment set-up. 84: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 2.5%. 84: The balanceable part of the MD step is 49%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 1.2%. 84: 84: 84: NOTE: 66 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.047 0.023 199.3 84: (ns/day) (hour/ns) 84: Performance: 62.863 0.382 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 2.7%. 84: The balanceable part of the MD step is 45%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 1.2%. 84: 84: 84: NOTE: 48 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.025 0.012 199.3 84: (ns/day) (hour/ns) 84: Performance: 118.653 0.202 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 4. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 4. 84: 84: 84: There were 5 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 2.0%. 84: The balanceable part of the MD step is 42%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.8%. 84: 84: 84: NOTE: 49 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.026 0.013 199.2 84: (ns/day) (hour/ns) 84: Performance: 112.147 0.214 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 5 NOTEs 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 0.3%. 84: The balanceable part of the MD step is 38%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.1%. 84: 84: 84: NOTE: 49 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.037 0.018 199.2 84: (ns/day) (hour/ns) 84: Performance: 79.408 0.302 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 5 NOTEs 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 2.9%. 84: The balanceable part of the MD step is 29%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.8%. 84: 84: 84: NOTE: 48 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.030 0.015 199.2 84: (ns/day) (hour/ns) 84: Performance: 98.330 0.244 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 5 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 3.7%. 84: The balanceable part of the MD step is 36%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 1.3%. 84: 84: 84: NOTE: 57 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.038 0.019 199.5 84: (ns/day) (hour/ns) 84: Performance: 76.828 0.312 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (2168 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 0.7%. 84: The balanceable part of the MD step is 51%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.4%. 84: 84: 84: NOTE: 49 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.042 0.021 199.6 84: (ns/day) (hour/ns) 84: Performance: 69.039 0.348 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 2.5%. 84: The balanceable part of the MD step is 2%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.1%. 84: 84: 84: NOTE: 49 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.058 0.029 199.7 84: (ns/day) (hour/ns) 84: Performance: 50.689 0.473 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 2.9%. 84: The balanceable part of the MD step is 44%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 1.3%. 84: 84: 84: NOTE: 62 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.066 0.043 153.6 84: (ns/day) (hour/ns) 84: Performance: 34.228 0.701 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 1.7%. 84: The balanceable part of the MD step is 35%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.6%. 84: 84: 84: NOTE: 65 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.043 0.025 167.8 84: (ns/day) (hour/ns) 84: Performance: 57.967 0.414 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 1.6%. 84: The balanceable part of the MD step is 42%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.6%. 84: 84: 84: NOTE: 49 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.031 0.015 199.4 84: (ns/day) (hour/ns) 84: Performance: 95.521 0.251 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB got disabled because it was unsuitable to use. 84: Average load imbalance: 7.2%. 84: The balanceable part of the MD step is 39%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 2.8%. 84: 84: 84: NOTE: 49 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.034 0.017 199.4 84: (ns/day) (hour/ns) 84: Performance: 87.092 0.276 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (2178 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 1.9%. 84: The balanceable part of the MD step is 40%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.8%. 84: 84: 84: NOTE: 49 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.050 0.025 199.6 84: (ns/day) (hour/ns) 84: Performance: 58.220 0.412 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 1.2%. 84: The balanceable part of the MD step is 44%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.5%. 84: 84: 84: NOTE: 62 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.048 0.034 141.8 84: (ns/day) (hour/ns) 84: Performance: 43.110 0.557 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 1.1%. 84: The balanceable part of the MD step is 41%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.4%. 84: 84: 84: NOTE: 54 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.030 0.015 199.3 84: (ns/day) (hour/ns) 84: Performance: 97.367 0.246 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: Reading energy frame 1 time 0.004 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB got disabled because it was unsuitable to use. 84: Average load imbalance: 33.2%. 84: The balanceable part of the MD step is 49%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 16.4%. 84: 84: NOTE: 16.4 % of the available CPU time was lost due to load imbalance 84: in the domain decomposition. 84: You can consider manually changing the decomposition (option -dd); 84: e.g. by using fewer domains along the box dimension in which there is 84: considerable inhomogeneity in the simulated system. 84: 84: NOTE: 16 % of the run time was spent in domain decomposition, 84: 0 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: NOTE: 42 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.661 0.331 200.0 84: (ns/day) (hour/ns) 84: Performance: 4.441 5.404 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_POpened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: eriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 1.4%. 84: The balanceable part of the MD step is 40%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.6%. 84: 84: 84: NOTE: 49 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.036 0.018 199.5 84: (ns/day) (hour/ns) 84: Performance: 82.331 0.292 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 0.5%. 84: The balanceable part of the MD step is 37%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.2%. 84: 84: 84: NOTE: 22 % of the run time was spent in domain decomposition, 84: 0 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: NOTE: 38 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.032 0.016 199.5 84: (ns/day) (hour/ns) 84: Performance: 92.224 0.260 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (2711 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.035 0.017 199.1 84: (ns/day) (hour/ns) 84: Performance: 84.523 0.284 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.033 0.016 199.0 84: (ns/day) (hour/ns) 84: Performance: 89.568 0.268 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.034 0.017 199.4 84: (ns/day) (hour/ns) 84: Performance: 86.330 0.278 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.036 0.018 199.5 84: (ns/day) (hour/ns) 84: Performance: 81.041 0.296 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: Core t (s) Wall t (s) (%) 84: Time: 0.026 0.013 199.2 84: (ns/day) (hour/ns) 84: Performance: 114.139 0.210 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.035 0.018 199.5 84: (ns/day) (hour/ns) 84: Performance: 83.242 0.288 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (1944 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 7 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.031 0.016 199.0 84: (ns/day) (hour/ns) 84: Performance: 94.578 0.254 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 29 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.048 0.024 199.5 84: (ns/day) (hour/ns) 84: Performance: 60.488 0.397 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.033 0.017 199.2 84: (ns/day) (hour/ns) 84: Performance: 88.683 0.271 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.048 0.024 199.3 84: (ns/day) (hour/ns) 84: Performance: 60.905 0.394 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 22 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.051 0.025 199.5 84: (ns/day) (hour/ns) 84: Performance: 57.935 0.414 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.028 0.014 198.4 84: (ns/day) (hour/ns) 84: Performance: 105.563 0.227 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (2129 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 36 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.074 0.047 157.5 84: (ns/day) (hour/ns) 84: Performance: 31.329 0.766 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.030 0.015 199.2 84: (ns/day) (hour/ns) 84: Performance: 98.166 0.244 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.023 0.011 199.2 84: (ns/day) (hour/ns) 84: Performance: 129.064 0.186 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.038 0.019 199.0 84: (ns/day) (hour/ns) 84: Performance: 77.162 0.311 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: Time: 0.024 0.012 199.3 84: (ns/day) (hour/ns) 84: Performance: 123.470 0.194 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.051 0.026 199.2 84: (ns/day) (hour/ns) 84: Performance: 57.003 0.421 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (1859 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.024 0.012 199.3 84: (ns/day) (hour/ns) 84: Performance: 124.004 0.194 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.027 0.014 199.5 84: (ns/day) (hour/ns) 84: Performance: 108.565 0.221 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 4. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 4. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.038 0.019 199.6 84: (ns/day) (hour/ns) 84: Performance: 77.389 0.310 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.034 0.017 199.6 84: (ns/day) (hour/ns) 84: Performance: 86.909 0.276 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.037 0.019 199.6 84: (ns/day) (hour/ns) 84: Performance: 79.143 0.303 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstr 84: This run will generate roughly 0 Mb of data 84: aints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.044 0.022 199.3 84: (ns/day) (hour/ns) 84: Performance: 65.856 0.364 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (2198 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.051 0.025 199.7 84: (ns/day) (hour/ns) 84: Performance: 57.911 0.414 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.021 0.010 199.0 84: (ns/day) (hour/ns) 84: Performance: 140.909 0.170 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstrOpened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 aints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.034 0.017 199.5 84: (ns/day) (hour/ns) 84: Performance: 86.275 0.278 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.041 0.021 199.4 84: (ns/day) (hour/ns) 84: Performance: 71.163 0.337 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: Core t (s) Wall t (s) (%) 84: Time: 0.029 0.015 199.1 84: (ns/day) (hour/ns) 84: Performance: 100.723 0.238 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.039 0.020 199.3 84: (ns/day) (hour/ns) 84: Performance: 74.717 0.321 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (2545 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.059 0.029 199.6 84: (ns/day) (hour/ns) 84: Performance: 49.825 0.482 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.028 0.014 199.4 84: (ns/day) (hour/ns) 84: Performance: 104.813 0.229 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.027 0.013 199.4 84: (ns/day) (hour/ns) 84: Performance: 108.825 0.221 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.039 0.020 199.6 84: (ns/day) (hour/ns) 84: Performance: 75.154 0.319 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.044 0.022 199.3 84: (ns/day) (hour/ns) 84: Performance: 66.558 0.361 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.055 0.028 198.2 84: (ns/day) (hour/ns) 84: Performance: 53.379 0.450 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (2177 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 0.0%. 84: The balanceable part of the MD step is 58%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.0%. 84: 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.038 0.023 162.8 84: (ns/day) (hour/ns) 84: Performance: 62.834 0.382 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 0.7%. 84: The balanceable part of the MD step is 55%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.4%. 84: 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.035 0.018 196.0 84: (ns/day) (hour/ns) 84: Performance: 81.507 0.294 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 4. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 4. 84: 84: 84: There were 5 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 2.9%. 84: The balanceable part of the MD step is 45%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 1.3%. 84: 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.031 0.015 198.6 84: (ns/day) (hour/ns) 84: Performance: 94.806 0.253 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 5 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 2.5%. 84: The balanceable part of the MD step is 43%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 1.1%. 84: 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.048 0.024 198.2 84: (ns/day) (hour/ns) 84: Performance: 60.256 0.398 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 5 NOTEs 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 0.9%. 84: The balanceable part of the MD step is 44%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.4%. 84: 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.048 0.024 196.9 84: (ns/day) (hour/ns) 84: Performance: 59.979 0.400 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstr 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: aints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 5 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 2.3%. 84: The balanceable part of the MD step is 44%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 1.0%. 84: 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.046 0.023 197.3 84: (ns/day) (hour/ns) 84: Performance: 63.369 0.379 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (1888 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 0.6%. 84: The balanceable part of the MD step is 49%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.3%. 84: 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.042 0.021 198.7 84: (ns/day) (hour/ns) 84: Performance: 69.537 0.345 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 1.6%. 84: The balanceable part of the MD step is 51%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.8%. 84: 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.048 0.024 197.3 84: (ns/day) (hour/ns) 84: Performance: 60.368 0.398 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 3.1%. 84: The balanceable part of the MD step is 48%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 1.5%. 84: 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.072 0.036 197.7 84: (ns/day) (hour/ns) 84: Performance: 40.512 0.592 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 0.9%. 84: The balanceable part of the MD step is 51%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.5%. 84: 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.038 0.019 198.5 84: (ns/day) (hour/ns) 84: Performance: 77.463 0.310 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 2.3%. 84: The balanceable part of the MD step is 49%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 1.1%. 84: 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.036 0.018 198.0 84: (ns/day) (hour/ns) 84: Performance: 81.452 0.295 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstr 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: aints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 2.6%. 84: The balanceable part of the MD step is 48%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 1.2%. 84: 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.060 0.030 198.8 84: (ns/day) (hour/ns) 84: Performance: 48.645 0.493 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (1712 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.037 0.019 198.7 84: (ns/day) (hour/ns) 84: Performance: 78.528 0.306 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.037 0.019 197.9 84: (ns/day) (hour/ns) 84: Performance: 77.562 0.309 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.046 0.023 198.4 84: (ns/day) (hour/ns) 84: Performance: 63.446 0.378 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.035 0.018 198.4 84: (ns/day) (hour/ns) 84: Performance: 83.519 0.287 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.041 0.021 198.5 84: (ns/day) (hour/ns) 84: Performance: 71.518 0.336 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.046 0.023 198.3 84: (ns/day) (hour/ns) 84: Performance: 63.681 0.377 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (1282 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.031 0.015 197.7 84: (ns/day) (hour/ns) 84: Performance: 94.823 0.253 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.022 0.011 197.6 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 (ns/day) (hour/ns) 84: Performance: 134.650 0.178 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.053 0.027 199.2 84: (ns/day) (hour/ns) 84: Performance: 55.127 0.435 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.035 0.018 198.6 84: (ns/day) (hour/ns) 84: Performance: 83.632 0.287 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.035 0.018 198.7 84: (ns/day) (hour/ns) 84: Performance: 83.500 0.287 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.033 0.017 198.5 84: (ns/day) (hour/ns) 84: Performance: 88.368 0.272 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (1237 ms) 84: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (26088 ms total) 84: 84: [----------] Global test environment tear-down 84: [==========] 13 tests from 1 test suite ran. (26131 ms total) 84: [ PASSED ] 13 tests. 84/91 Test #84: MdrunCoordinationConstraintsTests2Ranks ...... Passed 26.60 sec test 85 Start 85: MdrunFEPTests 85: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-fep-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunFEPTests.xml" 85: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 85: Test timeout computed to be: 600 85: [==========] Running 12 tests from 1 test suite. 85: [----------] Global test environment set-up. 85: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest 85: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp, line 149]: 85: For proper sampling of the (nearly) decoupled state, stochastic dynamics 85: should be used 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 85: The Berendsen thermostat does not generate the correct kinetic energy 85: distribution, and should not be used for new production simulations (in 85: our opinion). We would recommend the V-rescale thermostat. 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 355.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 85: The optimal PME mesh load for parallel simulations is below 0.5 85: and for highly parallel simulations between 0.25 and 0.33, 85: for higher performance, increase the cut-off and the PME grid spacing. 85: 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 85: For free energy simulations, the optimal load limit increases from 0.5 to 85: 0.667 85: 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Changing nstlist from 10 to 100, rlist from 1 to 1 85: 85: Using 1 MPI process 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'AA' 85: 20 steps, 0.0 ps. 85: Setting the LD random seed to -68193283 85: 85: Generated 153 of the 153 non-bonded parameter combinations 85: 85: Generated 153 of the 153 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'ASN' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Coupling 1 copies of molecule type 'ASN' 85: Analysing residue names: 85: There are: 1 Protein residues 85: There are: 56 Water residues 85: Analysing Protein... 85: 85: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 85: 85: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: Calculating fourier grid dimensions for X Y Z 85: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 85: 85: Estimate for the relative computational load of the PME mesh part: 0.94 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.088 0.044 199.7 85: (ns/day) (hour/ns) 85: Performance: 41.187 0.583 85: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_energy.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 trr version: GMX_trn_file (single precision) 85: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s (302 ms) 85: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp, line 148]: 85: For proper sampling of the (nearly) decoupled state, stochastic dynamics 85: should be used 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 85: The Berendsen thermostat does not generate the correct kinetic energy 85: distribution, and should not be used for new production simulations (in 85: our opinion). We would recommend the V-rescale thermostat. 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 355.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 85: The optimal PME mesh load for parallel simulations is below 0.5 85: and for highly parallel simulations between 0.25 and 0.33, 85: for higher performance, increase the cut-off and the PME grid spacing. 85: 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 85: For free energy simulations, the optimal load limit increases from 0.5 to 85: 0.667 85: 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Changing nstlist from 10 to 100, rlist from 1 to 1 85: 85: Using 1 MPI process 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'AA' 85: 20 steps, 0.0 ps. 85: Setting the LD random seed to -21334837 85: 85: Generated 153 of the 153 non-bonded parameter combinations 85: 85: Generated 153 of the 153 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'ASN' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Coupling 1 copies of molecule type 'ASN' 85: Analysing residue names: 85: There are: 1 Protein residues 85: There are: 56 Water residues 85: Analysing Protein... 85: 85: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 85: 85: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: Calculating fourier grid dimensions for X Y Z 85: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 85: 85: Estimate for the relative computational load of the PME mesh part: 0.94 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.175 0.088 199.8 85: (ns/day) (hour/ns) 85: Performance: 20.664 1.161 85: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_energy.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s (342 ms) 85: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp, line 147]: 85: For proper sampling of the (nearly) decoupled state, stochastic dynamics 85: should be used 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 85: With PME there is a minor soft core effect present at the cut-off, 85: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 85: energy conservation, but usually other effects dominate. With a common 85: sigma value of 0.34 nm the fraction of the particle-particle potential at 85: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 85: The Berendsen thermostat does not generate the correct kinetic energy 85: distribution, and should not be used for new production simulations (in 85: our opinion). We would recommend the V-rescale thermostat. 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 355.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 85: The optimal PME mesh load for parallel simulations is below 0.5 85: and for highly parallel simulations between 0.25 and 0.33, 85: for higher performance, increase the cut-off and the PME grid spacing. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 85: For free energy simulations, the optimal load limit increases from 0.5 to 85: 0.667 85: 85: 85: 85: There were 4 NOTEs 85: 85: There was 1 WARNING 85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Changing nstlist from 10 to 100, rlist from 1 to 1 85: 85: Using 1 MPI process 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'AA' 85: 20 steps, 0.0 ps. 85: Setting the LD random seed to -1230242177 85: 85: Generated 153 of the 153 non-bonded parameter combinations 85: 85: Generated 153 of the 153 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'ASN' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Coupling 1 copies of molecule type 'ASN' 85: Analysing residue names: 85: There are: 1 Protein residues 85: There are: 56 Water residues 85: Analysing Protein... 85: 85: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 85: 85: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: Calculating fourier grid dimensions for X Y Z 85: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 85: 85: Estimate for the relative computational load of the PME mesh part: 0.94 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.114 0.057 199.8 85: (ns/day) (hour/ns) 85: Performance: 31.670 0.758 85: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_energy.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s (160 ms) 85: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_s 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp, line 147]: 85: For proper sampling of the (nearly) decoupled state, stochastic dynamics 85: should be used 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 85: With PME there is a minor soft core effect present at the cut-off, 85: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 85: energy conservation, but usually other effects dominate. With a common 85: sigma value of 0.34 nm the fraction of the particle-particle potential at 85: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 85: The Berendsen thermostat does not generate the correct kinetic energy 85: distribution, and should not be used for new production simulations (in 85: our opinion). We would recommend the V-rescale thermostat. 85: 85: Generating 1-4 interactions: fudge = 0.5 85: 85: NOTE 3 [file topol.top, line 155]: 85: System has non-zero total charge: 1.000000 85: Total charge should normally be an integer. See 85: https://manual.gromacs.org/current/user-guide/floating-point.html 85: for discussion on how close it should be to an integer. 85: 85: 85: 85: 85: WARNING 2 [file topol.top, line 155]: 85: You are using Ewald electrostatics in a system with net charge. This can 85: lead to severe artifacts, such as ions moving into regions with low 85: dielectric, due to the uniform background charge. We suggest to 85: neutralize your system with counter ions, possibly in combination with a 85: physiological salt concentration. 85: 85: Setting the LD random seed to -1746934401 85: 85: Generated 171 of the 171 non-bonded parameter combinations 85: 85: Generated 171 of the 171 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'ASN' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Excluding 1 bonded neighbours molecule type 'NA' 85: 85: turning H bonds into constraints... 85: 85: Coupling 1 copies of molecule type 'ASN' 85: 85: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 85: J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof 85: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 85: Charge 85: J. Chem. Theory Comput. 10 (2014) pp. 381-393 85: -------- -------- --- Thank You --- -------- -------- 85: 85: Number of degrees of freedom in T-Coupling group System is 358.00 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 85: The optimal PME mesh load for parallel simulations is below 0.5 85: and for highly parallel simulations between 0.25 and 0.33, 85: for higher performance, increase the cut-off and the PME grid spacing. 85: 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 85: For free energy simulations, the optimal load limit increases from 0.5 to 85: 0.667 85: 85: 85: 85: There were 5 NOTEs 85: 85: There were 2 WARNINGs 85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Changing nstlist from 10 to 50, rlist from 1.004 to 1.101 85: 85: Using 1 MPI process 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'AA' 85: 20 steps, 0.0 ps. 85: Analysing residue names: 85: There are: 1 Protein residues 85: There are: 56 Water residues 85: There are: 1 Ion residues 85: Analysing Protein... 85: 85: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 85: 85: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: Calculating fourier grid dimensions for X Y Z 85: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 85: 85: Estimate for the relative computational load of the PME mesh part: 0.96 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.171 0.086 199.8 85: (ns/day) (hour/ns) 85: Performance: 21.191 1.133 85: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_s_energy.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_s (384 ms) 85: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_s 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp, line 147]: 85: For proper sampling of the (nearly) decoupled state, stochastic dynamics 85: should be used 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 85: With PME there is a minor soft core effect present at the cut-off, 85: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 85: energy conservation, but usually other effects dominate. With a common 85: sigma value of 0.34 nm the fraction of the particle-particle potential at 85: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 85: The Berendsen thermostat does not generate the correct kinetic energy 85: distribution, and should not be used for new production simulations (in 85: our opinion). We would recommend the V-rescale thermostat. 85: 85: Generating 1-4 interactions: fudge = 0.5 85: 85: NOTE 3 [file topol.top, line 165]: 85: System has non-zero total charge: 1.000000 85: Total charge should normally be an integer. See 85: https://manual.gromacs.org/current/user-guide/floating-point.html 85: for discussion on how close it should be to an integer. 85: 85: 85: 85: 85: WARNING 2 [file topol.top, line 165]: 85: You are using Ewald electrostatics in a system with net charge. This can 85: lead to severe artifacts, such as ions moving into regions with low 85: dielectric, due to the uniform background charge. We suggest to 85: neutralize your system with counter ions, possibly in combination with a 85: physiological salt concentration. 85: 85: Setting the LD random seed to -1114163 85: 85: Generated 190 of the 190 non-bonded parameter combinations 85: 85: Generated 190 of the 190 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'ASN' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Excluding 1 bonded neighbours molecule type 'NA' 85: 85: turning H bonds into constraints... 85: 85: Excluding 1 bonded neighbours molecule type 'CL' 85: 85: turning H bonds into constraints... 85: 85: Coupling 1 copies of molecule type 'CL' 85: 85: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 85: J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof 85: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 85: Charge 85: J. Chem. Theory Comput. 10 (2014) pp. 381-393 85: -------- -------- --- Thank You --- -------- -------- 85: 85: Number of degrees of freedom in T-Coupling group System is 361.00 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 85: The optimal PME mesh load for parallel simulations is below 0.5 85: and for highly parallel simulations between 0.25 and 0.33, 85: for higher performance, increase the cut-off and the PME grid spacing. 85: 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 85: For free energy simulations, the optimal load limit increases from 0.5 to 85: 0.667 85: 85: 85: 85: There were 5 NOTEs 85: 85: There were 2 WARNINGs 85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Changing nstlist from 10 to 50, rlist from 1.004 to 1.102 85: 85: Using 1 MPI process 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'AA' 85: 20 steps, 0.0 ps. 85: Analysing residue names: 85: There are: 1 Protein residues 85: There are: 56 Water residues 85: There are: 2 Ion residues 85: Analysing Protein... 85: 85: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 85: 85: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: Calculating fourier grid dimensions for X Y Z 85: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 85: 85: Estimate for the relative computational load of the PME mesh part: 0.96 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.109 0.054 199.8 85: (ns/day) (hour/ns) 85: Performance: 33.378 0.719 85: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_s_energy.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_s (84 ms) 85: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp, line 171]: 85: For proper sampling of the (nearly) decoupled state, stochastic dynamics 85: should be used 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 85: Replacing vdwtype=Shift by the equivalent combination of vdwtype=Cut-off 85: and vdw_modifier=Force-switch 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 85: The Berendsen thermostat does not generate the correct kinetic energy 85: distribution, and should not be used for new production simulations (in 85: our opinion). We would recommend the V-rescale thermostat. 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 355.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 85: The optimal PME mesh load for parallel simulations is below 0.5 85: and for highly parallel simulations between 0.25 and 0.33, 85: for higher performance, increase the cut-off and the PME grid spacing. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 85: For free energy simulations, the optimal load limit increases from 0.5 to 85: 0.667 85: 85: 85: 85: There were 4 NOTEs 85: 85: There was 1 WARNING 85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Changing nstlist from 10 to 100, rlist from 1 to 1 85: 85: Using 1 MPI process 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'AA' 85: 100 steps, 0.1 ps. 85: Setting the LD random seed to 1056948191 85: 85: Generated 153 of the 153 non-bonded parameter combinations 85: 85: Generated 153 of the 153 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'ASN' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Coupling 1 copies of molecule type 'ASN' 85: Analysing residue names: 85: There are: 1 Protein residues 85: There are: 56 Water residues 85: Analysing Protein... 85: 85: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 85: 85: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: Calculating fourier grid dimensions for X Y Z 85: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 85: 85: Estimate for the relative computational load of the PME mesh part: 0.94 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 0 % of the run time was spent in domain decomposition, 85: 12 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.329 0.165 199.9 85: (ns/day) (hour/ns) 85: Performance: 52.959 0.453 85: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_energy.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Reading energy frame 30 time 0.030 Reading energy frame 40 time 0.040 Reading energy frame 50 time 0.050 Reading energy frame 60 time 0.060 Reading energy frame 70 time 0.070 Reading energy frame 80 time 0.080 Reading energy frame 90 time 0.090 Reading energy frame 100 time 0.100 Last energy frame read 100 time 0.100 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s (264 ms) 85: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 85: The Berendsen thermostat does not generate the correct kinetic energy 85: distribution, and should not be used for new production simulations (in 85: our opinion). We would recommend the V-rescale thermostat. 85: 85: Generating 1-4 interactions: fudge = 0.5 85: 85: WARNING 2 [file topol.top, line 72]: 85: No default Bond types for perturbed atoms, using normal values 85: 85: 85: WARNING 3 [file topol.top, line 73]: 85: No default Bond types for perturbed atoms, using normal values 85: 85: 85: WARNING 4 [file topol.top, line 98]: 85: No default Angle types for perturbed atoms, using normal values 85: 85: 85: WARNING 5 [file topol.top, line 99]: 85: No default Angle types for perturbed atoms, using normal values 85: 85: 85: WARNING 6 [file topol.top, line 100]: 85: No default Angle types for perturbed atoms, using normal values 85: 85: 85: WARNING 7 [file topol.top, line 101]: 85: No default Angle types for perturbed atoms, using normal values 85: 85: 85: WARNING 8 [file topol.top, line 111]: 85: No default Ryckaert-Bell. types for perturbed atoms, using normal values 85: 85: 85: WARNING 9 [file topol.top, line 112]: 85: No default Ryckaert-Bell. types for perturbed atoms, using normal values 85: 85: 85: WARNING 10 [file topol.top, line 113]: 85: No default Ryckaert-Bell. types for perturbed atoms, using normal values 85: 85: 85: WARNING 11 [file topol.top, line 114]: 85: No default Ryckaert-Bell. types for perturbed atoms, using normal values 85: 85: Number of degrees of freedom in T-Coupling group System is 355.00 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 85: The optimal PME mesh load for parallel simulations is below 0.5 85: and for highly parallel simulations between 0.25 and 0.33, 85: for higher performance, increase the cut-off and the PME grid spacing. 85: 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 85: For free energy simulations, the optimal load limit increases from 0.5 to 85: 0.667 85: 85: 85: 85: There were 2 NOTEs 85: 85: There were 11 WARNINGs 85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Changing nstlist from 10 to 100, rlist from 1 to 1 85: 85: Using 1 MPI process 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'AA' 85: 20 steps, 0.0 ps. 85: Setting the LD random seed to -551953522 85: 85: Generated 136 of the 136 non-bonded parameter combinations 85: 85: Generated 136 of the 136 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'ASN' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: Analysing residue names: 85: There are: 1 Protein residues 85: There are: 56 Water residues 85: Analysing Protein... 85: 85: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 85: 85: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: Calculating fourier grid dimensions for X Y Z 85: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 85: 85: Estimate for the relative computational load of the PME mesh part: 0.94 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.218 0.109 199.8 85: (ns/day) (hour/ns) 85: Performance: 16.636 1.443 85: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_energy.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s (296 ms) 85: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 85: The Berendsen thermostat does not generate the correct kinetic energy 85: distribution, and should not be used for new production simulations (in 85: our opinion). We would recommend the V-rescale thermostat. 85: 85: Generating 1-4 interactions: fudge = 0.5 85: 85: WARNING 2 [file topol.top, line 72]: 85: No default Bond types for perturbed atoms, using normal values 85: 85: 85: WARNING 3 [file topol.top, line 73]: 85: No default Bond types for perturbed atoms, using normal values 85: 85: 85: WARNING 4 [file topol.top, line 98]: 85: No default Angle types for perturbed atoms, using normal values 85: 85: 85: WARNING 5 [file topol.top, line 99]: 85: No default Angle types for perturbed atoms, using normal values 85: 85: 85: WARNING 6 [file topol.top, line 100]: 85: No default Angle types for perturbed atoms, using normal values 85: 85: 85: WARNING 7 [file topol.top, line 101]: 85: No default Angle types for perturbed atoms, using normal values 85: 85: 85: WARNING 8 [file topol.top, line 111]: 85: No default Ryckaert-Bell. types for perturbed atoms, using normal values 85: 85: 85: WARNING 9 [file topol.top, line 112]: 85: No default Ryckaert-Bell. types for perturbed atoms, using normal values 85: 85: 85: WARNING 10 [file topol.top, line 113]: 85: No default Ryckaert-Bell. types for perturbed atoms, using normal values 85: 85: 85: WARNING 11 [file topol.top, line 114]: 85: No default Ryckaert-Bell. types for perturbed atoms, using normal values 85: 85: Number of degrees of freedom in T-Coupling group System is 355.00 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 85: Removing center of mass motion in the presence of position restraints 85: might cause artifacts. When you are using position restraints to 85: equilibrate a macro-molecule, the artifacts are usually negligible. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 85: The optimal PME mesh load for parallel simulations is below 0.5 85: and for highly parallel simulations between 0.25 and 0.33, 85: for higher performance, increase the cut-off and the PME grid spacing. 85: 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 85: For free energy simulations, the optimal load limit increases from 0.5 to 85: 0.667 85: 85: 85: 85: There were 3 NOTEs 85: 85: There were 11 WARNINGs 85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Changing nstlist from 10 to 100, rlist from 1 to 1 85: 85: Using 1 MPI process 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'AA' 85: 20 steps, 0.0 ps. 85: Setting the LD random seed to 66060222 85: 85: Generated 136 of the 136 non-bonded parameter combinations 85: 85: Generated 136 of the 136 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'ASN' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: Analysing residue names: 85: There are: 1 Protein residues 85: There are: 56 Water residues 85: Analysing Protein... 85: 85: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 85: 85: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: Calculating fourier grid dimensions for X Y Z 85: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 85: 85: Estimate for the relative computational load of the PME mesh part: 0.94 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.393 0.197 199.9 85: (ns/day) (hour/ns) 85: Performance: 9.221 2.603 85: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_energy.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s (311 ms) 85: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 85: The Berendsen thermostat does not generate the correct kinetic energy 85: distribution, and should not be used for new production simulations (in 85: our opinion). We would recommend the V-rescale thermostat. 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 355.00 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 85: The optimal PME mesh load for parallel simulations is below 0.5 85: and for highly parallel simulations between 0.25 and 0.33, 85: for higher performance, increase the cut-off and the PME grid spacing. 85: 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 85: For free energy simulations, the optimal load limit increases from 0.5 to 85: 0.667 85: 85: 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Changing nstlist from 10 to 100, rlist from 1 to 1 85: 85: Using 1 MPI process 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'AA' 85: 20 steps, 0.0 ps. 85: Setting the LD random seed to 1178532478 85: 85: Generated 136 of the 136 non-bonded parameter combinations 85: 85: Generated 136 of the 136 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'ASN' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: Analysing residue names: 85: There are: 1 Protein residues 85: There are: 56 Water residues 85: Analysing Protein... 85: 85: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 85: 85: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: Calculating fourier grid dimensions for X Y Z 85: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 85: 85: Estimate for the relative computational load of the PME mesh part: 0.88 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.075 0.037 199.6 85: (ns/day) (hour/ns) 85: Performance: 48.519 0.495 85: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_energy.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s (116 ms) 85: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 85: The Berendsen thermostat does not generate the correct kinetic energy 85: distribution, and should not be used for new production simulations (in 85: our opinion). We would recommend the V-rescale thermostat. 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 355.00 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 85: The optimal PME mesh load for parallel simulations is below 0.5 85: and for highly parallel simulations between 0.25 and 0.33, 85: for higher performance, increase the cut-off and the PME grid spacing. 85: 85: 85: 85: There was 1 NOTE 85: 85: There was 1 WARNING 85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Changing nstlist from 10 to 100, rlist from 1 to 1 85: 85: Using 1 MPI process 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'AA' 85: 20 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.028 0.014 199.1 85: (ns/day) (hour/ns) 85: Performance: 129.202 0.186 85: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_energy.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Setting the LD random seed to 1387830205 85: 85: Generated 136 of the 136 non-bonded parameter combinations 85: 85: Generated 136 of the 136 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'ASN' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: Analysing residue names: 85: There are: 1 Protein residues 85: There are: 56 Water residues 85: Analysing Protein... 85: 85: The largest distance between excluded atoms is 0.331 nm between atom 1 and 9 85: 85: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: Calculating fourier grid dimensions for X Y Z 85: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 85: 85: Estimate for the relative computational load of the PME mesh part: 0.88 85: 85: This run will generate roughly 0 Mb of data 85: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s (101 ms) 85: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 85: With PME there is a minor soft core effect present at the cut-off, 85: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 85: energy conservation, but usually other effects dominate. With a common 85: sigma value of 0.34 nm the fraction of the particle-particle potential at 85: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 85: The Berendsen thermostat does not generate the correct kinetic energy 85: distribution, and should not be used for new production simulations (in 85: our opinion). We would recommend the V-rescale thermostat. 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 355.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 85: The optimal PME mesh load for parallel simulations is below 0.5 85: and for highly parallel simulations between 0.25 and 0.33, 85: for higher performance, increase the cut-off and the PME grid spacing. 85: 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 85: For free energy simulations, the optimal load limit increases from 0.5 to 85: 0.667 85: 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Changing nstlist from 10 to 100, rlist from 1 to 1 85: 85: Using 1 MPI process 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'AA' 85: 20 steps, 0.0 ps. 85: Setting the LD random seed to 1040179167 85: 85: Generated 136 of the 136 non-bonded parameter combinations 85: 85: Generated 136 of the 136 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'ASN' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: Analysing residue names: 85: There are: 1 Protein residues 85: There are: 56 Water residues 85: Analysing Protein... 85: 85: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 85: 85: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: Calculating fourier grid dimensions for X Y Z 85: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 85: 85: Estimate for the relative computational load of the PME mesh part: 0.94 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.120 0.060 199.8 85: (ns/day) (hour/ns) 85: Performance: 30.288 0.792 85: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_energy.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s (167 ms) 85: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 85: With PME there is a minor soft core effect present at the cut-off, 85: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 85: energy conservation, but usually other effects dominate. With a common 85: sigma value of 0.34 nm the fraction of the particle-particle potential at 85: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 85: The Berendsen thermostat does not generate the correct kinetic energy 85: distribution, and should not be used for new production simulations (in 85: our opinion). We would recommend the V-rescale thermostat. 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 355.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 85: The optimal PME mesh load for parallel simulations is below 0.5 85: and for highly parallel simulations between 0.25 and 0.33, 85: for higher performance, increase the cut-off and the PME grid spacing. 85: 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 85: For free energy simulations, the optimal load limit increases from 0.5 to 85: 0.667 85: 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Changing nstlist from 10 to 100, rlist from 1 to 1 85: 85: Using 1 MPI process 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'AA' 85: 20 steps, 0.0 ps. 85: Setting the LD random seed to -1197689661 85: 85: Generated 136 of the 136 non-bonded parameter combinations 85: 85: Generated 136 of the 136 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'ASN' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: Analysing residue names: 85: There are: 1 Protein residues 85: There are: 56 Water residues 85: Analysing Protein... 85: 85: The largest distance between non-perturbed excluded atoms is 0.172 nm between atom 8 and 9 85: 85: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: Calculating fourier grid dimensions for X Y Z 85: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 85: 85: Estimate for the relative computational load of the PME mesh part: 0.88 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.100 0.050 199.7 85: (ns/day) (hour/ns) 85: Performance: 36.386 0.660 85: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_energy.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s (147 ms) 85: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest (2685 ms total) 85: 85: [----------] Global test environment tear-down 85: [==========] 12 tests from 1 test suite ran. (2702 ms total) 85: [ PASSED ] 12 tests. 85/91 Test #85: MdrunFEPTests ................................ Passed 3.00 sec test 86 Start 86: MdrunPullTests 86: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-pull-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunPullTests.xml" 86: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 86: Test timeout computed to be: 600 86: [==========] Running 4 tests from 1 test suite. 86: [----------] Global test environment set-up. 86: [----------] 4 tests from PullTest/PullIntegrationTest 86: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/0 86: Generating 1-4 interactions: fudge = 0.5 86: Pull group 1 'r_1' has 3 atoms 86: Pull group 2 'r_2' has 3 atoms 86: Number of degrees of freedom in T-Coupling group System is 1293.00 86: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 303.122 K for 86: determining the Verlet buffer size 86: 86: Pull group natoms pbc atom distance at start reference at t=0 86: 1 3 2 86: 2 3 5 0.575 nm 0.600 nm 86: 86: There was 1 NOTE 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 20 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.175 0.087 199.8 86: (ns/day) (hour/ns) 86: Performance: 20.768 1.156 86: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/0 (412 ms) 86: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/1 86: Generating 1-4 interactions: fudge = 0.5 86: Pull group 1 'r_1' has 3 atoms 86: Pull group 2 'r_2' has 3 atoms 86: Number of degrees of freedom in T-Coupling group System is 1293.00 86: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 303.122 K for 86: determining the Verlet buffer size 86: 86: Pull group natoms pbc atom distance at start reference at t=0 86: 1 3 2 86: 2 3 5 0.301 nm 0.400 nm 86: 86: There was 1 NOTE 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 20 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: NOTE: 25 % of the run time was spent in pair search, 86: you might want to increase nstlist (this has no effect on accuracy) 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.200 0.100 199.9 86: (ns/day) (hour/ns) 86: Performance: 18.118 1.325 86: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/1 (459 ms) 86: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/2 86: Generating 1-4 interactions: fudge = 0.5 86: Pull group 1 'r_1' has 3 atoms 86: Pull group 2 'r_2' has 3 atoms 86: Pull group 3 'r_3' has 3 atoms 86: Number of degrees of freedom in T-Coupling group System is 1292.00 86: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 303.357 K for 86: determining the Verlet buffer size 86: 86: Pull group natoms pbc atom distance at start reference at t=0 86: 1 3 2 86: 2 3 5 0.575 nm 0.500 nm 86: 1 3 2 86: 3 3 8 0.331 nm 0.400 nm 86: 86: There was 1 NOTE 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 20 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.357 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: NOTE: 18 % of the run time was spent in pair search, 86: you might want to increase nstlist (this has no effect on accuracy) 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.063 0.032 199.6 86: (ns/day) (hour/ns) 86: Performance: 57.415 0.418 86: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/2 (271 ms) 86: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/3 86: Generating 1-4 interactions: fudge = 0.5 86: Pull group 1 'r_1' has 3 atoms 86: Pull group 2 'r_2' has 3 atoms 86: Number of degrees of freedom in T-Coupling group System is 1293.00 86: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3_input.mdp]: 86: NVE simulation: will use the initial temperature of 303.122 K for 86: determining the Verlet buffer size 86: 86: Pull group natoms pbc atom distance at start reference at t=0 86: 1 3 2 86: 2 3 5 0.575 nm 0.000 nm 86: 1 3 2 86: 2 3 5 0.050 nm 0.000 nm 86: 86: There was 1 NOTE 86: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 20 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.100 0.050 199.8 86: (ns/day) (hour/ns) 86: Performance: 36.284 0.661 86: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/3 (295 ms) 86: [----------] 4 tests from PullTest/PullIntegrationTest (1440 ms total) 86: 86: [----------] Global test environment tear-down 86: [==========] 4 tests from 1 test suite ran. (1479 ms total) 86: [ PASSED ] 4 tests. 86/91 Test #86: MdrunPullTests ............................... Passed 1.82 sec test 87 Start 87: MdrunRotationTests 87: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-rotation-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunRotationTests.xml" 87: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 87: Test timeout computed to be: 600 87: [==========] Running 12 tests from 1 test suite. 87: [----------] Global test environment set-up. 87: [----------] 12 tests from RotationWorks/RotationTest 87: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 87: Enforced rotation: Group 0 (iso) normalized rot. vector: 0.267261 0.534522 0.801784 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: Rotation group 0 'system' has 4 atoms 87: Number of degrees of freedom in T-Coupling group rest is 9.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: Enforced rotation: group 0 has 4 reference positions. 87: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 87: trr version: GMX_trn_file (single precision) 87: 87: There were 2 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 1 MPI process 87: Using 2 OpenMP threads 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 87: 25 steps, 0.1 ps. 87: Setting the LD random seed to -285303053 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonA' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonB' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonC' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonD' 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.034 0.017 199.5 87: (ns/day) (hour/ns) 87: Performance: 266.616 0.090 87: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 87: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 (23 ms) 87: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 87: Enforced rotation: Group 0 (iso-pf) normalized rot. vector: 0.267261 0.534522 0.801784 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: Rotation group 0 'system' has 4 atoms 87: Number of degrees of freedom in T-Coupling group rest is 9.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: Enforced rotation: group 0 has 4 reference positions. 87: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 87: 87: There were 2 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 1 MPI process 87: Using 2 OpenMP threads 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 87: 25 steps, 0.1 ps. 87: Setting the LD random seed to -71368787 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonA' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonB' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonC' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonD' 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.072 0.036 199.6 87: (ns/day) (hour/ns) 87: Performance: 123.721 0.194 87: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 87: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 (42 ms) 87: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 87: Enforced rotation: Group 0 (pm) normalized rot. vector: 0.267261 0.534522 0.801784 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: Rotation group 0 'system' has 4 atoms 87: Number of degrees of freedom in T-Coupling group rest is 9.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: Enforced rotation: group 0 has 4 reference positions. 87: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 87: 87: There were 2 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 1 MPI process 87: Using 2 OpenMP threads 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 87: 25 steps, 0.1 ps. 87: Setting the LD random seed to 2147417013 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonA' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonB' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonC' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonD' 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.053 0.026 199.7 87: (ns/day) (hour/ns) 87: Performance: 169.969 0.141 87: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 87: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 (32 ms) 87: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 87: Enforced rotation: Group 0 (pm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: Rotation group 0 'system' has 4 atoms 87: Number of degrees of freedom in T-Coupling group rest is 9.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: Enforced rotation: group 0 has 4 reference positions. 87: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 87: 87: There were 2 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 1 MPI process 87: Using 2 OpenMP threads 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 87: 25 steps, 0.1 ps. 87: Setting the LD random seed to -709592065 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonA' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonB' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonC' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonD' 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.058 0.029 199.5 87: (ns/day) (hour/ns) 87: Performance: 155.832 0.154 87: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 87: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 (42 ms) 87: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 87: Enforced rotation: Group 0 (rm) normalized rot. vector: 0.267261 0.534522 0.801784 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: Rotation group 0 'system' has 4 atoms 87: Number of degrees of freedom in T-Coupling group rest is 9.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: Enforced rotation: group 0 has 4 reference positions. 87: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 87: 87: There were 2 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 1 MPI process 87: Using 2 OpenMP threads 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 87: 25 steps, 0.1 ps. 87: Setting the LD random seed to -539160681 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonA' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonB' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonC' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonD' 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.069 0.035 199.4 87: (ns/day) (hour/ns) 87: Performance: 129.741 0.185 87: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 87: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 (40 ms) 87: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 87: Enforced rotation: Group 0 (rm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: Rotation group 0 'system' has 4 atoms 87: Number of degrees of freedom in T-Coupling group rest is 9.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: Enforced rotation: group 0 has 4 reference positions. 87: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 87: 87: There were 2 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 1 MPI process 87: Using 2 OpenMP threads 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 87: 25 steps, 0.1 ps. 87: Setting the LD random seed to -1610956865 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonA' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonB' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonC' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonD' 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.097 0.049 199.6 87: (ns/day) (hour/ns) 87: Performance: 92.072 0.261 87: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 87: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 (55 ms) 87: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 87: Enforced rotation: Group 0 (rm2) normalized rot. vector: 0.267261 0.534522 0.801784 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: Rotation group 0 'system' has 4 atoms 87: Number of degrees of freedom in T-Coupling group rest is 9.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: Enforced rotation: group 0 has 4 reference positions. 87: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 87: 87: There were 2 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 1 MPI process 87: Using 2 OpenMP threads 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 87: 25 steps, 0.1 ps. 87: Setting the LD random seed to -671252997 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonA' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonB' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonC' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonD' 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.039 0.020 199.6 87: (ns/day) (hour/ns) 87: Performance: 228.891 0.105 87: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 87: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 (39 ms) 87: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 87: Enforced rotation: Group 0 (rm2-pf) normalized rot. vector: 0.267261 0.534522 0.801784 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: Rotation group 0 'system' has 4 atoms 87: Number of degrees of freedom in T-Coupling group rest is 9.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: Enforced rotation: group 0 has 4 reference positions. 87: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 87: 87: There were 2 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 1 MPI process 87: Using 2 OpenMP threads 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 87: 25 steps, 0.1 ps. 87: Setting the LD random seed to 2059334143 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonA' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonB' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonC' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonD' 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.040 0.020 198.8 87: (ns/day) (hour/ns) 87: Performance: 222.960 0.108 87: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 87: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 (29 ms) 87: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 87: Enforced rotation: Group 0 (flex) normalized rot. vector: 0.267261 0.534522 0.801784 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: Rotation group 0 'system' has 4 atoms 87: Number of degrees of freedom in T-Coupling group rest is 9.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: Enforced rotation: group 0 has 4 reference positions. 87: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 87: 87: There were 2 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 1 MPI process 87: Using 2 OpenMP threads 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 87: 25 steps, 0.1 ps. 87: Setting the LD random seed to 2147473405 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonA' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonB' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonC' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonD' 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.065 0.032 199.5 87: (ns/day) (hour/ns) 87: Performance: 138.371 0.173 87: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 87: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 (43 ms) 87: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 87: Enforced rotation: Group 0 (flex-t) normalized rot. vector: 0.267261 0.534522 0.801784 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: Rotation group 0 'system' has 4 atoms 87: Number of degrees of freedom in T-Coupling group rest is 9.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: Enforced rotation: group 0 has 4 reference positions. 87: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 87: 87: There were 2 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 1 MPI process 87: Using 2 OpenMP threads 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 87: 25 steps, 0.1 ps. 87: Setting the LD random seed to -536887747 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonA' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonB' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonC' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonD' 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.036 0.018 199.5 87: (ns/day) (hour/ns) 87: Performance: 251.712 0.095 87: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 87: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 (23 ms) 87: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 87: Enforced rotation: Group 0 (flex2) normalized rot. vector: 0.267261 0.534522 0.801784 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: Rotation group 0 'system' has 4 atoms 87: Number of degrees of freedom in T-Coupling group rest is 9.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: Enforced rotation: group 0 has 4 reference positions. 87: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 87: 87: There were 2 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 1 MPI process 87: Using 2 OpenMP threads 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 87: 25 steps, 0.1 ps. 87: Setting the LD random seed to -1616905860 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonA' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonB' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonC' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonD' 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.044 0.022 199.5 87: (ns/day) (hour/ns) 87: Performance: 205.828 0.117 87: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 87: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 (31 ms) 87: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 87: Enforced rotation: Group 0 (flex2-t) normalized rot. vector: 0.267261 0.534522 0.801784 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: Rotation group 0 'system' has 4 atoms 87: Number of degrees of freedom in T-Coupling group rest is 9.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: Enforced rotation: group 0 has 4 reference positions. 87: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 87: 87: There were 2 NOTEs 87: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 1 MPI process 87: Using 2 OpenMP threads 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 87: 25 steps, 0.1 ps. 87: Setting the LD random seed to -287572737 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonA' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonB' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonC' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonD' 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.055 0.028 199.5 87: (ns/day) (hour/ns) 87: Performance: 162.806 0.147 87: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 87: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 (35 ms) 87: [----------] 12 tests from RotationWorks/RotationTest (441 ms total) 87: 87: [----------] Global test environment tear-down 87: [==========] 12 tests from 1 test suite ran. (470 ms total) 87: [ PASSED ] 12 tests. 87/91 Test #87: MdrunRotationTests ........................... Passed 0.78 sec test 88 Start 88: MdrunSimulatorComparison 88: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-simulator-comparison-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunSimulatorComparison.xml" 88: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 88: Test timeout computed to be: 600 88: [==========] Running 0 tests from 0 test suites. 88: [==========] 0 tests from 0 test suites ran. (0 ms total) 88: [ PASSED ] 0 tests. 88: 88: YOU HAVE 82 DISABLED TESTS 88: 88/91 Test #88: MdrunSimulatorComparison ..................... Passed 0.33 sec test 89 Start 89: MdrunVirtualSiteTests 89: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-vsites-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunVirtualSiteTests.xml" 89: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 89: Test timeout computed to be: 600 89: [==========] Running 37 tests from 2 test suites. 89: [----------] Global test environment set-up. 89: [----------] 1 test from VirtualSiteVelocityTest 89: [ RUN ] VirtualSiteVelocityTest.ReferenceIsCorrect 89: [ OK ] VirtualSiteVelocityTest.ReferenceIsCorrect (0 ms) 89: [----------] 1 test from VirtualSiteVelocityTest (6 ms total) 89: 89: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 89: NVE simulation with an initial temperature of zero: will use a Verlet 89: buffer of 10%. Check your energy drift! 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 4 NOTEs 89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: 89: Dynamic load balancing report: 89: DLB was off during the run due to low measured imbalance. 89: Average load imbalance: 6.7%. 89: The balanceable part of the MD step is 40%, load imbalance is computed from this. 89: Part of the total run time spent waiting due to load imbalance: 2.7%. 89: 89: 89: NOTE: 48 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.032 0.016 198.7 89: (ns/day) (hour/ns) 89: Performance: 48.646 0.493 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading virtual site types... 89: Reading virtual site types... 89: trr version: GMX_trn_file (single precision) 89: trr version: GMX_trn_file (single precision) 89: 89: 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 (34 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 89: NVE simulation with an initial temperature of zero: will use a Verlet 89: buffer of 10%. Check your energy drift! 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: 89: This run will generate roughly 0 Mb of data 89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: 89: Dynamic load balancing report: 89: DLB was off during the run due to low measured imbalance. 89: Average load imbalance: 9.7%. 89: The balanceable part of the MD step is 38%, load imbalance is computed from this. 89: Part of the total run time spent waiting due to load imbalance: 3.7%. 89: 89: 89: NOTE: 49 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.041 0.020 199.5 89: (ns/day) (hour/ns) 89: Performance: 38.159 0.629 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 89: NVE simulation with an initial temperature of zero: will use a Verlet 89: buffer of 10%. Check your energy drift! 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: Reading virtual site types... 89: Reading virtual site types... 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 (28 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: 89: Dynamic load balancing report: 89: DLB was off during the run due to low measured imbalance. 89: Average load imbalance: 3.2%. 89: The balanceable part of the MD step is 41%, load imbalance is computed from this. 89: Part of the total run time spent waiting due to load imbalance: 1.3%. 89: 89: 89: NOTE: 49 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.052 0.026 199.3 89: (ns/day) (hour/ns) 89: Performance: 29.975 0.801 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpReading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading virtual site types... 89: ectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading virtual site types... 89: 89: 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 (30 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 89: There are 6 non-linear virtual site constructions. Their contribution to 89: the energy error is approximated. In most cases this does not affect the 89: error significantly. 89: 89: 89: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 4 NOTEs 89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 89: 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 57 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.058 0.030 196.7 89: (ns/day) (hour/ns) 89: Performance: 26.227 0.915 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading virtual site types... 89: 89: 89: Reading virtual site types... 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 (55 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 89: There are 6 non-linear virtual site constructions. Their contribution to 89: the energy error is approximated. In most cases this does not affect the 89: error significantly. 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 89: 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 48 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.045 0.022 199.4 89: (ns/day) (hour/ns) 89: Performance: 34.832 0.689 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 89: There are 6 non-linear virtual site constructions. Their contribution to 89: the energy error is approximated. In most cases this does not affect the 89: error significantly. 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 89: 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: Reading virtual site types... 89: Reading virtual site types... 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 (35 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 52 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.036 0.018 199.4 89: (ns/day) (hour/ns) 89: Performance: 43.149 0.556 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: 89: Reading virtual site types... 89: Reading virtual site types... 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 (30 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 89: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 89: 1 89: 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 89: There are 6 non-linear virtual site constructions. Their contribution to 89: the energy error is approximated. In most cases this does not affect the 89: error significantly. 89: 89: 89: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 5 NOTEs 89: 89: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 89: 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 54 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.028 0.014 199.1 89: (ns/day) (hour/ns) 89: Performance: 55.089 0.436 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 89: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 89: 1 89: 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 89: There are 6 non-linear virtual site constructions. Their contribution to 89: the energy error is approximated. In most cases this does not affect the 89: error significantly. 89: 89: 89: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 5 NOTEs 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: Reading virtual site types... 89: Reading virtual site types... 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 (32 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 89: 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 49 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.037 0.019 199.2 89: (ns/day) (hour/ns) 89: Performance: 41.575 0.577 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading virtual site types... 89: 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading virtual site types... 89: 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 (36 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 89: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 89: 1 89: 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 89: There are 6 non-linear virtual site constructions. Their contribution to 89: the energy error is approximated. In most cases this does not affect the 89: error significantly. 89: 89: 89: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 5 NOTEs 89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 89: 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 49 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.051 0.026 198.9 89: (ns/day) (hour/ns) 89: Performance: 30.401 0.789 89: Reading virtual site types... 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading virtual site types... 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 (40 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 89: 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: 89: This run will generate roughly 0 Mb of data 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 89: NVE simulation with an initial temperature of zero: will use a Verlet 89: buffer of 10%. Check your energy drift! 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: 89: Dynamic load balancing report: 89: DLB was off during the run due to low measured imbalance. 89: Average load imbalance: 4.4%. 89: The balanceable part of the MD step is 19%, load imbalance is computed from this. 89: Part of the total run time spent waiting due to load imbalance: 0.8%. 89: 89: 89: NOTE: 57 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.072 0.044 164.3 89: (ns/day) (hour/ns) 89: Performance: 17.783 1.350 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: Reading virtual site types... 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading virtual site types... 89: 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 (63 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: 89: This run will generate roughly 0 Mb of data 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 89: NVE simulation with an initial temperature of zero: will use a Verlet 89: buffer of 10%. Check your energy drift! 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: 89: Dynamic load balancing report: 89: DLB was off during the run due to low measured imbalance. 89: Average load imbalance: 5.0%. 89: The balanceable part of the MD step is 42%, load imbalance is computed from this. 89: Part of the total run time spent waiting due to load imbalance: 2.1%. 89: 89: 89: NOTE: 60 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.060 0.032 186.6 89: (ns/day) (hour/ns) 89: Performance: 24.365 0.985 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: 89: Reading virtual site types... 89: Reading virtual site types... 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 (36 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 (0 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 89: There are 6 non-linear virtual site constructions. Their contribution to 89: the energy error is approximated. In most cases this does not affect the 89: error significantly. 89: 89: 89: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 4 NOTEs 89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 89: 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 49 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: Reading virtual site types... 89: Core t (s) Wall t (s) (%) 89: Time: 0.039 0.019 199.4 89: 89: (ns/day) (hour/ns) 89: Performance: 40.209 0.597 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading virtual site types... 89: 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 (43 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 89: There are 6 non-linear virtual site constructions. Their contribution to 89: the energy error is approximated. In most cases this does not affect the 89: error significantly. 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 89: 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 49 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.026 0.013 199.3 89: (ns/day) (hour/ns) 89: Performance: 58.610 0.409 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: Reading virtual site types... 89: Reading virtual site types... 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 (33 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 (0 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 89: There are 6 non-linear virtual site constructions. Their contribution to 89: the energy error is approximated. In most cases this does not affect the 89: error significantly. 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: 89: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 89: 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 49 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.053 0.026 199.5 89: (ns/day) (hour/ns) 89: Performance: 29.394 0.817 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: Reading virtual site types... 89: Reading virtual site types... 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 (46 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 89: There are 6 non-linear virtual site constructions. Their contribution to 89: the energy error is approximated. In most cases this does not affect the 89: error significantly. 89: 89: 89: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 89: 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 49 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.051 0.026 198.3 89: (ns/day) (hour/ns) 89: Performance: 30.293 0.792 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: Reading virtual site types... 89: Reading virtual site types... 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 (47 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 (0 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 89: There are 6 non-linear virtual site constructions. Their contribution to 89: the energy error is approximated. In most cases this does not affect the 89: error significantly. 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 89: 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 49 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.032 0.016 199.3 89: (ns/day) (hour/ns) 89: Performance: 48.542 0.494 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: Reading virtual site types... 89: Reading virtual site types... 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 (38 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 89: There are 6 non-linear virtual site constructions. Their contribution to 89: the energy error is approximated. In most cases this does not affect the 89: error significantly. 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: 89: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 89: 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 48 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.031 0.016 198.8 89: (ns/day) (hour/ns) 89: Performance: 49.097 0.489 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading virtual site types... 89: 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading virtual site types... 89: 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 (29 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 89: There are 6 non-linear virtual site constructions. Their contribution to 89: the energy error is approximated. In most cases this does not affect the 89: error significantly. 89: 89: 89: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 89: 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 48 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.044 0.022 197.8 89: (ns/day) (hour/ns) 89: Performance: 35.299 0.680 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: Reading virtual site types... 89: Reading virtual site types... 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 (44 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 (0 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 (0 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 (0 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 (0 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 (0 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 (0 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 89: There are 6 non-linear virtual site constructions. Their contribution to 89: the energy error is approximated. In most cases this does not affect the 89: error significantly. 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 89: 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 48 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.034 0.017 198.6 89: (ns/day) (hour/ns) 89: Performance: 45.331 0.529 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading virtual site types... 89: 89: Reading virtual site types... 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 (35 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 89: There are 6 non-linear virtual site constructions. Their contribution to 89: the energy error is approximated. In most cases this does not affect the 89: error significantly. 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 89: 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 49 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.072 0.036 199.3 89: (ns/day) (hour/ns) 89: Performance: 21.568 1.113 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: Reading virtual site types... 89: Reading virtual site types... 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 (65 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 89: There are 6 non-linear virtual site constructions. Their contribution to 89: the energy error is approximated. In most cases this does not affect the 89: error significantly. 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: 89: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: Compiled SIMD is SSE4.1, but AVX2_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 89: 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 49 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.052 0.026 199.5 89: (ns/day) (hour/ns) 89: Performance: 29.767 0.806 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: 89: Reading virtual site types... 89: Reading virtual site types... 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 (51 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 (0 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 (0 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 (0 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 (0 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 (0 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 (0 ms) 89: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest (883 ms total) 89: 89: [----------] Global test environment tear-down 89: [==========] 37 tests from 2 test suites ran. (942 ms total) 89: [ PASSED ] 37 tests. 89/91 Test #89: MdrunVirtualSiteTests ........................ Passed 1.38 sec test 90 Start 90: EnsembleHistogramPotentialPlugin.ForceCalc 90: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/gmxapi_extension_histogram-test "--gtest_filter=EnsembleHistogramPotentialPlugin.ForceCalc" 90: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/tests 90: Test timeout computed to be: 1500 90: Running main() from ./src/external/googletest/googletest/src/gtest_main.cc 90: Note: Google Test filter = EnsembleHistogramPotentialPlugin.ForceCalc 90: [==========] Running 1 test from 1 test suite. 90: [----------] Global test environment set-up. 90: [----------] 1 test from EnsembleHistogramPotentialPlugin 90: [ RUN ] EnsembleHistogramPotentialPlugin.ForceCalc 90: [ OK ] EnsembleHistogramPotentialPlugin.ForceCalc (0 ms) 90: [----------] 1 test from EnsembleHistogramPotentialPlugin (0 ms total) 90: 90: [----------] Global test environment tear-down 90: [==========] 1 test from 1 test suite ran. (0 ms total) 90: [ PASSED ] 1 test. 90/91 Test #90: EnsembleHistogramPotentialPlugin.ForceCalc ... Passed 0.28 sec test 91 Start 91: EnsembleBoundingPotentialPlugin.ForceCalc 91: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/gmxapi_extension_bounding-test "--gtest_filter=EnsembleBoundingPotentialPlugin.ForceCalc" 91: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/tests 91: Test timeout computed to be: 1500 91: Running main() from ./src/external/googletest/googletest/src/gtest_main.cc 91: Note: Google Test filter = EnsembleBoundingPotentialPlugin.ForceCalc 91: [==========] Running 1 test from 1 test suite. 91: [----------] Global test environment set-up. 91: [----------] 1 test from EnsembleBoundingPotentialPlugin 91: [ RUN ] EnsembleBoundingPotentialPlugin.ForceCalc 91: [ OK ] EnsembleBoundingPotentialPlugin.ForceCalc (0 ms) 91: [----------] 1 test from EnsembleBoundingPotentialPlugin (0 ms total) 91: 91: [----------] Global test environment tear-down 91: [==========] 1 test from 1 test suite ran. (0 ms total) 91: [ PASSED ] 1 test. 91/91 Test #91: EnsembleBoundingPotentialPlugin.ForceCalc .... Passed 0.26 sec 100% tests passed, 0 tests failed out of 91 Label Time Summary: GTest = 427.79 sec*proc (87 tests) IntegrationTest = 276.06 sec*proc (30 tests) MpiTest = 325.77 sec*proc (23 tests) QuickGpuTest = 88.60 sec*proc (20 tests) SlowGpuTest = 256.11 sec*proc (14 tests) SlowTest = 123.43 sec*proc (13 tests) UnitTest = 28.31 sec*proc (44 tests) Total Test time (real) = 204.56 sec touch build-mpi dh_testdir (mkdir -p build/documentation ; cd build/documentation; \ LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2024.4/build/documentation/lib cmake /build/reproducible-path/gromacs-2024.4 \ -DCMAKE_BUILD_TYPE=Debug -DGMX_OPENMP=OFF -DGMX_SIMD=None -DGMXAPI=ON \ -DGMX_PYTHON_PACKAGE=ON -DGMX_GPU=OFF -DCMAKE_VERBOSE_MAKEFILE=ON \ -DCMAKE_RULE_MESSAGES=OFF -DGMX_BUILD_MANUAL=ON -DGMX_BUILD_HELP=ON \ -DGMX_VERSION_STRING_OF_FORK="Debian-2024.4-1") -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.12.7", minimum required is "3.7") found components: Interpreter Development Development.Module Development.Embed -- Performing Test CFLAGS_PRAGMA -- Performing Test CFLAGS_PRAGMA - Success -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_PRAGMA -- Performing Test CXXFLAGS_PRAGMA - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- GROMACS is being built without library MPI support (-DGMX_MPI=no). However MPI is potentially useful for the gmxapi Python API, so we will search for MPI anyway. If this causes problems, disable the check with -DCMAKE_DISABLE_FIND_PACKAGE_MPI=on. -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") found components: CXX -- Using default binary suffix: "" -- Using default library suffix: "" -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- SIMD instructions disabled -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - AMD -- Detected build CPU brand - AMD EPYC-Rome Processor -- Detected build CPU family - 23 -- Detected build CPU model - 49 -- Detected build CPU stepping - 0 -- Detected build CPU features - aes amd apic avx avx2 clfsh cmov cx8 cx16 f16c fma lahf misalignsse mmx msr pclmuldq pdpe1gb popcnt pse rdrnd rdtscp sha sse2 sse3 sse4a sse4.1 sse4.2 ssse3 x2apic -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3f' -- Found fftw3f, version 3.3.10 -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/x86_64-linux-gnu/liblapack.so;/usr/lib/x86_64-linux-gnu/libblas.so -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed CMake Deprecation Warning at src/external/googletest/CMakeLists.txt:4 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. CMake Deprecation Warning at src/external/googletest/googlemock/CMakeLists.txt:39 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. CMake Deprecation Warning at src/external/googletest/googletest/CMakeLists.txt:49 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Found Python: /usr/bin/python3 (found version "3.12.7") found components: Interpreter -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAVE_NO_DEBUG_DISABLES_OPTIMIZATION -- Performing Test HAVE_NO_DEBUG_DISABLES_OPTIMIZATION - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test HAS_WARNING_NO_ARRAY_BOUNDS -- Performing Test HAS_WARNING_NO_ARRAY_BOUNDS - Success -- Performing Test HAS_WARNING_NO_DEPRECATED_NON_PROTOTYPE -- Performing Test HAS_WARNING_NO_DEPRECATED_NON_PROTOTYPE - Success -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Performing Test HAS_FLTO -- Performing Test HAS_FLTO - Success -- Configuring Python package for gmxapi version 0.4.0 -- Using /build/reproducible-path/gromacs-2024.4/build/documentation/bin/gmx from build tree. -- Found pybind11: /usr/include (found version "2.13.6") -- Found Python interpreter: /usr/bin/python3 -- Python site-packages directory is /usr/lib/python./site-packages -- Found Doxygen: /usr/bin/doxygen (found version "1.9.8") found components: doxygen dot -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "7.4.7", minimum required is "4.0.0") found components: pygments -- Found LATEX: /usr/bin/latex -- Configuring done (36.8s) -- Generating done (1.6s) -- Build files have been written to: /build/reproducible-path/gromacs-2024.4/build/documentation /usr/bin/make -j12 manual -C build/documentation make[1]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/cmake -P /build/reproducible-path/gromacs-2024.4/build/documentation/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2024.4 -B/build/reproducible-path/gromacs-2024.4/build/documentation --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 manual make[2]: Entering directory 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/build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/selection /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/selection /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_zlib.dir/build.make src/gromacs/CMakeFiles/tng_io_zlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/CMakeFiles/tng_io_zlib.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f _deps/muparser-build/CMakeFiles/muparser.dir/build.make _deps/muparser-build/CMakeFiles/muparser.dir/depend /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make 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/build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/external/muparser /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/_deps/muparser-build /build/reproducible-path/gromacs-2024.4/build/documentation/_deps/muparser-build/CMakeFiles/muparser.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/options /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/options /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" /usr/bin/make -f docs/CMakeFiles/sphinx-image-conversion.dir/build.make docs/CMakeFiles/sphinx-image-conversion.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/errhandler.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/gm convert 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VERSION_OUT=/build/reproducible-path/gromacs-2024.4/build/documentation/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2024.4-1 -P /build/reproducible-path/gromacs-2024.4/cmake/gmxGenerateVersionInfoWithoutGit.cmake cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -MF 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make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/programs /build/reproducible-path/gromacs-2024.4/build/documentation/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY 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-I/build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/lz77.c make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [ 0%] Built target lmfit_objlib cd 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src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/tng_compress.c cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2024.4/docs/reference-manual/algorithms/plots/dd-tric.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/dd-tric.png cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/collective.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-deprecated-non-prototype -MD -MT src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/inftrees.c.o -MF CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/inftrees.c.o.d -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/inftrees.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/external/zlib/inftrees.c [ 0%] Built target energyanalysis cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2024.4/docs/reference-manual/algorithms/plots/flowchart.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch 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/build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/vals16.c cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/warnmalloc.c cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline 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/build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -MF CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o.d -o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/legacymodules.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/options/basicoptions.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-deprecated-non-prototype -MD -MT src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/uncompr.c.o -MF CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/uncompr.c.o.d -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/uncompr.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/external/zlib/uncompr.c [ 0%] Built target linearalgebra cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvar_neuralnetworkcompute.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/reduce_fast.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-deprecated-non-prototype -MD -MT src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/zutil.c.o -MF CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/zutil.c.o.d -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/zutil.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/external/zlib/zutil.c make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [ 1%] Built target tng_io_zlib cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 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/build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/group.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/scanner.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/tmpi_init.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/lib/tng_io.c cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/topology.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/_deps/muparser-build && /usr/bin/c++ -DGMX_DOUBLE=0 -DMUPARSERLIB_EXPORTS -DMUPARSER_DLL -D_DEBUG -Dmuparser_EXPORTS -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-long-long -pedantic -g -std=c++11 -fPIC -MD -MT _deps/muparser-build/CMakeFiles/muparser.dir/src/muParserDLL.cpp.o -MF CMakeFiles/muparser.dir/src/muParserDLL.cpp.o.d -o CMakeFiles/muparser.dir/src/muParserDLL.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/muparser/src/muParserDLL.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [ 1%] Built target gmx_objlib /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/programs /build/reproducible-path/gromacs-2024.4/build/documentation/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fno-inline 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src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/list.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/type.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/scan.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/numa_malloc.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2024.4/docs/reference-manual/algorithms/plots/free2.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/free2.png make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [ 1%] Built target scanner cd /build/reproducible-path/gromacs-2024.4/build/documentation/_deps/muparser-build && /usr/bin/c++ -DGMX_DOUBLE=0 -DMUPARSERLIB_EXPORTS -DMUPARSER_DLL -D_DEBUG -Dmuparser_EXPORTS -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-long-long -pedantic -g -std=c++11 -fPIC -MD -MT _deps/muparser-build/CMakeFiles/muparser.dir/src/muParserError.cpp.o -MF CMakeFiles/muparser.dir/src/muParserError.cpp.o.d -o CMakeFiles/muparser.dir/src/muParserError.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/muparser/src/muParserError.cpp /usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/docs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/docs /build/reproducible-path/gromacs-2024.4/build/documentation/docs/CMakeFiles/sphinx-input-rst.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/reference-manual/analysis/plots/sgangle.pdf /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/reference-manual/analysis/plots/sgangle.pdf cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2024.4/build/documentation/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2024.4/docs/conf.cmakein.py -D VERSION_OUT=/build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/conf.py -D CMAKE_MINIMUM_REQUIRED_VERSION=3.18.4 -D EXPECTED_DOXYGEN_VERSION=1.8.5 -D EXPECTED_SPHINX_VERSION=4.0.0 -D GMX_ADMIN_DIR=/build/reproducible-path/gromacs-2024.4/admin -D GMX_LMFIT_REQUIRED_VERSION=7.0 -D "GMX_MANUAL_DOI_STRING=This is not a release build of GROMACS, so please reference one of the GROMACS papers and the base release of the manual." -D GMX_TNG_MINIMUM_REQUIRED_VERSION=1.7.10 -D "GMX_SOURCE_DOI_STRING=This is not a release build of GROMACS. Please reference one of the GROMACS papers, as well as the base release that this version is built from. Also, please state what modifcations have been performed or where the version was sourced from." -D GMXAPI_PYTHON_STAGING_DIR=/build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi/gmxapi_staging -D IMAGE_CONVERT_STRING=gmx_image_convert_possible -D REGRESSIONTEST_VERSION=2024.4 -D REQUIRED_CUDA_COMPUTE_CAPABILITY=3.5 -D REQUIRED_CUDA_VERSION=11.0 -D REQUIRED_OPENCL_MIN_VERSION= -D REGRESSIONTEST_MD5SUM_STRING=unknown -D RELENG_PATH= -D SOURCE_MD5SUM=unknown -D SPHINX_EXTENSION_PATH=/build/reproducible-path/gromacs-2024.4/docs -D "GMX_CURRENT_CONTRIBUTORS_STRING=Mark Abraham, Andrey Alekseenko, Vladimir Basov, Cathrine Bergh, Eliane Briand, Ania Brown, Mahesh Doijade, Giacomo Fiorin, Stefan Fleischmann, Sergey Gorelov, Gilles Gouaillardet, Alan Gray, M. Eric Irrgang, Farzaneh Jalalypour, Joe Jordan, Carsten Kutzner, Justin A. Lemkul, Magnus Lundborg, Pascal Merz, Vedran Miletic, Dmitry Morozov, Julien Nabet, Szilard Pall, Andrea Pasquadibisceglie, Michele Pellegrino, Hubert Santuz, Roland Schulz, Tatiana Shugaeva, Alexey Shvetsov, Philip Turner, Alessandra Villa, Sebastian Wingbermuehle" -D "GMX_PREVIOUS_CONTRIBUTORS_STRING=Emile Apol, Rossen Apostolov, James Barnett, Paul Bauer, Herman J.C. Berendsen, Par Bjelkmar, Christian Blau, Viacheslav Bolnykh, Kevin Boyd, Aldert van Buuren, Carlo Camilloni, Rudi van Drunen, Anton Feenstra, Oliver Fleetwood, Vytas Gapsys, Gaurav Garg, Gerrit Groenhof, Bert de Groot, Anca Hamuraru, Vincent Hindriksen, Victor Holanda, Aleksei Iupinov, Christoph Junghans, Prashanth Kanduri, Dimitrios Karkoulis, Peter Kasson, Sebastian Kehl, Sebastian Keller, Jiri Kraus, Per Larsson, Viveca Lindahl, Erik Marklund, Pieter Meulenhoff, Teemu Murtola, Sander Pronk, Michael Shirts, Alfons Sijbers, Balint Soproni, David van der Spoel, Peter Tieleman, Carsten Uphoff, Jon Vincent, Teemu Virolainen, Christian Wennberg, Maarten Wolf, Artem Zhmurov" -D "GMX_CURRENT_PROJECT_LEADERS_STRING=Berk Hess, Erik Lindahl" -P /build/reproducible-path/gromacs-2024.4/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/conf.py cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/index.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/index.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/texindex.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/texindex.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/download.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/download.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/links.dat /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/links.dat cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/api/gmxlibs.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/api/gmxlibs.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/api/index.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/api/index.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/build-system.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/build-system.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/change-management.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/change-management.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/commitstyle.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/commitstyle.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/documentation-generation.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/documentation-generation.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/contribute.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/contribute.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/doxygen.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/doxygen.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2024.4/docs/reference-manual/algorithms/plots/leapfrog.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/leapfrog.png cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/once.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/error-handling.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/error-handling.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/formatting.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/formatting.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/gitlab-ci.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/gitlab-ci.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/gmxtree.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/gmxtree.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/includestyle.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/includestyle.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/index.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/index.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/infrastructure.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/infrastructure.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2024.4/docs/reference-manual/algorithms/plots/lincs.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/lincs.png make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/known-issues.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/known-issues.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/language-features.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/language-features.rst [ 3%] Built target thread_mpi cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/naming.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/naming.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/_deps/muparser-build && /usr/bin/c++ -DGMX_DOUBLE=0 -DMUPARSERLIB_EXPORTS -DMUPARSER_DLL -D_DEBUG -Dmuparser_EXPORTS -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-long-long -pedantic -g -std=c++11 -fPIC -MD -MT _deps/muparser-build/CMakeFiles/muparser.dir/src/muParserInt.cpp.o -MF CMakeFiles/muparser.dir/src/muParserInt.cpp.o.d -o CMakeFiles/muparser.dir/src/muParserInt.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/muparser/src/muParserInt.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/overview.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/overview.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/physical_validation.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/physical_validation.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/redmine-states.png /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/redmine-states.png cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/relocatable-binaries.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/relocatable-binaries.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/reportstyle.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/reportstyle.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/style.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/style.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/testutils.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/testutils.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2024.4/docs/reference-manual/algorithms/plots/maxwell.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/maxwell.png cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/tools.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/tools.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/code-formatting.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/code-formatting.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/fragments/doxygen-links.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/fragments/doxygen-links.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/how-to/index.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/how-to/index.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2024.4/docs/reference-manual/algorithms/plots/mpmd-pme.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/mpmd-pme.png cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/how-to/beginners.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/how-to/beginners.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/how-to/topology.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/how-to/topology.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/how-to/special.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/how-to/special.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/how-to/visualize.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/how-to/visualize.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/install-guide/index.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/install-guide/index.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/install-guide/exotic.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/install-guide/exotic.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/reference-manual/plots/GMX_logos/gmx_logo_blue.svg /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/reference-manual/plots/GMX_logos/gmx_logo_blue.svg cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2024.4/docs/reference-manual/algorithms/plots/nstric.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/nstric.png cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/release-notes/index.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/release-notes/index.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/release-notes/2024/2024.1.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/release-notes/2024/2024.1.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/release-notes/2024/2024.2.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/release-notes/2024/2024.2.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/release-notes/2024/2024.3.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/release-notes/2024/2024.3.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/release-notes/2024/2024.4.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/release-notes/2024/2024.4.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/release-notes/2024/major/highlights.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/release-notes/2024/major/highlights.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/release-notes/2024/major/features.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/release-notes/2024/major/features.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/release-notes/2024/major/performance.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/release-notes/2024/major/performance.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/release-notes/2024/major/tools.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/release-notes/2024/major/tools.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/release-notes/2024/major/bugs-fixed.rst 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/build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input//reference-manual/analysis/plots/rdf.png cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarbias_restraint.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong 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CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_coordnums.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_distances.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/_deps/muparser-build && /usr/bin/cmake -E cmake_link_script CMakeFiles/muparser.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-long-long -pedantic -g -Wl,--dependency-file,CMakeFiles/muparser.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libmuparser.so.2 -o ../../lib/libmuparser.so.2.3.4 CMakeFiles/muparser.dir/src/muParser.cpp.o CMakeFiles/muparser.dir/src/muParserBase.cpp.o CMakeFiles/muparser.dir/src/muParserBytecode.cpp.o CMakeFiles/muparser.dir/src/muParserCallback.cpp.o CMakeFiles/muparser.dir/src/muParserDLL.cpp.o CMakeFiles/muparser.dir/src/muParserError.cpp.o CMakeFiles/muparser.dir/src/muParserInt.cpp.o CMakeFiles/muparser.dir/src/muParserTest.cpp.o CMakeFiles/muparser.dir/src/muParserTokenReader.cpp.o -Wl,-rpath,"\$ORIGIN/../lib" cd /build/reproducible-path/gromacs-2024.4/build/documentation/_deps/muparser-build && /usr/bin/cmake -E cmake_symlink_library ../../lib/libmuparser.so.2.3.4 ../../lib/libmuparser.so.2 ../../lib/libmuparser.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [ 35%] Built target muparser /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/pulling /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/output.cpp.o -MF CMakeFiles/pulling.dir/output.cpp.o.d -o CMakeFiles/pulling.dir/output.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/output.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_gpath.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [ 35%] Built target options cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 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-std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -MF CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/compositesimulatorelement.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src 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CMakeFiles/taskassignment.dir/taskassignment.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/taskassignment.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/firstorderpressurecoupling.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/forceelement.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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/build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -MF CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o.d -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/modularsimulator.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/mttk.cpp.o -MF CMakeFiles/modularsimulator.dir/mttk.cpp.o.d -o CMakeFiles/modularsimulator.dir/mttk.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/mttk.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [ 38%] Built target colvars_objlib cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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-std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/nosehooverchains.cpp.o -MF CMakeFiles/modularsimulator.dir/nosehooverchains.cpp.o.d -o CMakeFiles/modularsimulator.dir/nosehooverchains.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/nosehooverchains.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [ 38%] Built target taskassignment cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [ 40%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2024.4/build/documentation/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2024.4/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H 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-D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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-Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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-Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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-D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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-DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include 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-Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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-DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include 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-Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include 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-Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include 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-D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/atomdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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-Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_confrms.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_covar.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_current.cpp /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_anaeig.cpp: In function 'void project(const char*, const t_topology*, PbcType, real (*)[3], const char*, const char*, const char*, const char*, const char*, int, const char*, gmx_bool, real, int, const t_atoms*, int, int*, gmx_bool, real (*)[3], int, int*, real*, const real*, real (*)[3], int*, real (**)[3], int, int*, gmx_bool, const gmx_output_env_t*)': /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_anaeig.cpp:841:24: warning: '%s' directive writing up to 4095 bytes into a region of size 4094 [-Wformat-overflow=] 841 | sprintf(c, "%%d%s", str2); /* append '%s' and extention to filename */ | ^~ ~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_anaeig.cpp:42: In function 'int sprintf(char*, const char*, ...)', inlined from 'void project(const char*, const t_topology*, PbcType, real (*)[3], const char*, const char*, const char*, const char*, const char*, int, const char*, gmx_bool, real, int, const t_atoms*, int, int*, gmx_bool, real (*)[3], int, int*, real*, const real*, real (*)[3], int*, real (**)[3], int, int*, gmx_bool, const gmx_output_env_t*)' at /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_anaeig.cpp:841:16: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 3 and 4098 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_anaeig.cpp: In function 'void project(const char*, const t_topology*, PbcType, real (*)[3], const char*, const char*, const char*, const char*, const char*, int, const char*, gmx_bool, real, int, const t_atoms*, int, int*, gmx_bool, real (*)[3], int, int*, real*, const real*, real (*)[3], int*, real (**)[3], int, int*, gmx_bool, const gmx_output_env_t*)': /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_anaeig.cpp:841:24: warning: '%s' directive writing up to 4095 bytes into a region of size 4094 [-Wformat-overflow=] 841 | sprintf(c, "%%d%s", str2); /* append '%s' and extention to filename */ | ^~ ~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'void project(const char*, const t_topology*, PbcType, real (*)[3], const char*, const char*, const char*, const char*, const char*, int, const char*, gmx_bool, real, int, const t_atoms*, int, int*, gmx_bool, real (*)[3], int, int*, real*, const real*, real (*)[3], int*, real (**)[3], int, int*, gmx_bool, const gmx_output_env_t*)' at /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_anaeig.cpp:841:16: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 3 and 4098 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_anaeig.cpp: In function 'void project(const char*, const t_topology*, PbcType, real (*)[3], const char*, const char*, const char*, const char*, const char*, int, const char*, gmx_bool, real, int, const t_atoms*, int, int*, gmx_bool, real (*)[3], int, int*, real*, const real*, real (*)[3], int*, real (**)[3], int, int*, gmx_bool, const gmx_output_env_t*)': /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_anaeig.cpp:841:24: warning: '%s' directive writing up to 4095 bytes into a region of size 4094 [-Wformat-overflow=] 841 | sprintf(c, "%%d%s", str2); /* append '%s' and extention to filename */ | ^~ ~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'void project(const char*, const t_topology*, PbcType, real (*)[3], const char*, const char*, const char*, const char*, const char*, int, const char*, gmx_bool, real, int, const t_atoms*, int, int*, gmx_bool, real (*)[3], int, int*, real*, const real*, real (*)[3], int*, real (**)[3], int, int*, gmx_bool, const gmx_output_env_t*)' at /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_anaeig.cpp:841:16: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 3 and 4098 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ At global scope: cc1plus: note: unrecognized command-line option '-Wno-cast-function-type-strict' may have been intended to silence earlier diagnostics cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include 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/build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_densmap.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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/build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_same.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_simple.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -MF CMakeFiles/libgromacs.dir/selection/symrec.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/symrec.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wl,--dependency-file,CMakeFiles/libgromacs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgromacs.so.9 -o ../../lib/libgromacs.so.9.0.0 @CMakeFiles/libgromacs.dir/objects1.rsp -Wl,-rpath,"\$ORIGIN/../lib" -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so -lm /usr/lib/x86_64-linux-gnu/liblapack.so -lm ../../lib/libmuparser.so.2.3.4 cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs.so.9.0.0 ../../lib/libgromacs.so.9 ../../lib/libgromacs.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [ 98%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/programs 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/build/reproducible-path/gromacs-2024.4/build/documentation/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/gmx.dir/link.d CMakeFiles/gmx_objlib.dir/gmx.cpp.o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../bin/gmx -Wl,-rpath,"\$ORIGIN/../lib" ../../lib/libgromacs.so.9.0.0 -lm -Wl,-rpath-link,/build/reproducible-path/gromacs-2024.4/build/documentation/lib make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [ 98%] Built target gmx cd /build/reproducible-path/gromacs-2024.4/build/documentation/api/gmxapi && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong 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/usr/bin/cmake -E cmake_symlink_library ../../lib/libgmxapi.so.0.4.0 ../../lib/libgmxapi.so.0 ../../lib/libgmxapi.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [100%] Built target gmxapi /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi /build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/gmxapi/include -isystem /usr/include/python3.12 -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. 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/build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/export_system.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/gmxapi/include -isystem /usr/include/python3.12 -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fvisibility=hidden -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/export_tprfile.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/export_tprfile.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/export_tprfile.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/export_tprfile.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/gmxapi/include -isystem /usr/include/python3.12 -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. 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-I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/gmxapi/include -isystem /usr/include/python3.12 -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fvisibility=hidden -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/pysystem.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/pysystem.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/pysystem.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/pysystem.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/gmxapi/include -isystem /usr/include/python3.12 -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fvisibility=hidden -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/wrapped_exceptions_0_3_1.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/wrapped_exceptions_0_3_1.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/wrapped_exceptions_0_3_1.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/wrapped_exceptions_0_3_1.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/gmxapi/include -isystem /usr/include/python3.12 -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fvisibility=hidden -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/mpi_bindings.cpp.o -MF 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(https://github.com/pybind/pybind11/pull/4772) [-Wdeprecated-declarations] 131 | baseException(message.c_str()); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/gmxpy_exceptions.h:51, from /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/gmxpy_exceptions.cpp:49: /usr/include/pybind11/pybind11.h:2625:10: note: declared here 2625 | void operator()(const char *message) const { set_error(*this, message); } | ^~~~~~~~ /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/gmxpy_exceptions.cpp:137:29: warning: 'void pybind11::exception::operator()(const char*) const [with type = gmxpy::detail::export_exceptions(pybind11::module&)::UnknownExceptionPlaceHolder]' is deprecated: Please use py::set_error() instead (https://github.com/pybind/pybind11/pull/4772) [-Wdeprecated-declarations] 137 | unknownException(message.c_str()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /usr/include/pybind11/pybind11.h:2625:10: note: declared here 2625 | void operator()(const char *message) const { set_error(*this, message); } | ^~~~~~~~ cd /build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi && /usr/bin/cmake -E cmake_link_script CMakeFiles/_gmxapi.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wl,-rpath -Wl,/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,--dependency-file,CMakeFiles/_gmxapi.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o gmxapi_staging/gmxapi/_gmxapi.cpython-312-x86_64-linux-gnu.so CMakeFiles/_gmxapi.dir/src/cpp/launch_0_2_1.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/module.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/export_context.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/export_system.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/export_tprfile.cpp.o 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[568 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 8}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.58167 \clearpage pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 8}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.58167 \clearpage ] [569] [570] [571] [572] [573] [574] [575] [576] [577] Chapter 6. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:module-gmxapi' on page 578 undefined on input line 59922. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:module-gmxapi' on pa ge 578 undefined on input line 59922. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:module-gmxapi' on page 578 undefined on input line 59938. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:module-gmxapi' on pa ge 578 undefined on input line 59938. 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LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi.MDSes sion' on page 611 undefined on input line 63415. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi .SimulationParameters' on page 611 undefined on input line 63436. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi.Simul ationParameters' on page 611 undefined on input line 63436. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi .TprFile' on page 611 undefined on input line 63501. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi.TprFi le' on page 611 undefined on input line 63501. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi .SimulationParameters' on page 611 undefined on input line 63501. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi.Simul ationParameters' on page 611 undefined on input line 63501. [611] [612] Chapter 7. [613] [614] [615] [616] [617] Underfull \hbox (badness 10000) in paragraph at lines 64070--64070 []\T1/ptm/m/n/10 Bool Underfull \hbox (badness 10000) in paragraph at lines 64070--64070 []\T1/ptm/m/n/10 Ker-nel SIMD type (\T1/pcr/m/n/10 SimdAuto\T1/ptm/m/n/10 /\T1/ pcr/m/n/10 SimdNo\T1/ptm/m/n/10 /\T1/pcr/m/n/10 Simd4XM\T1/ptm/m/n/10 / Underfull \hbox (badness 10000) in paragraph at lines 64070--64070 []\T1/pcr/m/n/10 useHalfLJOptimizat Underfull \hbox (badness 10000) in paragraph at lines 64070--64070 []\T1/ptm/m/n/10 Bool Underfull \hbox (badness 10000) in paragraph at lines 64070--64070 []\T1/pcr/m/n/10 computeVirialAndEn Underfull \hbox (badness 10000) in paragraph at lines 64070--64070 []\T1/ptm/m/n/10 Bool Underfull \hbox (badness 10000) in paragraph at lines 64070--64070 []\T1/ptm/m/n/10 Coulomb in-ter-ac-tion func-tion Underfull \hbox (badness 10000) in paragraph at lines 64070--64070 []\T1/pcr/m/n/10 useTabulatedEwaldC Underfull \hbox (badness 10000) in paragraph at lines 64070--64070 []\T1/ptm/m/n/10 Bool Underfull \hbox (badness 10000) in paragraph at lines 64070--64070 []\T1/ptm/m/n/10 Bool [618] [619] Chapter 8. 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[440 <./vsite-4fdn.pdf>] [441] [442] [443] [444 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.28 7}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.45266 \end{equation} ] [445 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.29 4}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.45344 \paragraph{Using LJ\sphinxhyphen{}PME} pdfTeX warning (ext4): destination with the same identifier (name{equation.5.29 5}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.45344 \paragraph{Using LJ\sphinxhyphen{}PME} ] [446] [447] [448] [449] [450] [451] [452] [453] [454] [455] [456] [457] [458] [459] [460] [461] [462] [463] Overfull \hbox (10.25368pt too wide) in paragraph at lines 47482--47484 []|\T1/pcr/m/n/10 dihedraltypes$[]$| Overfull \hbox (11.40642pt too wide) in paragraph at lines 47495--47497 []|\T1/pcr/m/n/10 constrainttypes| Underfull \hbox (badness 10000) in paragraph at lines 47511--47513 []|\T1/pcr/m/n/10 nonbond_- Underfull \hbox (badness 10000) in paragraph at lines 47527--47529 []|\T1/pcr/m/n/10 nonbond_- Underfull \hbox (badness 10000) in paragraph at lines 47536--47540 []|$\OML/cmm/m/it/10 a [][]$ \T1/ptm/m/n/10 ; Underfull \hbox (badness 10000) in paragraph at lines 47536--47540 \OML/cmm/m/it/10 b [][]$\T1/ptm/m/n/10 ; $\OML/cmm/m/it/10 c[]$ Underfull \hbox (badness 10000) in paragraph at lines 47577--47579 []|\T1/ptm/m/n/10 molecule name; Underfull \hbox (badness 10000) in paragraph at lines 47590--47594 \T1/ptm/m/n/10 num-ber; residue [464] Underfull \hbox (badness 10000) in paragraph at lines 47728--47730 []|\T1/phv/m/n/10 Topol-ogy file Underfull \hbox (badness 10000) in paragraph at lines 47731--47734 []|\T1/phv/m/n/10 num. 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<./awh-pmfs.pdf>] [506] [507] [508] [509] [510] [511 <./rotation.pdf>] [512 <./equipotential.pdf>] [513 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.34 3}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.52732 \subsubsection{Radial Motion Potential} ] [514] [515 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.35 8}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.52971 \begin{equation} \label{equation:reference-manual/special/enforced-ro... ] [516 <./gaussians.pdf>] pdfTeX warning (ext4): destination with the same identifier (name{equation.5.36 7}) has been already used, duplicate ignored \relax l.53053 \begin{equation} \label{equation:reference-manual/special/enforced-ro... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.36 7}) has been already used, duplicate ignored 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[519] [520 <./field.pdf>] [521] [522 <./compelsetup.pdf>] [523] [524] [525 <./dumtypes.pdf>] [526 <./dumaro.pdf>] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548 <./rdf.pdf> <./rdfO-O.pdf pdfTeX warning: /usr/bin/pdflatex (file ./rdfO-O.pdf): PDF inclusion: multiple pdfs with page group included in a single page >] [549] [550] [551] [552] [553 <./msdwater.pdf> <./dih-def.pdf pdfTeX warning: /usr/bin/pdflatex (file ./dih-def.pdf): PDF inclusion: multiple pdfs with page group included in a single page >] [554 <./sgangle.pdf>] [555 <./distm.pdf>] [556] [557] [558 <./hbond.pdf> <./hbond-insert.pdf pdfTeX warning: /usr/bin/pdflatex (file ./hbond-insert.pdf): PDF inclusion: mul tiple pdfs with page group included in a single page >] [559 <./phipsi.pdf>] [560 <./rama.pdf> <./hpr-wheel.pdf pdfTeX warning: /usr/bin/pdflatex (file ./hpr-wheel.pdf): PDF inclusion: multip le pdfs with page group included in a single page >] [561] [562] [563 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.44 9}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.57673 \sphinxAtStartPar ] [564] [565] [566 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.46 2}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.57969 \end{equation} ] [567] [568 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 4}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.58122 \end{equation} pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 4}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.58122 \end{equation} ] [569 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 8}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.58167 \clearpage pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 8}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.58167 \clearpage ] [570] [571] [572] [573] [574] [575] [576] [577] [578] Chapter 6. [579] [580] [581] [582] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 60279. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 60279. [583] [584] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 60466. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 60466. Overfull \vbox (1.84944pt too high) detected at line 60523 [585] [586] Underfull \hbox (badness 10000) in paragraph at lines 60665--60668 []\T1/ptm/m/n/10 The fol-low-ing in-struc-tions are para-phrased from [][]$http s : / / pip . pypa . io / en / stable / user _ guide / [587] [588] [589] [590] [591] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61110. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61110. [592] [593] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61275. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61275. 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[621] [622] [623] pdfTeX warning: /usr/bin/pdflatex (file ./graphviz-d18d8687359a04d68afb2d653619 8981190fe142.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> allowed [624] [625 <./graphviz-d18d8687359a04d68afb2d6536198981190fe142.pdf>] [626] [627] [628] [629] [630] [631] [632] [633] [634] [635] [636] [637] [638] [639] [640] [641] [642] Underfull \hbox (badness 10000) in paragraph at lines 66702--66708 []\T1/ptm/m/n/10 The above logic to find the in-stal-la-tion pre-fix is in \T1/ pcr/m/n/10 src/gromacs/commandline/ [643] [644] [645] [646] [647] [648] [649] [650] [651] [652] Underfull \hbox (badness 6575) in paragraph at lines 67784--67790 []\T1/ptm/m/n/10 Use smart point-ers for mem-ory man-age-ment. 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[440 <./vsite-4fdn.pdf>] [441] [442] [443] [444 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.28 7}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.45266 \end{equation} ] [445 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.29 4}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.45344 \paragraph{Using LJ\sphinxhyphen{}PME} pdfTeX warning (ext4): destination with the same identifier (name{equation.5.29 5}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.45344 \paragraph{Using LJ\sphinxhyphen{}PME} ] [446] [447] [448] [449] [450] [451] [452] [453] [454] [455] [456] [457] [458] [459] [460] [461] [462] [463] Overfull \hbox (10.25368pt too wide) in paragraph at lines 47482--47484 []|\T1/pcr/m/n/10 dihedraltypes$[]$| Overfull \hbox (11.40642pt too wide) in paragraph at lines 47495--47497 []|\T1/pcr/m/n/10 constrainttypes| Underfull \hbox (badness 10000) in paragraph at lines 47511--47513 []|\T1/pcr/m/n/10 nonbond_- Underfull \hbox (badness 10000) in paragraph at lines 47527--47529 []|\T1/pcr/m/n/10 nonbond_- Underfull \hbox (badness 10000) in paragraph at lines 47536--47540 []|$\OML/cmm/m/it/10 a [][]$ \T1/ptm/m/n/10 ; Underfull \hbox (badness 10000) in paragraph at lines 47536--47540 \OML/cmm/m/it/10 b [][]$\T1/ptm/m/n/10 ; $\OML/cmm/m/it/10 c[]$ Underfull \hbox (badness 10000) in paragraph at lines 47577--47579 []|\T1/ptm/m/n/10 molecule name; Underfull \hbox (badness 10000) in paragraph at lines 47590--47594 \T1/ptm/m/n/10 num-ber; residue [464] Underfull \hbox (badness 10000) in paragraph at lines 47728--47730 []|\T1/phv/m/n/10 Topol-ogy file Underfull \hbox (badness 10000) in paragraph at lines 47731--47734 []|\T1/phv/m/n/10 num. 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./awh-sampleweights.pdf): PDF inclusion : multiple pdfs with page group included in a single page >] [505 <./awh-pmfs.pdf>] [506] [507] [508] [509] [510] [511 <./rotation.pdf>] [512 <./equipotential.pdf>] [513 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.34 3}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.52732 \subsubsection{Radial Motion Potential} ] [514] [515 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.35 8}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.52971 \begin{equation} \label{equation:reference-manual/special/enforced-ro... ] [516 <./gaussians.pdf>] pdfTeX warning (ext4): destination with the same identifier (name{equation.5.36 7}) has been already used, duplicate ignored \relax l.53053 \begin{equation} \label{equation:reference-manual/special/enforced-ro... pdfTeX warning 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[519] [520 <./field.pdf>] [521] [522 <./compelsetup.pdf>] [523] [524] [525 <./dumtypes.pdf>] [526 <./dumaro.pdf>] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548 <./rdf.pdf> <./rdfO-O.pdf pdfTeX warning: /usr/bin/pdflatex (file ./rdfO-O.pdf): PDF inclusion: multiple pdfs with page group included in a single page >] [549] [550] [551] [552] [553 <./msdwater.pdf> <./dih-def.pdf pdfTeX warning: /usr/bin/pdflatex (file ./dih-def.pdf): PDF inclusion: multiple pdfs with page group included in a single page >] [554 <./sgangle.pdf>] [555 <./distm.pdf>] [556] [557] [558 <./hbond.pdf> <./hbond-insert.pdf pdfTeX warning: /usr/bin/pdflatex (file ./hbond-insert.pdf): PDF inclusion: mul tiple pdfs with page group included in a single page >] [559 <./phipsi.pdf>] [560 <./rama.pdf> <./hpr-wheel.pdf pdfTeX warning: /usr/bin/pdflatex (file ./hpr-wheel.pdf): PDF inclusion: multip le pdfs with page group included in a single page >] [561] [562] [563 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.44 9}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.57673 \sphinxAtStartPar ] [564] [565] [566 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.46 2}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.57969 \end{equation} ] [567] [568 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 4}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.58122 \end{equation} pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 4}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.58122 \end{equation} ] [569 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 8}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.58167 \clearpage pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 8}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.58167 \clearpage ] [570] [571] [572] [573] [574] [575] [576] [577] [578] Chapter 6. [579] [580] [581] [582] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 60279. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 60279. [583] [584] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 60466. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 60466. Overfull \vbox (1.84944pt too high) detected at line 60523 [585] [586] Underfull \hbox (badness 10000) in paragraph at lines 60665--60668 []\T1/ptm/m/n/10 The fol-low-ing in-struc-tions are para-phrased from [][]$http s : / / pip . pypa . io / en / stable / user _ guide / [587] [588] [589] [590] [591] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61110. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61110. [592] [593] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61275. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61275. 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[614] [615] [616] [617] [618] Underfull \hbox (badness 10000) in paragraph at lines 64070--64070 []\T1/ptm/m/n/10 Bool Underfull \hbox (badness 10000) in paragraph at lines 64070--64070 []\T1/ptm/m/n/10 Ker-nel SIMD type (\T1/pcr/m/n/10 SimdAuto\T1/ptm/m/n/10 /\T1/ pcr/m/n/10 SimdNo\T1/ptm/m/n/10 /\T1/pcr/m/n/10 Simd4XM\T1/ptm/m/n/10 / Underfull \hbox (badness 10000) in paragraph at lines 64070--64070 []\T1/pcr/m/n/10 useHalfLJOptimizat Underfull \hbox (badness 10000) in paragraph at lines 64070--64070 []\T1/ptm/m/n/10 Bool Underfull \hbox (badness 10000) in paragraph at lines 64070--64070 []\T1/pcr/m/n/10 computeVirialAndEn Underfull \hbox (badness 10000) in paragraph at lines 64070--64070 []\T1/ptm/m/n/10 Bool Underfull \hbox (badness 10000) in paragraph at lines 64070--64070 []\T1/ptm/m/n/10 Coulomb in-ter-ac-tion func-tion Underfull \hbox (badness 10000) in paragraph at lines 64070--64070 []\T1/pcr/m/n/10 useTabulatedEwaldC Underfull \hbox (badness 10000) in paragraph at lines 64070--64070 []\T1/ptm/m/n/10 Bool Underfull \hbox (badness 10000) in paragraph at lines 64070--64070 []\T1/ptm/m/n/10 Bool [619] [620] Chapter 8. [621] [622] [623] pdfTeX warning: /usr/bin/pdflatex (file ./graphviz-d18d8687359a04d68afb2d653619 8981190fe142.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> allowed [624] [625 <./graphviz-d18d8687359a04d68afb2d6536198981190fe142.pdf>] [626] [627] [628] [629] [630] [631] [632] [633] [634] [635] [636] [637] [638] [639] [640] [641] [642] Underfull \hbox (badness 10000) in paragraph at lines 66702--66708 []\T1/ptm/m/n/10 The above logic to find the in-stal-la-tion pre-fix is in \T1/ pcr/m/n/10 src/gromacs/commandline/ [643] [644] [645] [646] [647] [648] [649] [650] [651] [652] Underfull \hbox (badness 6575) in paragraph at lines 67784--67790 []\T1/ptm/m/n/10 Use smart point-ers for mem-ory man-age-ment. By de-fault, use \T1/pcr/m/n/10 std::unique_-ptr \T1/ptm/m/n/10 and [653] [654] [655 <./redmine-states.png>] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666] Underfull \vbox (badness 1590) detected at line 69174 [667] Underfull \vbox (badness 10000) detected at line 69174 Underfull \vbox (badness 10000) detected at line 69174 [668] [669] [670] [671] [672] [673] [674] [675] [676] [677] [678] [679] [680] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 70418. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 70418. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 70418. 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Underfull \hbox (badness 10000) in paragraph at lines 72302--72306 \T1/ptm/m/n/10 (page 702[]) can be found at \T1/pcr/m/n/10 $GROMACS_-ROOT/share /cmake/gromacs$GROMACS_-SUFFIX/ [700] [701] [702] Underfull \hbox (badness 7344) in paragraph at lines 72652--72656 []\T1/ptm/m/n/10 CMake tar-get \T1/pcr/m/n/10 Gromacs::libgromacs\T1/ptm/m/n/10 , en-abled by [][]\T1/pcr/m/sl/10 GMX_-INSTALL_-LEGACY_-API[][] [703] Chapter 11. [704] [705] [706] [707] [708] [709] [710] [711] Underfull \hbox (badness 7168) in paragraph at lines 73283--73288 []\T1/ptm/m/n/10 In some cases, GRO-MACS could ran-domly crash on neighbor-sear ch steps with \T1/pcr/m/n/10 hip_-queue: [712] [713] Underfull \hbox (badness 10000) in paragraph at lines 73441--73445 []\T1/pcr/m/n/10 NbnxmSetupTest.CanCreateNbnxmGPU \T1/ptm/m/n/10 could crash in GPU builds with an er-ror in [714] [715] [716] [717] [718] [719] [720] [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] Underfull \hbox (badness 7722) in paragraph at lines 74751--74756 []\T1/ptm/m/n/10 De-pend-ing on the build en-vi-ron-ment, GRO-MACS 2023 and 202 3.1 could in-stall a mal-formed [731] [732] [733] [734] [735] [736] [737] [738] [739] [740] [741] [742] [743] [744] [745] [746] [747] [748] [749] [750] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776] [777] [778] [779] [780] [781] [782] [783] [784] [785] [786] [787] [788] [789] [790] [791] [792] [793] [794] [795] [796] [797] [798] [799] [800] [801] [802] [803] [804] [805] [806] [807] [808] [809] [810] [811] [812] [813] [814] [815] [816] [817] [818] [819] [820] [821] [822] [823] [824] [825] [826] [827] [828] [829] [830] [831] [832] [833] [834] [835] [836] [837] [838] [839] [840] [841] [842] [843] [844] [845] [846] [847] [848] [849] [850] [851] [852] [853] [854] [855] [856] [857] [858] [859] [860] [861] [862] [863] [864] [865] [866] [867] [868] [869] [870] [871] [872] [873] [874] [875] Overfull \hbox (18.01631pt too wide) in paragraph at lines 85908--85911 []\T1/ptm/m/n/10 Changed multi-simulation nsteps be-haviour ^^P^^Q^^Q^^Q^^Q^^Q^ ^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^ Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q ^^Q^^Q^^Q^^Q^^Q^^Q^^Q- Underfull \hbox (badness 10000) in paragraph at lines 85908--85911 [876] [877] [878] [879] [880] [881] [882] [883] [884] [885] [886] [887] [888] [889] [890] [891] No file gromacs.ind. (./gromacs.aux) LaTeX Warning: There were multiply-defined labels. ) (see the transcript file for additional information) < /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/symbols/msbm10.pfb> Output written on gromacs.pdf (901 pages, 13745698 bytes). 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'_deps/muparser-build/CMakeFiles/muparser.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build [ 4%] Built target sphinx-image-conversion [ 4%] Built target lmfit_objlib make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend [ 6%] Built target tng_io_obj /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/programs /build/reproducible-path/gromacs-2024.4/build/documentation/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" [ 7%] Built target tng_io_zlib make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/programs /build/reproducible-path/gromacs-2024.4/build/documentation/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" [ 7%] Built target release-version-info [ 7%] Built target linearalgebra make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [ 7%] Built target energyanalysis [ 9%] Built target thread_mpi [ 9%] Built target muparser /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/docs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/docs /build/reproducible-path/gromacs-2024.4/build/documentation/docs/CMakeFiles/sphinx-input-rst.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/pulling /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'src/programs/CMakeFiles/gmx_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 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'docs/CMakeFiles/sphinx-input-rst.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [ 9%] Built target gmx_objlib [ 12%] Built target colvars_objlib make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build [ 12%] Built target options [ 38%] Built target sphinx-input-rst make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [ 38%] Built target mdrun_objlib make[4]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [ 38%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/taskassignment /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [ 38%] Built target taskassignment make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [ 40%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs 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'/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/gmxapi /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/api/gmxapi /build/reproducible-path/gromacs-2024.4/build/documentation/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/programs 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'/build/reproducible-path/gromacs-2024.4/build/documentation' [100%] Built target gmxapi /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi /build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [100%] Built target _gmxapi /usr/bin/make -f docs/CMakeFiles/sphinx-input.dir/build.make docs/CMakeFiles/sphinx-input.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/docs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/docs /build/reproducible-path/gromacs-2024.4/build/documentation/docs/CMakeFiles/sphinx-input.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-input.dir/build.make docs/CMakeFiles/sphinx-input.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'docs/CMakeFiles/sphinx-input.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [100%] Built target sphinx-input /usr/bin/make -f docs/CMakeFiles/sphinx-programs.dir/build.make docs/CMakeFiles/sphinx-programs.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/docs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/docs /build/reproducible-path/gromacs-2024.4/build/documentation/docs/CMakeFiles/sphinx-programs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-programs.dir/build.make docs/CMakeFiles/sphinx-programs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'docs/CMakeFiles/sphinx-programs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [100%] Built target sphinx-programs /usr/bin/make -f docs/CMakeFiles/man.dir/build.make docs/CMakeFiles/man.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/docs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/docs /build/reproducible-path/gromacs-2024.4/build/documentation/docs/CMakeFiles/man.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f docs/CMakeFiles/man.dir/build.make docs/CMakeFiles/man.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/sphinx-build -q -b man -w sphinx-man.log -d /build/reproducible-path/gromacs-2024.4/build/documentation/docs/_man_doctrees -t do_man /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input /build/reproducible-path/gromacs-2024.4/build/documentation/docs/man WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by NameResolutionError(": Failed to resolve 'docs.python.org' ([Errno -3] Temporary failure in name resolution)")) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://mpi4py.readthedocs.io/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='mpi4py.readthedocs.io', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by NameResolutionError(": Failed to resolve 'mpi4py.readthedocs.io' ([Errno -3] Temporary failure in name resolution)")) /build/reproducible-path/gromacs-2024.4/admin/trigger-post-merge.py:53: UserWarning: This tool requires the `gitlab` package. Try `pip install python-gitlab`. warnings.warn( make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [100%] Built target man make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2024.4/build/documentation/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[1]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -j12 webpage -C build/documentation make[1]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/cmake -P /build/reproducible-path/gromacs-2024.4/build/documentation/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2024.4 -B/build/reproducible-path/gromacs-2024.4/build/documentation --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 webpage make[2]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/cmake -P /build/reproducible-path/gromacs-2024.4/build/documentation/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2024.4 -B/build/reproducible-path/gromacs-2024.4/build/documentation --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2024.4/build/documentation/CMakeFiles 65 /usr/bin/make -f CMakeFiles/Makefile2 docs/CMakeFiles/webpage.dir/all make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-image-conversion.dir/build.make docs/CMakeFiles/sphinx-image-conversion.dir/depend /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend 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make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend /usr/bin/make -f _deps/muparser-build/CMakeFiles/muparser.dir/build.make _deps/muparser-build/CMakeFiles/muparser.dir/depend /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/selection /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/selection /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f _deps/muparser-build/CMakeFiles/muparser.dir/build.make _deps/muparser-build/CMakeFiles/muparser.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'src/gromacs/options/CMakeFiles/options.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Leaving directory 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Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [ 4%] Built target sphinx-image-conversion [ 4%] Built target scanner /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend [ 6%] Built target tng_io_zlib /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-source-timestamp.dir/build.make docs/doxygen/CMakeFiles/doxygen-source-timestamp.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 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'/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/programs /build/reproducible-path/gromacs-2024.4/build/documentation/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" [ 6%] Built target lmfit_objlib make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [ 7%] Built target release-version-info [ 7%] Built target energyanalysis [ 7%] Built target thread_mpi make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make 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12%] Built target colvars_objlib make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/pulling /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen && /usr/bin/cmake -E touch 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&& /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2024.4/build/documentation/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2024.4/docs/doxygen/Doxyfile-version.cmakein -D VERSION_OUT=Doxyfile-version -P /build/reproducible-path/gromacs-2024.4/cmake/gmxConfigureVersionInfo.cmake make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'docs/CMakeFiles/sphinx-input-rst.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [ 12%] Built target gmx_objlib make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [ 12%] Built target mdrun_objlib make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [ 38%] Built target sphinx-input-rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen && /usr/bin/cmake -E touch Doxyfile-version [ 38%] Built target doxygen-source-timestamp [ 38%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/taskassignment /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" [ 38%] Built target doxygen-version /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-xml.dir/build.make docs/doxygen/CMakeFiles/doxygen-xml.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/docs/doxygen /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen/CMakeFiles/doxygen-xml.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-xml.dir/build.make docs/doxygen/CMakeFiles/doxygen-xml.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [ 38%] Built target taskassignment cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen && /usr/bin/cmake -E make_directory /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen/depgraphs make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen && /usr/bin/cmake -DDOCTYPE=xml -P RunDoxygen.cmake [ 40%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend NOTE: You are using Doxygen version 1.9.8. The documentation is designed for 1.8.5. Other versions may or may not work, but very likely produce extra warnings. Running Doxygen... warning: Tag 'MSCGEN_PATH' at line 40 of file 'Doxyfile-common' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'CLASS_DIAGRAMS' at line 15 of file 'Doxyfile-xml' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 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'/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/gmxapi /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/api/gmxapi /build/reproducible-path/gromacs-2024.4/build/documentation/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'src/programs/CMakeFiles/gmx.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [ 98%] Built target gmx make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'api/gmxapi/CMakeFiles/gmxapi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [100%] Built target gmxapi /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi /build/reproducible-path/gromacs-2024.4/build/documentation 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/usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/docs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/docs /build/reproducible-path/gromacs-2024.4/build/documentation/docs/CMakeFiles/sphinx-input.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-input.dir/build.make docs/CMakeFiles/sphinx-input.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'docs/CMakeFiles/sphinx-input.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [100%] Built target sphinx-input /usr/bin/make -f docs/CMakeFiles/sphinx-programs.dir/build.make docs/CMakeFiles/sphinx-programs.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/docs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/docs /build/reproducible-path/gromacs-2024.4/build/documentation/docs/CMakeFiles/sphinx-programs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-programs.dir/build.make docs/CMakeFiles/sphinx-programs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'docs/CMakeFiles/sphinx-programs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [100%] Built target sphinx-programs /usr/bin/make -f docs/manual/CMakeFiles/pdf.dir/build.make docs/manual/CMakeFiles/pdf.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/docs/manual /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/docs/manual /build/reproducible-path/gromacs-2024.4/build/documentation/docs/manual/CMakeFiles/pdf.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f docs/manual/CMakeFiles/pdf.dir/build.make docs/manual/CMakeFiles/pdf.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'docs/manual/CMakeFiles/pdf.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [100%] Built target pdf /usr/bin/make -f docs/manual/CMakeFiles/manual.dir/build.make docs/manual/CMakeFiles/manual.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/docs/manual /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/docs/manual /build/reproducible-path/gromacs-2024.4/build/documentation/docs/manual/CMakeFiles/manual.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f docs/manual/CMakeFiles/manual.dir/build.make docs/manual/CMakeFiles/manual.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'docs/manual/CMakeFiles/manual.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [100%] Built target manual /usr/bin/make -f docs/CMakeFiles/webpage-sphinx.dir/build.make docs/CMakeFiles/webpage-sphinx.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/docs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/docs /build/reproducible-path/gromacs-2024.4/build/documentation/docs/CMakeFiles/webpage-sphinx.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f docs/CMakeFiles/webpage-sphinx.dir/build.make docs/CMakeFiles/webpage-sphinx.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/sphinx-build -q -b html -w sphinx-html.log -d /build/reproducible-path/gromacs-2024.4/build/documentation/docs/_html_doctrees -t do_html /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input /build/reproducible-path/gromacs-2024.4/build/documentation/docs/html WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://mpi4py.readthedocs.io/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='mpi4py.readthedocs.io', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by NameResolutionError(": Failed to resolve 'mpi4py.readthedocs.io' ([Errno -3] Temporary failure in name resolution)")) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by NameResolutionError(": Failed to resolve 'docs.python.org' ([Errno -3] Temporary failure in name resolution)")) /build/reproducible-path/gromacs-2024.4/admin/trigger-post-merge.py:53: UserWarning: This tool requires the `gitlab` package. Try `pip install python-gitlab`. warnings.warn( The following warnings were produced by Doxygen: /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/energyhistory.cpp:44: warning: Conditional section with label 'INTERNAL' does not have a corresponding \endcond command within this file. /build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/restraintmdmodule.cpp:49: warning: no matching class member found for gmx::RestraintForceProvider::RestraintForceProvider(std::shared_ptr< gmx::IRestraintPotential > restraint, const std::vector< int > &sites) Possible candidates: 'gmx::RestraintForceProvider::RestraintForceProvider()=delete' at line 212 of file /build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/restraintmdmodule_impl.h 'gmx::RestraintForceProvider::RestraintForceProvider(std::shared_ptr< gmx::IRestraintPotential > restraint, const std::vector< int > &sites)' at line 223 of file /build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/restraintmdmodule_impl.h /build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/restraintmdmodule.cpp:153: warning: no matching class member found for gmx::RestraintMDModuleImpl::RestraintMDModuleImpl(std::shared_ptr< gmx::IRestraintPotential > restraint, const std::vector< int > &sites) Possible candidates: 'gmx::RestraintMDModuleImpl::RestraintMDModuleImpl()=delete' at line 271 of file /build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/restraintmdmodule_impl.h 'gmx::RestraintMDModuleImpl::RestraintMDModuleImpl(std::shared_ptr< gmx::IRestraintPotential > restraint, const std::vector< int > &sites)' at line 278 of file /build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/restraintmdmodule_impl.h 'gmx::RestraintMDModuleImpl::RestraintMDModuleImpl(RestraintMDModuleImpl &&) noexcept=default' at line 286 of file /build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/restraintmdmodule_impl.h /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/arrayref.h:314: warning: @copybrief or @copydoc target 'arrayRefFromArray' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:81: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:117: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/options/abstractoptionstorage.h:144: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:268: warning: @copybrief or @copydoc target 'CheckpointData::subCheckpointData' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:92: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:97: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/electricfield.cpp:174: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:118: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:123: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:58: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:403: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:247: warning: @copybrief or @copydoc target 'CheckpointData::scalar' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:169: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:98: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:142: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_insolidangle.cpp:99: warning: unable to resolve reference to 'sm_insolidangle' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:300: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd_memory.h:154: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd_memory.h:163: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:345: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/filestream.h:158: warning: @copybrief or @copydoc target 'TextInputFile::TextInputFile(const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/selection/selectionenums.h:82: warning: explicit link request to 'SelectionFlag' could not be resolved /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:62: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/selection/selectionenums.h:82: warning: explicit link request to 'SelectionFlag' could not be resolved /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:81: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:98: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:117: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:142: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:58: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:62: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:169: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:300: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:345: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:403: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:81: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:98: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:117: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:142: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/options/abstractoptionstorage.h:144: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/selection/selectionenums.h:82: warning: explicit link request to 'SelectionFlag' could not be resolved /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:92: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:97: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:118: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:123: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:169: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:81: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:98: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:117: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:142: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:58: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:62: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:300: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:345: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:403: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:247: warning: @copybrief or @copydoc target 'CheckpointData::scalar' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:268: warning: @copybrief or @copydoc target 'CheckpointData::subCheckpointData' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/filestream.h:158: warning: @copybrief or @copydoc target 'TextInputFile::TextInputFile(const std::string &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/electricfield.cpp:174: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd_memory.h:154: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd_memory.h:163: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/options/abstractoptionstorage.h:144: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/options/abstractoptionstorage.h:145: warning: @copydetails or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/electricfield.cpp:174: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/electricfield.cpp:175: warning: @copydetails or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:247: warning: @copybrief or @copydoc target 'CheckpointData::scalar' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:248: warning: @copydetails or @copydoc target 'CheckpointData::scalar' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:255: warning: @copybrief or @copydoc target 'CheckpointData::arrayRef' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:255: warning: @copydetails or @copydoc target 'CheckpointData::arrayRef' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:265: warning: @copybrief or @copydoc target 'CheckpointData::tensor' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:265: warning: @copydetails or @copydoc target 'CheckpointData::tensor' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:268: warning: @copybrief or @copydoc target 'CheckpointData::subCheckpointData' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:269: warning: @copydetails or @copydoc target 'CheckpointData::subCheckpointData' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd_memory.h:154: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd_memory.h:155: warning: @copydetails or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd_memory.h:163: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd_memory.h:164: warning: @copydetails or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/filestream.h:158: warning: @copybrief or @copydoc target 'TextInputFile::TextInputFile(const std::string &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/filestream.h:159: warning: @copydetails or @copydoc target 'TextInputFile::TextInputFile(const std::string &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:300: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:310: warning: unable to resolve reference to 'SimdIBool' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:345: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:357: warning: unable to resolve reference to 'SimdBool' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:358: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:358: warning: unable to resolve reference to 'SimdIBool' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:359: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:361: warning: unable to resolve reference to 'cvtB2IB' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:361: warning: unable to resolve reference to 'cvtIB2B' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:403: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/selection/selectionenums.h:82: warning: explicit link request to 'SelectionFlag' could not be resolved /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:58: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:62: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/correlationhistory.h:61: warning: unable to resolve reference to 'updateCorrelationGridHistory' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:92: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:93: warning: @copydetails or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:97: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:98: warning: @copydetails or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:118: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:119: warning: @copydetails or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:123: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:124: warning: @copydetails or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:169: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/topology/index.h:102: warning: Illegal command @param found as part of a \p command /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/topology/index.h:99: warning: The following parameter of write_index(const char *outf, gmx::ArrayRef< const IndexGroup > indexGroups, bool duplicate, int numAtoms) is not documented: parameter 'numAtoms' /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/iframeconverter.h:116: warning: invalid argument for command '\iline' /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/warninp.h:153: warning: @copybrief or @copydoc target 'warning_error_and_exit(WarningHandler*,const char *,int,const char *,int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/warninp.h:154: warning: @copydetails or @copydoc target 'warning_error_and_exit(WarningHandler*,const char *,int,const char *,int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/warninp.h:153: warning: @copybrief or @copydoc target 'warning_error_and_exit(WarningHandler*,const char *,int,const char *,int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/warninp.h:154: warning: @copydetails or @copydoc target 'warning_error_and_exit(WarningHandler*,const char *,int,const char *,int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_insolidangle.cpp:99: warning: unable to resolve reference to 'sm_insolidangle' for \ref command /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/topology/index.h:102: warning: Illegal command @param found as part of a \p command /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/topology/index.h:99: warning: The following parameter of write_index(const char *outf, gmx::ArrayRef< const IndexGroup > indexGroups, bool duplicate, int numAtoms) is not documented: parameter 'numAtoms' /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_double.h:171: warning: @copydetails or @copydoc target 'c_simdBestPairAlignmentFloat' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_float.h:151: warning: unable to resolve reference to 'c_simdBestPairAlignmentFloat' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_float.h:152: warning: unable to resolve reference to 'c_simdBestPairAlignmentDouble' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/errorcodes.h:111: warning: explicit link request to 'eeUnknownError' could not be resolved /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:113: warning: @copydetails or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:119: warning: @copydetails or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:179: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:184: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:189: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:81: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copydetails or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:98: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copydetails or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:117: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copydetails or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:142: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copydetails or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copydetails or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copydetails or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen/doxygen-xml-timestamp.txt make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [100%] Built target doxygen-xml /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-user.dir/build.make docs/doxygen/CMakeFiles/doxygen-user.dir/depend /usr/bin/make -f docs/doxygen/CMakeFiles/dep-graphs-dot.dir/build.make docs/doxygen/CMakeFiles/dep-graphs-dot.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/docs/doxygen /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen/CMakeFiles/doxygen-user.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/docs/doxygen /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen/CMakeFiles/dep-graphs-dot.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/dep-graphs-dot.dir/build.make docs/doxygen/CMakeFiles/dep-graphs-dot.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen && /usr/bin/python3 /build/reproducible-path/gromacs-2024.4/docs/doxygen/graphbuilder.py -S /build/reproducible-path/gromacs-2024.4 -B /build/reproducible-path/gromacs-2024.4/build/documentation -o /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen/depgraphs make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-user.dir/build.make docs/doxygen/CMakeFiles/doxygen-user.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen && /usr/bin/cmake -E make_directory /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen/depgraphs cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen && /usr/bin/cmake -DDOCTYPE=user -P RunDoxygen.cmake NOTE: You are using Doxygen version 1.9.8. The documentation is designed for 1.8.5. Other versions may or may not work, but very likely produce extra warnings. Running Doxygen... /build/reproducible-path/gromacs-2024.4/docs/doxygen/doxygenxml.py:35: SyntaxWarning: invalid escape sequence '\l' """Doxygen XML output parser. /build/reproducible-path/gromacs-2024.4/docs/doxygen/doxygenxml.py:349: SyntaxWarning: invalid escape sequence '\i' self, "\internal does not cover whole documentation" /build/reproducible-path/gromacs-2024.4/docs/doxygen/doxygenxml.py:356: SyntaxWarning: invalid escape sequence '\l' self, "\libinternal should not be used inside \internal" warning: Tag 'MSCGEN_PATH' at line 40 of file 'Doxyfile-common' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" Scanning source tree... Reading source files... Reading Doxygen XML files... Writing graphs... cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen/dep-graphs-dot-timestamp.txt make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [100%] Built target dep-graphs-dot /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-full.dir/build.make docs/doxygen/CMakeFiles/doxygen-full.dir/depend /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-lib.dir/build.make docs/doxygen/CMakeFiles/doxygen-lib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/docs/doxygen /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen/CMakeFiles/doxygen-full.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/docs/doxygen /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen/CMakeFiles/doxygen-lib.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-full.dir/build.make docs/doxygen/CMakeFiles/doxygen-full.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen && /usr/bin/cmake -E make_directory /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen/depgraphs make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-lib.dir/build.make docs/doxygen/CMakeFiles/doxygen-lib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen && /usr/bin/cmake -E make_directory /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen/depgraphs cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen && /usr/bin/cmake -DDOCTYPE=full -P RunDoxygen.cmake cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen && /usr/bin/cmake -DDOCTYPE=lib -P RunDoxygen.cmake NOTE: You are using Doxygen version 1.9.8. The documentation is designed for 1.8.5. Other versions may or may not work, but very likely produce extra warnings. Running Doxygen... NOTE: You are using Doxygen version 1.9.8. The documentation is designed for 1.8.5. Other versions may or may not work, but very likely produce extra warnings. Running Doxygen... warning: Tag 'MSCGEN_PATH' at line 40 of file 'Doxyfile-common' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'MSCGEN_PATH' at line 40 of file 'Doxyfile-common' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" libpath/shortest.c:324: triangulation failed libpath/shortest.c:324: triangulation failed libpath/shortest.c:324: triangulation failed libpath/shortest.c:324: triangulation failed The following warnings were produced by Doxygen: /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/energyhistory.cpp:44: warning: Conditional section with label 'INTERNAL' does not have a corresponding \endcond command within this file. /build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/helpwritercontext.cpp:246: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/testasserts.h:738: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2024.4/src/testutils/testasserts.cpp:182: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/int64_to_int.h:57: warning: Member int64_to_int found in multiple @ingroup groups! The member will be put in group module_utility, and not in group group_libraryapi /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/basedefinitions.h:208: warning: documentation for unknown define GMX_IGNORE_RETURN_VALUE found. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:81: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:117: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:92: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:97: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:118: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:123: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:58: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:169: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:98: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:142: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:62: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/selectioncollection.cpp:964: warning: Member swap(SelectionCollection &lhs, SelectionCollection &rhs) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:81: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:98: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:117: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:142: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/iframeconverter.h:109: warning: invalid argument for command '\iline' /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:57: warning: Member SYCL_ASSERT(condition) (macro definition) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:78: warning: Member compilingForHost() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:94: warning: Member compilingForSubGroupSize() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:108: warning: Member skipKernelCompilation() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:130: warning: Member atomicAddDefault(T &val, const T delta) (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:167: warning: Member atomicFetchAddLocal(T &val, const T delta) (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:321: warning: Member __attribute__((always_inline)) static AmdPackedFloat3 operator*(const AmdPackedFloat3 &v (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:321: warning: Member s (variable) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:325: warning: Member v (variable) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:217: warning: Member gmx_call(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:218: warning: Member gmx_comm(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:219: warning: Member gmx_file(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:220: warning: Member gmx_impl(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:221: warning: Member gmx_incons(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:222: warning: Member gmx_input(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:223: warning: Member gmx_mem(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:224: warning: Member gmx_open(fn) (macro definition) of file fatalerror.h is not documented. :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initOptions()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::optionsFinished()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initAnalysis()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initAfterFirstFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishAnalysis()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::writeOutput()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::startFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::startFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishFrames()' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/utility.h:109: warning: explicit link request to 'GMX_IGNORE_RETURN_VALUE' could not be resolved /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:81: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:98: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:117: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:142: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:117: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copydetails or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:98: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copydetails or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:142: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copydetails or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/errorcodes.h:111: warning: explicit link request to 'eeUnknownError' could not be resolved /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/int64_to_int.h:48: warning: Found unknown command '\file' /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copydetails or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copydetails or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:81: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copydetails or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:214: warning: Member __attribute__((ext_vector_type(2))) Native_float2_ (typedef) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:214: warning: Member __attribute__((packed)) (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:240: warning: Member __attribute__((always_inline)) float operator[](Index i) const (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:250: warning: Member __attribute__((always_inline)) float &operator[](Index i) (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:260: warning: Member __attribute__((always_inline)) float x() const (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:261: warning: Member __attribute__((always_inline)) float y() const (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:262: warning: Member __attribute__((always_inline)) Native_float2_ xy() const (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:263: warning: Member __attribute__((always_inline)) float z() const (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:267: warning: Member AmdPackedFloat3(float x, float y, float z) (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:269: warning: Member AmdPackedFloat3(Native_float2_ xy, float z) (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:271: warning: Member AmdPackedFloat3(Float3 r) (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:273: warning: Member operator Float3() const (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/constraint_gpu_helpers.h:51: warning: Member AtomsAdjacencyListElement(int indexOfSecondConstrainedAtom, int indexOfConstraint, int signFactor) (function) of struct AtomsAdjacencyListElement is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/dlbtiming.h:215: warning: Member impl_ (variable) of class BalanceRegion is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/commrec.h:66: warning: Member bUse (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/commrec.h:67: warning: Member comm_intra (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/commrec.h:68: warning: Member rank_intra (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/commrec.h:69: warning: Member comm_inter (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlist.h:241: warning: Member PackedJClusterList(const gmx::PinningPolicy pinningPolicy) (function) of class PackedJClusterList is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/fcdata.h:216: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(t_oriresdata) (function) of struct t_oriresdata is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/warninp.h:71: warning: Member WarningHandler(bool allowWarnings, int maxNumberWarnings) (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/warninp.h:89: warning: Member errorCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/warninp.h:91: warning: Member warningCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/warninp.h:93: warning: Member noteCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/warninp.h:95: warning: Member maxWarningCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_force_sender_gpu_impl.h:70: warning: Member CacheLineAlignedFlag (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:875: warning: Member mode (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/oclraii.h:131: warning: Member ClCommandQueue (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/oclraii.h:132: warning: Member ClProgram (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/oclraii.h:133: warning: Member ClKernel (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft.h:67: warning: Member FftBackend (enumeration) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:67: warning: Member CheckpointDataOperation (enumeration) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/referencetemperaturemanager.h:66: warning: Member ReferenceTemperatureChangeAlgorithm (enumeration) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:63: warning: Member packSendBufKernel(Float3 *__restrict__ gm_dataPacked, const Float3 *__restrict__ gm_data, const int *__restrict__ gm_map, int mapSize, Float3 coordinateShift) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:117: warning: Member launchPackSendBufKernel(const DeviceStream &deviceStream, int xSendSize, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:131: warning: Member launchUnpackRecvBufKernel(const DeviceStream &deviceStream, int fRecvSize, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_cufftmp.cpp:102: warning: Member handleCufftError(cufftResult_t status, const char *msg) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:251: warning: Member launchVkFft(const DeviceBuffer< float > &realGrid, const DeviceBuffer< float > &complexGrid, NativeQueue queue, gmx_fft_direction fftDirection, VkFFTApplication *application, VkFFTLaunchParams *launchParams) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:92: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:97: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:118: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:123: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/massrepartitioning.cpp:44: warning: Member smallestAtomMass(const gmx_mtop_t &mtop) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_impl_gpu.cpp:67: warning: Member chooseSubGroupSizeForDevice(const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:878: warning: Member bondedKernel(sycl::handler &cgh, const BondedGpuKernelParameters &kernelParams, const DeviceBuffer< t_iatom > gm_iatoms_[numFTypesOnGpu], float *__restrict__ gm_vTot, const t_iparams *__restrict__ gm_forceParams_, const sycl::float4 *__restrict__ gm_xq_, Float3 *__restrict__ gm_f_, Float3 *__restrict__ gm_fShift_) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:169: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/lincs_gpu_internal_sycl.cpp:451: warning: Member launchLincsKernel(const DeviceStream &deviceStream, const int numConstraintsThreads, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:88: warning: Member makeCheckpointArrayRef(T &container) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:108: warning: Member makeCheckpointArrayRefFromArray(T *begin, size_t size) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:733: warning: Member hasStartVelocityScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:742: warning: Member hasEndVelocityScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:749: warning: Member hasPositionScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:755: warning: Member hasParrinelloRahmanScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:881: warning: Member getConnection(Propagator< integrationStage > gmx_unused *propagator, const PropagatorTag &propagatorTag) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/pullelement.cpp:125: warning: Member doCheckpointData(CheckpointData< operation > *checkpointData, ArrayRef< double > previousStepCom) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/simulatoralgorithm.h:608: warning: Member getElementPointer(LegacySimulatorData *legacySimulatorData, ModularSimulatorAlgorithmBuilderHelper *builderHelper, StatePropagatorData *statePropagatorData, EnergyData *energyData, FreeEnergyPerturbationData *freeEnergyPerturbationData, GlobalCommunicationHelper *globalCommunicationHelper, ObservablesReducer *observablesReducer, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:62: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:74: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:86: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:98: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:110: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:122: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:134: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:146: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:158: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:170: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:182: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:194: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:206: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:218: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:230: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:242: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:254: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:266: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:278: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:290: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:302: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:314: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:326: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:338: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:350: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:362: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:374: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:386: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:398: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:410: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:423: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:435: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:447: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:459: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:471: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:483: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:495: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:507: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:519: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:531: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:543: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:555: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:567: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:579: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:591: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:603: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:615: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:627: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:639: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:651: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:663: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:675: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:687: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:699: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:711: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:723: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:735: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:747: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:759: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:771: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:784: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:796: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:808: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:820: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:832: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:844: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:856: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:868: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:880: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:892: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:904: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:916: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:928: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:940: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:952: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:964: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:976: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:988: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1000: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1012: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1024: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1036: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1048: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1060: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1072: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1084: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1096: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1108: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1120: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1132: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:62: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:74: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:86: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:98: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:110: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:122: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:134: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:146: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:158: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:170: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:182: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:194: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:206: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:218: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:230: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:242: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:254: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:266: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:278: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:290: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:302: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:314: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:326: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:338: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:350: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:362: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:374: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:386: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:398: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:410: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:423: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:435: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:447: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:459: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:471: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:483: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:495: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:507: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:519: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:531: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:543: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:555: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:567: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:579: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:591: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:603: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:615: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:627: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:639: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:651: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:663: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:675: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:687: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:699: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:711: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:723: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:735: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:747: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:759: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:771: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:784: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:796: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:808: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:820: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:832: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:844: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:856: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:868: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:880: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:892: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:904: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:916: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:928: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:940: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:952: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:964: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:976: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:988: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1000: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1012: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1024: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1036: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1048: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1060: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1072: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1084: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1096: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1108: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1120: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1132: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/compiler.cpp:2586: warning: Member compileSelection(SelectionCollection *coll) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/selectioncollection.cpp:964: warning: Member swap(SelectionCollection &lhs, SelectionCollection &rhs) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/decidegpuusage.cpp:165: warning: Member decideWhetherToUseGpusForPmeFft(const TaskTarget pmeFftTarget) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/decidegpuusage.cpp:172: warning: Member canUseGpusForPme(const bool useGpuForNonbonded, const TaskTarget pmeTarget, const TaskTarget pmeFftTarget, const t_inputrec &inputrec, std::string *errorMessage) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/template_mp.h:87: warning: Member dispatchTemplatedFunction(Function &&f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/stringutil.cpp:132: warning: Member formatString(gmx_fmtstr const char *fmt,...) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:81: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:98: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:117: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:142: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinput.h:120: warning: Member globalSimulationState(const SimulationInput &) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinput.h:121: warning: Member applyGlobalInputRecord(const SimulationInput &, t_inputrec *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinput.h:122: warning: Member applyGlobalTopology(const SimulationInput &, gmx_mtop_t *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/vec.h:625: warning: Member norm2(T *v) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/tests/colvarsoptions.cpp:80: warning: Member colvarsConfig (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:58: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:62: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/forcebuffers.cpp:55: warning: Member c_forces (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/nosehooverchains.cpp:67: warning: Member nhcUsageNames (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:55: warning: Member c_centralShiftIndex (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:56: warning: Member c_numShiftVectors (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/decidegpuusage.cpp:118: warning: Member c_gpuBuildSyclWithoutGpuFft (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:83: warning: Member c_angstrom (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:84: warning: Member c_kilo (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:85: warning: Member c_nano (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:86: warning: Member c_pico (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:87: warning: Member c_nm2A (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:88: warning: Member c_cal2Joule (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:89: warning: Member c_electronCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:91: warning: Member c_amu (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:92: warning: Member c_boltzmann (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:93: warning: Member c_avogadro (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:94: warning: Member c_universalGasConstant (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:95: warning: Member c_boltz (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:96: warning: Member c_faraday (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:97: warning: Member c_planck1 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:98: warning: Member c_planck (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:100: warning: Member c_epsilon0Si (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:102: warning: Member c_epsilon0 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:105: warning: Member c_speedOfLight (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:108: warning: Member c_rydberg (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:110: warning: Member c_one4PiEps0 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:115: warning: Member c_barMdunits (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:116: warning: Member c_presfac (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:121: warning: Member c_debye2Enm (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:122: warning: Member c_enm2Debye (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:126: warning: Member c_fieldfac (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:129: warning: Member c_hartree2Kj (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:130: warning: Member c_bohr2Nm (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:131: warning: Member c_hartreeBohr2Md (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:133: warning: Member c_rad2Deg (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:134: warning: Member c_deg2Rad (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:64: warning: Member sc_atomInfo_HasPerturbedCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:65: warning: Member sc_atomInfo_Exclusion (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:66: warning: Member sc_atomInfo_Constraint (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:67: warning: Member sc_atomInfo_Settle (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:68: warning: Member sc_atomInfo_BondCommunication (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:69: warning: Member sc_atomInfo_HasVdw (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:70: warning: Member sc_atomInfo_HasCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:44: warning: Member c_dBoxY (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:45: warning: Member c_dBoxX (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/correlationhistory.h:61: warning: unable to resolve reference to 'updateCorrelationGridHistory' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:97: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:98: warning: @copydetails or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:92: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:93: warning: @copydetails or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:123: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:124: warning: @copydetails or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:118: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:119: warning: @copydetails or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:62: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:58: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/booltype.h:72: warning: Member value_ (variable) of struct gmx::BoolType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_coulomb_functions.h:134: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldAnalytical > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_coulomb_functions.h:145: warning: Member force(const std::array< SimdReal, nR > &rSquaredV, const std::array< SimdReal, nR > gmx_unused &dummyRInvV, const std::array< SimdReal, nR > &rInvExclV, const std::array< SimdBool, nR > &withinCutoffV) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldAnalytical > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_coulomb_functions.h:194: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldTabulated > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_coulomb_functions.h:83: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::RF > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_diagonal_masker.h:108: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeEqualsISize > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_diagonal_masker.h:132: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsDoubleISize > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_diagonal_masker.h:163: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsHalfISize > is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:440: warning: Member operator()(const std::string &lhs, const std::string &rhs) const (function) of class gmx::EqualCaseInsensitive is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:137: warning: Member value (variable) of struct gmx::IsSerializableEnum is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_lennardjones_functions.h:332: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< calculateEnergies, InteractionModifiers::ForceSwitch > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_lennardjones_functions.h:483: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< calculateEnergies, InteractionModifiers::PotSwitch > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_lennardjones_functions.h:179: warning: Member LennardJonesCalculator(const interaction_const_t gmx_unused &ic) (function) of class gmx::LennardJonesCalculator< false, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_lennardjones_functions.h:209: warning: Member forceSigmaEpsilon(const std::array< SimdReal, inputSize > &rInvV, const std::array< SimdBool, interactSize > &interactV, SimdBool *withinCutoffV, const std::array< SimdReal, nR > &sigmaV, const std::array< SimdReal, nR > &epsilonV, SimdReal sixth, SimdReal twelfth, std::array< SimdReal, nR > &frLJV, std::array< SimdReal, vljvSize > &vLJV) (function) of class gmx::LennardJonesCalculator< false, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_lennardjones_functions.h:231: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< true, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_lennardjones_functions.h:270: warning: Member forceSigmaEpsilon(const std::array< SimdReal, inputSize > &rInvV, const std::array< SimdBool, interactSize > &interactV, SimdBool *withinCutoffV, const std::array< SimdReal, nR > &sigmaV, const std::array< SimdReal, nR > &epsilonV, SimdReal sixth, SimdReal twelfth, std::array< SimdReal, nR > &frLJV, std::array< SimdReal, vljvSize > &vLJV) (function) of class gmx::LennardJonesCalculator< true, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:218: warning: Member allocator_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:219: warning: Member size_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:220: warning: Member reference (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:221: warning: Member const_reference (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:222: warning: Member storage_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:223: warning: Member pointer (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:224: warning: Member const_pointer (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:225: warning: Member iterator (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:226: warning: Member const_iterator (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:227: warning: Member difference_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:351: warning: Member data() const noexcept (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:353: warning: Member begin() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:354: warning: Member end() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:356: warning: Member cbegin() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:357: warning: Member cend() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:359: warning: Member begin() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:360: warning: Member end() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:362: warning: Member cbegin() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:363: warning: Member cend() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/selection/selectioncollection.h:144: warning: Member SelectionCollection(const SelectionCollection &rhs) (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/selection/selectioncollection.h:145: warning: Member operator=(SelectionCollection rhs) (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/selection/selectioncollection.h:146: warning: Member swap(SelectionCollection &rhs) (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:125: warning: Member mode (typedef) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/grid.cpp:122: warning: Member getMaxNumCells(const Grid::Geometry &geometry, const int numAtoms, const int numColumns) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/gridset.cpp:135: warning: Member getGridOffset(gmx::ArrayRef< const Grid > grids, int gridIndex) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_buffer_ops.cpp:63: warning: Member nbnxn_gpu_x_to_nbat_x(const Nbnxm::Grid &grid, NbnxmGpu *nb, DeviceBuffer< gmx::RVec > d_x, GpuEventSynchronizer *xReadyOnDevice, const gmx::AtomLocality locality, int gridId, int numColumnsMax, bool mustInsertNonLocalDependency) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:83: warning: Member init_ewald_coulomb_force_table(const EwaldCorrectionTables &tables, NBParamGpu *nbp, const DeviceContext &deviceContext) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:97: warning: Member useTabulatedEwaldByDefault(const DeviceInformation &deviceInfo) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:128: warning: Member nbnxn_gpu_pick_ewald_kernel_type(const interaction_const_t &ic, const DeviceInformation &deviceInfo) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:178: warning: Member set_cutoff_parameters(NBParamGpu *nbp, const interaction_const_t &ic, const PairlistParams &listParams) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:202: warning: Member initPlistSorting(gpuPlistSorting *sorting) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:225: warning: Member init_plist(gpu_plist *pl) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:253: warning: Member init_timings(gmx_wallclock_gpu_nbnxn_t *t) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:302: warning: Member nbnxmGpuPickVdwKernelType(const interaction_const_t &ic, LJCombinationRule ljCombinationRule) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:356: warning: Member nbnxmGpuPickElectrostaticsKernelType(const interaction_const_t &ic, const DeviceInformation &deviceInfo) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:442: warning: Member gpu_init(const gmx::DeviceStreamManager &deviceStreamManager, const interaction_const_t *ic, const PairlistParams &listParams, const nbnxn_atomdata_t *nbat, const bool bLocalAndNonlocal) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:511: warning: Member gpu_pme_loadbal_update_param(nonbonded_verlet_t *nbv, const interaction_const_t &ic) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:528: warning: Member gpu_upload_shiftvec(NbnxmGpu *nb, const nbnxn_atomdata_t *nbatom) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:689: warning: Member gpu_init_atomdata(NbnxmGpu *nb, const nbnxn_atomdata_t *nbat) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:792: warning: Member gpu_clear_outputs(NbnxmGpu *nb, bool computeVirial) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:823: warning: Member gpu_is_kernel_ewald_analytical(const NbnxmGpu *nb) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:829: warning: Member setupGpuShortRangeWork(NbnxmGpu *nb, const gmx::ListedForcesGpu *listedForcesGpu, const gmx::InteractionLocality iLocality) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:842: warning: Member haveGpuShortRangeWork(const NbnxmGpu *nb, const gmx::InteractionLocality interactionLocality) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:981: warning: Member nbnxnInsertNonlocalGpuDependency(NbnxmGpu *nb, const InteractionLocality interactionLocality) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1076: warning: Member nbnxn_gpu_init_x_to_nbat_x(const Nbnxm::GridSet &gridSet, NbnxmGpu *gpu_nbv) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1286: warning: Member gpuGetNBAtomData(NbnxmGpu *nb) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1292: warning: Member gpu_get_f(NbnxmGpu *nb) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_setup.cpp:355: warning: Member getENbnxnInitCombRule(const t_forcerec &forcerec) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.cpp:53: warning: Member getNbnxmSubGroupSize(const DeviceInformation &deviceInfo) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:1455: warning: Member launchNbnxmKernelHelper(NbnxmGpu *nb, const gmx::StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:106: warning: Member elecEwald (variable) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:109: warning: Member elecEwaldTab (variable) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:112: warning: Member ljEwald (variable) of namespace Nbnxm is not documented. cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen/doxygen-user-timestamp.txt make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [100%] Built target doxygen-user libpath/shortest.c:324: triangulation failed libpath/shortest.c:324: triangulation failed The following warnings were produced by Doxygen: /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/energyhistory.cpp:44: warning: Conditional section with label 'INTERNAL' does not have a corresponding \endcond command within this file. /build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/helpwritercontext.cpp:246: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2024.4/src/testutils/testasserts.cpp:182: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/basedefinitions.h:208: warning: documentation for unknown define GMX_IGNORE_RETURN_VALUE found. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:81: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:117: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:92: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:97: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:118: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:123: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:58: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:403: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:169: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:98: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:142: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:300: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:62: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:345: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme.h:316: warning: unable to resolve reference to 'pme_gpu_supports_input' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/filestream.h:158: warning: @copybrief or @copydoc target 'TextInputFile::TextInputFile(const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/selectioncollection.cpp:964: warning: Member swap(SelectionCollection &lhs, SelectionCollection &rhs) (function) of namespace gmx is not documented. warning: Included by graph for 'basedefinitions.h' not generated, too many nodes (65), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'real.h' not generated, too many nodes (71), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:81: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:98: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:117: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:142: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/mp11.h:76: warning: Member mp_with_index(std::size_t i, F &&f) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:87: warning: Member Ensures(cond) (macro definition) of file pointers.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:194: warning: Member operator!=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() !=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:200: warning: Member operator<(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()< rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:206: warning: Member operator<=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()<=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:212: warning: Member operator>(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() > rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:218: warning: Member operator>=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() >=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/iframeconverter.h:116: warning: invalid argument for command '\iline' /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/domdec_struct.h:113: warning: Member gmx_domdec_zone_size_t (typedef) of file domdec_struct.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme.h:316: warning: unable to resolve reference to 'pme_gpu_supports_input' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme.h:221: warning: unable to resolve reference to 'gmx_pme_reinit' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme.h:316: warning: unable to resolve reference to 'pme_gpu_supports_input' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_types_host.h:72: warning: Member PmeGpuHaloExchange (typedef) of file pme_gpu_types_host.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/devicebuffer_ocl.h:386: warning: Member asMpiPointer(DeviceBuffer< ValueType > &) (function) of file devicebuffer_ocl.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/devicebuffer_sycl.h:437: warning: Member asMpiPointer(DeviceBuffer< ValueType > &buffer) (function) of file devicebuffer_sycl.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gmxopencl.h:56: warning: Member CL_USE_DEPRECATED_OPENCL_2_0_APIS (macro definition) of file gmxopencl.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:61: warning: unable to resolve reference to 'GpuEventSynchronizer::markEvent' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:62: warning: unable to resolve reference to 'GpuEventSynchronizer::waitForEvent' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:63: warning: unable to resolve reference to 'GpuEventSynchronizer::enqueueWaitEvent' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:77: warning: unable to resolve reference to 'GpuEventSynchronizer::reset' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:79: warning: unable to resolve reference to 'GpuEventSynchronizer::consume' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:81: warning: unable to resolve reference to 'GpuEventSynchronizer::markEvent' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:84: warning: unable to resolve reference to 'GpuEventSynchronizer::waitForEvent' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:86: warning: unable to resolve reference to 'GpuEventSynchronizer::enqueueWaitEvent' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:91: warning: unable to resolve reference to 'GpuEventSynchronizer::markEvent' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:92: warning: unable to resolve reference to 'GpuEventSynchronizer::enqueueWaitEvent' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:92: warning: unable to resolve reference to 'GpuEventSynchronizer::enqueueWaitEvent' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gputraits.h:63: warning: Member DeviceTexture (typedef) of file gputraits.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gputraits_ocl.h:50: warning: Member DeviceTexture (typedef) of file gputraits_ocl.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/oclraii.h:131: warning: Member ClCommandQueue (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/oclraii.h:132: warning: Member ClProgram (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/oclraii.h:133: warning: Member ClKernel (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:57: warning: Member SYCL_ASSERT(condition) (macro definition) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:78: warning: Member compilingForHost() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:94: warning: Member compilingForSubGroupSize() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:108: warning: Member skipKernelCompilation() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:130: warning: Member atomicAddDefault(T &val, const T delta) (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:167: warning: Member atomicFetchAddLocal(T &val, const T delta) (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:321: warning: Member __attribute__((always_inline)) static AmdPackedFloat3 operator*(const AmdPackedFloat3 &v (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:321: warning: Member s (variable) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:325: warning: Member v (variable) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/nrjac.h:55: warning: Member jacobi(double **a, int numDimensions, double *eigenvalues, double **eigenvectors, int *numRotations) (function) of file nrjac.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/nrjac.h:65: warning: Member jacobi(gmx::ArrayRef< gmx::DVec > a, gmx::ArrayRef< double > eigenvalues, gmx::ArrayRef< gmx::DVec > eigenvectors) (function) of file nrjac.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/nrjac.h:67: warning: Member m_inv_gen(const real *m, int n, real *minv) (function) of file nrjac.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/nrjac.cpp:52: warning: Member do_rotate(MatrixType a, int i, int j, int k, int l, double tau, double s) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/nrjac.cpp:62: warning: Member jacobi(MatrixType a, const int n, double d[], MatrixType v) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/nrjac.cpp:175: warning: Member jacobi(double **a, const int numDimensions, double *eigenvalues, double **eigenvectors, int *numRotations) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/nrjac.cpp:185: warning: Member jacobi(gmx::ArrayRef< gmx::DVec > a, gmx::ArrayRef< double > eigenvalues, gmx::ArrayRef< gmx::DVec > eigenvectors) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/nrjac.cpp:194: warning: Member m_inv_gen(const real *m, int n, real *minv) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/energyoutput.h:84: warning: Member pvEnergyFieldName (variable) of file energyoutput.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/energyoutput.h:86: warning: Member enthalpyEnergyFieldName (variable) of file energyoutput.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/energyoutput.h:88: warning: Member virialEnergyFieldNames (variable) of file energyoutput.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinput.h:120: warning: Member globalSimulationState(const SimulationInput &) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinput.h:121: warning: Member applyGlobalInputRecord(const SimulationInput &, t_inputrec *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinput.h:122: warning: Member applyGlobalTopology(const SimulationInput &, gmx_mtop_t *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:64: warning: Member sc_atomInfo_HasPerturbedCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:65: warning: Member sc_atomInfo_Exclusion (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:66: warning: Member sc_atomInfo_Constraint (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:67: warning: Member sc_atomInfo_Settle (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:68: warning: Member sc_atomInfo_BondCommunication (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:69: warning: Member sc_atomInfo_HasVdw (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:70: warning: Member sc_atomInfo_HasCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:88: warning: Member makeCheckpointArrayRef(T &container) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:108: warning: Member makeCheckpointArrayRefFromArray(T *begin, size_t size) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include/gromacs/pbcutil/pbc_aiuc_sycl.h:50: warning: Member xyzToShiftIndex(int x, int y, int z) (function) of file pbc_aiuc_sycl.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:647: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_FLOAT (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:658: warning: Member GMX_SIMD4N_FLOAT_WIDTH (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:693: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_DOUBLE (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:704: warning: Member GMX_SIMD4N_DOUBLE_WIDTH (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:738: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_REAL (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:747: warning: Member GMX_SIMD4N_REAL_WIDTH (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:657: warning: Member Simd4NFloat (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:703: warning: Member Simd4NDouble (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:746: warning: Member Simd4NReal (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:517: warning: Member load(const std::enable_if_t< std::is_arithmetic_v< T >, T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:523: warning: Member load(const AlignedArray< internal::SimdTraitsT< T >, N > &m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:541: warning: Member loadU(const std::enable_if_t< std::is_arithmetic_v< T >, T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:547: warning: Member loadU(const AlignedArray< internal::SimdTraitsT< T >, N > &m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:628: warning: Member load(const internal::Simd4TraitsT< T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:633: warning: Member loadU(const internal::Simd4TraitsT< T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:662: warning: Member loadUNDuplicate4(const float *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:666: warning: Member load4DuplicateN(const float *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:670: warning: Member loadU4NOffset(const float *f, int) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:708: warning: Member loadUNDuplicate4(const double *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:712: warning: Member load4DuplicateN(const double *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:716: warning: Member loadU4NOffset(const double *f, int) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:300: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:345: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:403: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:379: warning: Member c_simdBestPairAlignment (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:484: warning: Member SimdTraitsT (typedef) of namespace gmx::internal is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:623: warning: Member Simd4TraitsT (typedef) of namespace gmx::internal is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/tables/forcetable.h:79: warning: Member TableFormat (enumeration) of file forcetable.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include/gromacs/timing/gpu_timing.h:57: warning: Member PmeStage (enumeration) of file gpu_timing.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include/gromacs/topology/mtop_atomloops.h:212: warning: Member gmx_mtop_atomloop_block_t (typedef) of file mtop_atomloops.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include/gromacs/topology/mtop_atomloops.h:216: warning: Member gmx_mtop_atomloop_block_init(const gmx_mtop_t &mtop) (function) of file mtop_atomloops.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include/gromacs/topology/mtop_atomloops.h:231: warning: Member gmx_mtop_atomloop_block_next(gmx_mtop_atomloop_block_t aloop, const t_atom **atom, int *nmol) (function) of file mtop_atomloops.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:217: warning: Member gmx_call(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:218: warning: Member gmx_comm(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:219: warning: Member gmx_file(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:220: warning: Member gmx_impl(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:221: warning: Member gmx_incons(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:222: warning: Member gmx_input(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:223: warning: Member gmx_mem(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:224: warning: Member gmx_open(fn) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:64: warning: Member ivec[3] (typedef) of file iserializer.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:200: warning: Member toString(bool t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:204: warning: Member toString(int t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:208: warning: Member toString(int64_t t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:212: warning: Member toString(float t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:216: warning: Member toString(double t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:220: warning: Member toString(unsigned char t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:224: warning: Member toString(std::string t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/template_mp.h:87: warning: Member dispatchTemplatedFunction(Function &&f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:85: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(p) &this->mask(a)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:86: warning: Member deallocate(p, 1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:93: warning: Member v(10) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:94: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(v.data()) &this->mask(v.get_allocator())) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:99: warning: Member for(std::size_t i=1000;i<=10000;i+=1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:125: warning: Member v1(1) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:127: warning: Member EXPECT_NE(data, nullptr) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:128: warning: Member v2(std::move(v1)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:129: warning: Member EXPECT_EQ(data, v2.data()) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:82: warning: Member a (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:83: warning: Member p (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:126: warning: Member data (variable) of namespace gmx::test is not documented. :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initOptions()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::optionsFinished()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initAnalysis()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initAfterFirstFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishAnalysis()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::writeOutput()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::startFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::startFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishFrames()' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_float.h:151: warning: unable to resolve reference to 'c_simdBestPairAlignmentFloat' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_float.h:152: warning: unable to resolve reference to 'c_simdBestPairAlignmentDouble' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_double.h:171: warning: @copydetails or @copydoc target 'c_simdBestPairAlignmentFloat' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility.h:109: warning: explicit link request to 'GMX_IGNORE_RETURN_VALUE' could not be resolved /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:200: warning: Member toString(bool t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:204: warning: Member toString(int t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:208: warning: Member toString(int64_t t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:212: warning: Member toString(float t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:216: warning: Member toString(double t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:220: warning: Member toString(unsigned char t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:224: warning: Member toString(std::string t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:81: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:98: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:117: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:142: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:117: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copydetails or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:184: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:98: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copydetails or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:142: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copydetails or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:119: warning: @copydetails or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:113: warning: @copydetails or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/errorcodes.h:111: warning: explicit link request to 'eeUnknownError' could not be resolved /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:179: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copydetails or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copydetails or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:81: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copydetails or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:189: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:214: warning: Member __attribute__((ext_vector_type(2))) Native_float2_ (typedef) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:214: warning: Member __attribute__((packed)) (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:240: warning: Member __attribute__((always_inline)) float operator[](Index i) const (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:250: warning: Member __attribute__((always_inline)) float &operator[](Index i) (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:260: warning: Member __attribute__((always_inline)) float x() const (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:261: warning: Member __attribute__((always_inline)) float y() const (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:262: warning: Member __attribute__((always_inline)) Native_float2_ xy() const (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:263: warning: Member __attribute__((always_inline)) float z() const (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:267: warning: Member AmdPackedFloat3(float x, float y, float z) (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:269: warning: Member AmdPackedFloat3(Native_float2_ xy, float z) (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:271: warning: Member AmdPackedFloat3(Float3 r) (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:273: warning: Member operator Float3() const (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/constraint_gpu_helpers.h:51: warning: Member AtomsAdjacencyListElement(int indexOfSecondConstrainedAtom, int indexOfConstraint, int signFactor) (function) of struct AtomsAdjacencyListElement is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/dlbtiming.h:215: warning: Member impl_ (variable) of class BalanceRegion is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/device_information.h:176: warning: Member supportedSubGroupSizes() const (function) of struct DeviceInformation is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/device_information.h:175: warning: Member supportedSubGroupSizesSize (variable) of struct DeviceInformation is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/device_information.h:181: warning: Member gpuAwareMpiStatus (variable) of struct DeviceInformation is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/commrec.h:66: warning: Member bUse (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/commrec.h:67: warning: Member comm_intra (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/commrec.h:68: warning: Member rank_intra (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/commrec.h:69: warning: Member comm_inter (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/grompp_impl.h:68: warning: Member aj() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/grompp_impl.h:69: warning: Member ak() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/grompp_impl.h:70: warning: Member al() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/grompp_impl.h:71: warning: Member am() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/grompp_impl.h:73: warning: Member c0() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/grompp_impl.h:74: warning: Member c1() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/grompp_impl.h:75: warning: Member c2() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/grompp_impl.h:77: warning: Member interactionTypeName() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm.h:482: warning: Member setupFepThreadedForceBuffer(int numAtomsForce) (function) of struct nonbonded_verlet_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlist.h:241: warning: Member PackedJClusterList(const gmx::PinningPolicy pinningPolicy) (function) of class PackedJClusterList is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/fcdata.h:216: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(t_oriresdata) (function) of struct t_oriresdata is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/warninp.h:71: warning: Member WarningHandler(bool allowWarnings, int maxNumberWarnings) (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/warninp.h:89: warning: Member errorCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/warninp.h:91: warning: Member warningCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/warninp.h:93: warning: Member noteCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/warninp.h:95: warning: Member maxWarningCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_force_sender_gpu_impl.h:70: warning: Member CacheLineAlignedFlag (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:875: warning: Member mode (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/oclraii.h:131: warning: Member ClCommandQueue (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/oclraii.h:132: warning: Member ClProgram (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/oclraii.h:133: warning: Member ClKernel (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft.h:67: warning: Member FftBackend (enumeration) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/referencetemperaturemanager.h:66: warning: Member ReferenceTemperatureChangeAlgorithm (enumeration) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:63: warning: Member packSendBufKernel(Float3 *__restrict__ gm_dataPacked, const Float3 *__restrict__ gm_data, const int *__restrict__ gm_map, int mapSize, Float3 coordinateShift) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:117: warning: Member launchPackSendBufKernel(const DeviceStream &deviceStream, int xSendSize, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:131: warning: Member launchUnpackRecvBufKernel(const DeviceStream &deviceStream, int fRecvSize, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_cufftmp.cpp:102: warning: Member handleCufftError(cufftResult_t status, const char *msg) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:251: warning: Member launchVkFft(const DeviceBuffer< float > &realGrid, const DeviceBuffer< float > &complexGrid, NativeQueue queue, gmx_fft_direction fftDirection, VkFFTApplication *application, VkFFTLaunchParams *launchParams) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:92: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:97: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:118: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:123: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/massrepartitioning.cpp:44: warning: Member smallestAtomMass(const gmx_mtop_t &mtop) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/simd_support.cpp:70: warning: Member simdString(SimdType s) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/simd_support.cpp:199: warning: Member simdCompiled() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_impl_gpu.cpp:67: warning: Member chooseSubGroupSizeForDevice(const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:878: warning: Member bondedKernel(sycl::handler &cgh, const BondedGpuKernelParameters &kernelParams, const DeviceBuffer< t_iatom > gm_iatoms_[numFTypesOnGpu], float *__restrict__ gm_vTot, const t_iparams *__restrict__ gm_forceParams_, const sycl::float4 *__restrict__ gm_xq_, Float3 *__restrict__ gm_f_, Float3 *__restrict__ gm_fShift_) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:169: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/lincs_gpu_internal_sycl.cpp:451: warning: Member launchLincsKernel(const DeviceStream &deviceStream, const int numConstraintsThreads, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:88: warning: Member makeCheckpointArrayRef(T &container) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:108: warning: Member makeCheckpointArrayRefFromArray(T *begin, size_t size) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:733: warning: Member hasStartVelocityScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:742: warning: Member hasEndVelocityScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:749: warning: Member hasPositionScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:755: warning: Member hasParrinelloRahmanScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:881: warning: Member getConnection(Propagator< integrationStage > gmx_unused *propagator, const PropagatorTag &propagatorTag) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/pullelement.cpp:125: warning: Member doCheckpointData(CheckpointData< operation > *checkpointData, ArrayRef< double > previousStepCom) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/simulatoralgorithm.h:608: warning: Member getElementPointer(LegacySimulatorData *legacySimulatorData, ModularSimulatorAlgorithmBuilderHelper *builderHelper, StatePropagatorData *statePropagatorData, EnergyData *energyData, FreeEnergyPerturbationData *freeEnergyPerturbationData, GlobalCommunicationHelper *globalCommunicationHelper, ObservablesReducer *observablesReducer, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:62: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:74: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:86: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:98: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:110: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:122: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:134: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:146: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:158: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:170: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:182: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:194: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:206: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:218: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:230: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:242: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:254: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:266: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:278: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:290: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:302: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:314: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:326: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:338: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:350: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:362: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:374: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:386: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:398: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:410: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:423: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:435: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:447: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:459: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:471: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:483: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:495: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:507: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:519: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:531: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:543: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:555: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:567: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:579: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:591: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:603: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:615: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:627: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:639: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:651: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:663: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:675: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:687: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:699: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:711: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:723: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:735: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:747: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:759: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:771: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:784: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:796: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:808: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:820: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:832: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:844: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:856: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:868: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:880: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:892: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:904: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:916: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:928: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:940: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:952: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:964: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:976: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:988: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1000: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1012: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1024: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1036: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1048: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1060: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1072: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1084: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1096: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1108: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1120: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1132: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:62: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:74: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:86: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:98: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:110: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:122: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:134: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:146: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:158: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:170: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:182: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:194: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:206: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:218: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:230: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:242: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:254: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:266: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:278: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:290: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:302: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:314: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:326: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:338: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:350: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:362: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:374: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:386: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:398: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:410: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:423: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:435: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:447: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:459: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:471: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:483: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:495: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:507: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:519: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:531: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:543: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:555: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:567: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:579: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:591: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:603: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:615: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:627: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:639: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:651: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:663: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:675: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:687: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:699: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:711: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:723: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:735: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:747: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:759: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:771: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:784: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:796: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:808: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:820: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:832: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:844: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:856: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:868: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:880: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:892: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:904: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:916: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:928: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:940: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:952: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:964: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:976: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:988: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1000: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1012: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1024: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1036: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1048: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1060: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1072: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1084: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1096: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1108: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1120: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1132: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/compiler.cpp:2586: warning: Member compileSelection(SelectionCollection *coll) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/selectioncollection.cpp:964: warning: Member swap(SelectionCollection &lhs, SelectionCollection &rhs) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/decidegpuusage.cpp:165: warning: Member decideWhetherToUseGpusForPmeFft(const TaskTarget pmeFftTarget) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/decidegpuusage.cpp:172: warning: Member canUseGpusForPme(const bool useGpuForNonbonded, const TaskTarget pmeTarget, const TaskTarget pmeFftTarget, const t_inputrec &inputrec, std::string *errorMessage) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/template_mp.h:87: warning: Member dispatchTemplatedFunction(Function &&f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/stringutil.cpp:132: warning: Member formatString(gmx_fmtstr const char *fmt,...) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:81: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:98: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:117: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:142: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinput.h:120: warning: Member globalSimulationState(const SimulationInput &) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinput.h:121: warning: Member applyGlobalInputRecord(const SimulationInput &, t_inputrec *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinput.h:122: warning: Member applyGlobalTopology(const SimulationInput &, gmx_mtop_t *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:200: warning: Member toString(bool t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:204: warning: Member toString(int t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:208: warning: Member toString(int64_t t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:212: warning: Member toString(float t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:216: warning: Member toString(double t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:220: warning: Member toString(unsigned char t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:224: warning: Member toString(std::string t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/vec.h:625: warning: Member norm2(T *v) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/tests/colvarsoptions.cpp:80: warning: Member colvarsConfig (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:58: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:62: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/forcebuffers.cpp:55: warning: Member c_forces (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/nosehooverchains.cpp:67: warning: Member nhcUsageNames (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:55: warning: Member c_centralShiftIndex (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:56: warning: Member c_numShiftVectors (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/decidegpuusage.cpp:118: warning: Member c_gpuBuildSyclWithoutGpuFft (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:83: warning: Member c_angstrom (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:84: warning: Member c_kilo (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:85: warning: Member c_nano (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:86: warning: Member c_pico (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:87: warning: Member c_nm2A (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:88: warning: Member c_cal2Joule (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:89: warning: Member c_electronCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:91: warning: Member c_amu (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:92: warning: Member c_boltzmann (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:93: warning: Member c_avogadro (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:94: warning: Member c_universalGasConstant (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:95: warning: Member c_boltz (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:96: warning: Member c_faraday (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:97: warning: Member c_planck1 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:98: warning: Member c_planck (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:100: warning: Member c_epsilon0Si (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:102: warning: Member c_epsilon0 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:105: warning: Member c_speedOfLight (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:108: warning: Member c_rydberg (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:110: warning: Member c_one4PiEps0 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:115: warning: Member c_barMdunits (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:116: warning: Member c_presfac (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:121: warning: Member c_debye2Enm (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:122: warning: Member c_enm2Debye (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:126: warning: Member c_fieldfac (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:129: warning: Member c_hartree2Kj (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:130: warning: Member c_bohr2Nm (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:131: warning: Member c_hartreeBohr2Md (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:133: warning: Member c_rad2Deg (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:134: warning: Member c_deg2Rad (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:64: warning: Member sc_atomInfo_HasPerturbedCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:65: warning: Member sc_atomInfo_Exclusion (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:66: warning: Member sc_atomInfo_Constraint (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:67: warning: Member sc_atomInfo_Settle (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:68: warning: Member sc_atomInfo_BondCommunication (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:69: warning: Member sc_atomInfo_HasVdw (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:70: warning: Member sc_atomInfo_HasCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:44: warning: Member c_dBoxY (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:45: warning: Member c_dBoxX (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:300: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:345: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:403: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:379: warning: Member c_simdBestPairAlignment (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:657: warning: Member Simd4NFloat (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:703: warning: Member Simd4NDouble (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:746: warning: Member Simd4NReal (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:517: warning: Member load(const std::enable_if_t< std::is_arithmetic_v< T >, T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:523: warning: Member load(const AlignedArray< internal::SimdTraitsT< T >, N > &m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:541: warning: Member loadU(const std::enable_if_t< std::is_arithmetic_v< T >, T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:547: warning: Member loadU(const AlignedArray< internal::SimdTraitsT< T >, N > &m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:628: warning: Member load(const internal::Simd4TraitsT< T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:633: warning: Member loadU(const internal::Simd4TraitsT< T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:662: warning: Member loadUNDuplicate4(const float *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:666: warning: Member load4DuplicateN(const float *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:670: warning: Member loadU4NOffset(const float *f, int) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:708: warning: Member loadUNDuplicate4(const double *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:712: warning: Member load4DuplicateN(const double *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:716: warning: Member loadU4NOffset(const double *f, int) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:403: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:300: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:310: warning: unable to resolve reference to 'SimdIBool' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:345: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:357: warning: unable to resolve reference to 'SimdBool' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:358: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:358: warning: unable to resolve reference to 'SimdIBool' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:359: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:361: warning: unable to resolve reference to 'cvtB2IB' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:361: warning: unable to resolve reference to 'cvtIB2B' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/correlationhistory.h:61: warning: unable to resolve reference to 'updateCorrelationGridHistory' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:97: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:98: warning: @copydetails or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:92: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:93: warning: @copydetails or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:123: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:124: warning: @copydetails or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:118: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:119: warning: @copydetails or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:62: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:58: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/booltype.h:72: warning: Member value_ (variable) of struct gmx::BoolType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/clfftinitializer.h:96: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(ClfftInitializer) (function) of class gmx::ClfftInitializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/mdmodulesnotifiers.h:157: warning: Member coordinates_ (variable) of struct gmx::CoordinatesAndBoxPreprocessed is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/mdmodulesnotifiers.h:158: warning: Member box_ (variable) of struct gmx::CoordinatesAndBoxPreprocessed is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/mdmodulesnotifiers.h:159: warning: Member pbc_ (variable) of struct gmx::CoordinatesAndBoxPreprocessed is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_coulomb_functions.h:134: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldAnalytical > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_coulomb_functions.h:145: warning: Member force(const std::array< SimdReal, nR > &rSquaredV, const std::array< SimdReal, nR > gmx_unused &dummyRInvV, const std::array< SimdReal, nR > &rInvExclV, const std::array< SimdBool, nR > &withinCutoffV) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldAnalytical > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_coulomb_functions.h:194: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldTabulated > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_coulomb_functions.h:83: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::RF > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_diagonal_masker.h:108: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeEqualsISize > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_diagonal_masker.h:132: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsDoubleISize > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_diagonal_masker.h:163: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsHalfISize > is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:251: warning: Member const_iterator (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:252: warning: Member reverse_iterator (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:253: warning: Member const_reverse_iterator (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:275: warning: Member const_pointer (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:230: warning: Member operator[](const std::size_t arrayIndex) const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:236: warning: Member operator[](const EnumType enumIndex) (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:241: warning: Member operator[](const EnumType enumIndex) const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:259: warning: Member end() (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:260: warning: Member begin() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:261: warning: Member end() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:267: warning: Member rend() (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:268: warning: Member rbegin() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:269: warning: Member rend() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:182: warning: Member end() const (function) of class gmx::EnumerationWrapper is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:440: warning: Member operator()(const std::string &lhs, const std::string &rhs) const (function) of class gmx::EqualCaseInsensitive is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/iforceprovider.h:106: warning: Member homenr_ (variable) of class gmx::ForceProviderInput is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/iforceprovider.h:107: warning: Member chargeA_ (variable) of class gmx::ForceProviderInput is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/iforceprovider.h:108: warning: Member massT_ (variable) of class gmx::ForceProviderInput is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/gpuhaloexchange.h:100: warning: Member GpuHaloExchange(GpuHaloExchange &&source) noexcept (function) of class gmx::GpuHaloExchange is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/gpuhaloexchange.h:101: warning: Member operator=(GpuHaloExchange &&source) noexcept (function) of class gmx::GpuHaloExchange is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:86: warning: Member doUChar(unsigned char *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:87: warning: Member doChar(char *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:88: warning: Member doUShort(unsigned short *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:89: warning: Member doInt(int *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:90: warning: Member doInt32(int32_t *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:91: warning: Member doInt64(int64_t *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:92: warning: Member doFloat(float *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:93: warning: Member doDouble(double *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:94: warning: Member doReal(real *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:95: warning: Member doIvec(ivec *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:96: warning: Member doRvec(rvec *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:97: warning: Member doString(std::string *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:98: warning: Member doOpaque(char *data, std::size_t size)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:112: warning: Member doCharArray(char *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:119: warning: Member doUCharArray(unsigned char *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:126: warning: Member doUShortArray(unsigned short *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:133: warning: Member doIntArray(int *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:140: warning: Member doInt32Array(int32_t *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:147: warning: Member doInt64Array(int64_t *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:154: warning: Member doFloatArray(float *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:161: warning: Member doDoubleArray(double *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:168: warning: Member doRealArray(real *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:175: warning: Member doIvecArray(ivec *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:182: warning: Member doRvecArray(rvec *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:137: warning: Member value (variable) of struct gmx::IsSerializableEnum is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:143: warning: Member ddrank_opt_choices[static_cast< int >(DdRankOrder::Count)+1] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:148: warning: Member dddlb_opt_choices[static_cast< int >(DlbOption::Count)+1] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:153: warning: Member thread_aff_opt_choices[static_cast< int >(ThreadAffinity::Count)+1] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:158: warning: Member nbpu_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:159: warning: Member pme_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:160: warning: Member pme_fft_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:161: warning: Member bonded_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:162: warning: Member update_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:163: warning: Member devicesSelectedByUser (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:164: warning: Member userGpuTaskAssignment (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:167: warning: Member imdOptions (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:169: warning: Member pa[48] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_lennardjones_functions.h:332: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< calculateEnergies, InteractionModifiers::ForceSwitch > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_lennardjones_functions.h:483: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< calculateEnergies, InteractionModifiers::PotSwitch > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_lennardjones_functions.h:179: warning: Member LennardJonesCalculator(const interaction_const_t gmx_unused &ic) (function) of class gmx::LennardJonesCalculator< false, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_lennardjones_functions.h:209: warning: Member forceSigmaEpsilon(const std::array< SimdReal, inputSize > &rInvV, const std::array< SimdBool, interactSize > &interactV, SimdBool *withinCutoffV, const std::array< SimdReal, nR > &sigmaV, const std::array< SimdReal, nR > &epsilonV, SimdReal sixth, SimdReal twelfth, std::array< SimdReal, nR > &frLJV, std::array< SimdReal, vljvSize > &vLJV) (function) of class gmx::LennardJonesCalculator< false, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_lennardjones_functions.h:231: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< true, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_lennardjones_functions.h:270: warning: Member forceSigmaEpsilon(const std::array< SimdReal, inputSize > &rInvV, const std::array< SimdBool, interactSize > &interactV, SimdBool *withinCutoffV, const std::array< SimdReal, nR > &sigmaV, const std::array< SimdReal, nR > &epsilonV, SimdReal sixth, SimdReal twelfth, std::array< SimdReal, nR > &frLJV, std::array< SimdReal, vljvSize > &vLJV) (function) of class gmx::LennardJonesCalculator< true, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/mdmodulesnotifiers.h:85: warning: Member MDModulesAtomsRedistributedSignal(const matrix box, gmx::ArrayRef< const RVec > x) (function) of struct gmx::MDModulesAtomsRedistributedSignal is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/runner.h:145: warning: Member operator=(Mdrunner &&handle) noexcept (function) of class gmx::Mdrunner is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/runner.h:391: warning: Member operator=(MdrunnerBuilder &&builder) noexcept (function) of class gmx::MdrunnerBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/message_string_collector.h:67: warning: Member MessageStringCollector(MessageStringCollector &&) noexcept (function) of class gmx::MessageStringCollector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/message_string_collector.h:68: warning: Member operator=(MessageStringCollector &&) noexcept (function) of class gmx::MessageStringCollector is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:218: warning: Member allocator_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:219: warning: Member size_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:220: warning: Member reference (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:221: warning: Member const_reference (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:222: warning: Member storage_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:223: warning: Member pointer (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:224: warning: Member const_pointer (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:225: warning: Member iterator (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:226: warning: Member const_iterator (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:227: warning: Member difference_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:351: warning: Member data() const noexcept (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:353: warning: Member begin() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:354: warning: Member end() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:356: warning: Member cbegin() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:357: warning: Member cend() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:359: warning: Member begin() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:360: warning: Member end() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:362: warning: Member cbegin() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:363: warning: Member cend() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_force_sender_gpu.h:112: warning: Member waitForEvents() (function) of class gmx::PmeForceSenderGpu is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/manager.h:89: warning: Member operator=(const RestraintManager &)=default (function) of class gmx::RestraintManager is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/manager.h:90: warning: Member RestraintManager(RestraintManager &&) noexcept=default (function) of class gmx::RestraintManager is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/manager.h:91: warning: Member operator=(RestraintManager &&) noexcept=default (function) of class gmx::RestraintManager is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/selection/selectioncollection.h:144: warning: Member SelectionCollection(const SelectionCollection &rhs) (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/selection/selectioncollection.h:145: warning: Member operator=(SelectionCollection rhs) (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/selection/selectioncollection.h:146: warning: Member swap(SelectionCollection &rhs) (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:341: warning: Member add(MembedHolder &&membedHolder) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:343: warning: Member add(std::unique_ptr< StopHandlerBuilder > stopHandlerBuilder) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:348: warning: Member add(SimulatorStateData &&simulatorStateData) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:353: warning: Member add(SimulatorConfig &&simulatorConfig) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:360: warning: Member add(SimulatorEnv &&simulatorEnv) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:365: warning: Member add(Profiling &&profiling) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:367: warning: Member add(ConstraintsParam &&constraintsParam) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:372: warning: Member add(LegacyInput &&legacyInput) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:377: warning: Member add(ReplicaExchangeParameters &&replicaExchangeParameters) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:379: warning: Member add(InteractiveMD &&interactiveMd) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:384: warning: Member add(SimulatorModules &&simulatorModules) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:389: warning: Member add(CenterOfMassPulling &¢erOfMassPulling) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:394: warning: Member add(IonSwapping &&ionSwapping) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:399: warning: Member add(TopologyData &&topologyData) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:404: warning: Member add(BoxDeformationHandle &&boxDeformation) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/filestream.h:158: warning: @copybrief or @copydoc target 'TextInputFile::TextInputFile(const std::string &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/filestream.h:158: warning: @copybrief or @copydoc target 'TextInputFile::TextInputFile(const std::string &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/filestream.h:159: warning: @copydetails or @copydoc target 'TextInputFile::TextInputFile(const std::string &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/updategroups.h:112: warning: Member useUpdateGroups() const (function) of class gmx::UpdateGroups is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/updategroups.h:113: warning: Member maxUpdateGroupRadius() const (function) of class gmx::UpdateGroups is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/updategroups.h:114: warning: Member updateGroupingPerMoleculeType() const (function) of class gmx::UpdateGroups is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:412: warning: Member empty() const (function) of class gmx::WriteCheckpointDataHolder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/mp11.h:76: warning: Member mp_with_index(std::size_t i, F &&f) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:194: warning: Member operator!=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() !=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:200: warning: Member operator<(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()< rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:206: warning: Member operator<=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()<=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:212: warning: Member operator>(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() > rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:218: warning: Member operator>=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() >=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:134: warning: Member not_null(const not_null &other)=default (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:135: warning: Member operator=(const not_null &other)=default (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:146: warning: Member operator T() const (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:147: warning: Member operator->() const (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests/fft_mpi.cpp:72: warning: Member GpuFftTestParams (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests/fft_mpi.cpp:77: warning: Member GpuFftTestGridParams (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/gyrate.cpp:70: warning: Member GyrateTestParamsMerge (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/hbond.cpp:70: warning: Member HbondTestParamsMerge (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulatorcomparison.h:60: warning: Member SimulationOptionTuple (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/moduletest.h:69: warning: Member SimulationRunnerMdpSource (enumeration) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/awh_setup.cpp:68: warning: Member awhDimParamSerialized(AwhCoordinateProviderType inputCoordinateProvider, int inputCoordIndex, double inputOrigin, double inputEnd, double inputPeriod, double inputDiffusion) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/awh_setup.cpp:110: warning: Member awhBiasParamSerialized(AwhHistogramGrowthType eawhgrowth, double beta, double inputErrorScaling, ArrayRef< const std::vector< char > > dimensionParameterBuffers, int shareGroup, bool inputUserData, AwhTargetType eTargetType, bool scaleTargetByMetric) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/awh_setup.cpp:167: warning: Member awhParamSerialized(AwhHistogramGrowthType eawhgrowth, AwhPotentialType eawhpotential, double beta, double inputErrorScaling, int64_t inputSeed, ArrayRef< const std::vector< char > > dimensionParameterBuffers, int biasShareGroup, bool inputUserData, AwhTargetType eTargetType, bool scaleTargetByMetric) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests/fft_mpi.cpp:79: warning: Member getGpuAwareMpiStatusForFftBackend(const FftBackend fftBackend) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/tests/device_availability.cpp:66: warning: Member getRequiredNumberOfDevices() (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:85: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(p) &this->mask(a)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:86: warning: Member deallocate(p, 1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:93: warning: Member v(10) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:94: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(v.data()) &this->mask(v.get_allocator())) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:99: warning: Member for(std::size_t i=1000;i<=10000;i+=1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:125: warning: Member v1(1) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:127: warning: Member EXPECT_NE(data, nullptr) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:128: warning: Member v2(std::move(v1)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:129: warning: Member EXPECT_EQ(data, v2.data()) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/moduletest.cpp:398: warning: Member getNumberOfTestOpenMPThreads() (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulatorcomparison.cpp:61: warning: Member runGrompp(SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulatorcomparison.cpp:74: warning: Member runMdrun(SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulatorcomparison.cpp:87: warning: Member compareEnergies(const std::string &edr1Name, const std::string &edr2Name, const EnergyTermsToCompare &energyTermsToCompare, const MaxNumFrames maxNumFrames) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulatorcomparison.cpp:108: warning: Member compareTrajectories(const std::string &trajectory1Name, const std::string &trajectory2Name, const TrajectoryComparison &trajectoryComparison) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmegathertest.cpp:429: warning: Member registerDynamicalPmeGatherTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmesolvetest.cpp:414: warning: Member registerDynamicalPmeSolveTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/trajectorycomparison.cpp:408: warning: Member checkTrajectoryAgainstReferenceData(const std::string &trajectoryFilename, const TrajectoryComparison &trajectoryComparison, TestReferenceChecker *checker) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/trajectorycomparison.cpp:416: warning: Member checkTrajectoryAgainstReferenceData(const std::string &trajectoryFilename, const TrajectoryComparison &trajectoryComparison, TestReferenceChecker *checker, MaxNumFrames maxNumFrames) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/friction_metric.cpp:68: warning: Member g_sampleWeightCentral (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/friction_metric.cpp:69: warning: Member g_sampleWeightNeighbor (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/friction_metric.cpp:70: warning: Member g_sampleTimeStep (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/friction_metric.cpp:71: warning: Member g_numPointsPerDim (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests/fft_mpi.cpp:263: warning: Member inputGrids (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests/fft_mpi.cpp:267: warning: Member inputBackends (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:783: warning: Member testKernelTypes (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:82: warning: Member a (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:83: warning: Member p (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:126: warning: Member data (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:125: warning: Member mode (typedef) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/grid.cpp:122: warning: Member getMaxNumCells(const Grid::Geometry &geometry, const int numAtoms, const int numColumns) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/gridset.cpp:135: warning: Member getGridOffset(gmx::ArrayRef< const Grid > grids, int gridIndex) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_buffer_ops.cpp:63: warning: Member nbnxn_gpu_x_to_nbat_x(const Nbnxm::Grid &grid, NbnxmGpu *nb, DeviceBuffer< gmx::RVec > d_x, GpuEventSynchronizer *xReadyOnDevice, const gmx::AtomLocality locality, int gridId, int numColumnsMax, bool mustInsertNonLocalDependency) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:83: warning: Member init_ewald_coulomb_force_table(const EwaldCorrectionTables &tables, NBParamGpu *nbp, const DeviceContext &deviceContext) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:97: warning: Member useTabulatedEwaldByDefault(const DeviceInformation &deviceInfo) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:128: warning: Member nbnxn_gpu_pick_ewald_kernel_type(const interaction_const_t &ic, const DeviceInformation &deviceInfo) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:178: warning: Member set_cutoff_parameters(NBParamGpu *nbp, const interaction_const_t &ic, const PairlistParams &listParams) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:202: warning: Member initPlistSorting(gpuPlistSorting *sorting) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:225: warning: Member init_plist(gpu_plist *pl) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:253: warning: Member init_timings(gmx_wallclock_gpu_nbnxn_t *t) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:302: warning: Member nbnxmGpuPickVdwKernelType(const interaction_const_t &ic, LJCombinationRule ljCombinationRule) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:356: warning: Member nbnxmGpuPickElectrostaticsKernelType(const interaction_const_t &ic, const DeviceInformation &deviceInfo) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:442: warning: Member gpu_init(const gmx::DeviceStreamManager &deviceStreamManager, const interaction_const_t *ic, const PairlistParams &listParams, const nbnxn_atomdata_t *nbat, const bool bLocalAndNonlocal) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:511: warning: Member gpu_pme_loadbal_update_param(nonbonded_verlet_t *nbv, const interaction_const_t &ic) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:528: warning: Member gpu_upload_shiftvec(NbnxmGpu *nb, const nbnxn_atomdata_t *nbatom) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:689: warning: Member gpu_init_atomdata(NbnxmGpu *nb, const nbnxn_atomdata_t *nbat) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:792: warning: Member gpu_clear_outputs(NbnxmGpu *nb, bool computeVirial) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:823: warning: Member gpu_is_kernel_ewald_analytical(const NbnxmGpu *nb) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:829: warning: Member setupGpuShortRangeWork(NbnxmGpu *nb, const gmx::ListedForcesGpu *listedForcesGpu, const gmx::InteractionLocality iLocality) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:842: warning: Member haveGpuShortRangeWork(const NbnxmGpu *nb, const gmx::InteractionLocality interactionLocality) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:981: warning: Member nbnxnInsertNonlocalGpuDependency(NbnxmGpu *nb, const InteractionLocality interactionLocality) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1076: warning: Member nbnxn_gpu_init_x_to_nbat_x(const Nbnxm::GridSet &gridSet, NbnxmGpu *gpu_nbv) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1286: warning: Member gpuGetNBAtomData(NbnxmGpu *nb) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1292: warning: Member gpu_get_f(NbnxmGpu *nb) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_setup.cpp:355: warning: Member getENbnxnInitCombRule(const t_forcerec &forcerec) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.cpp:53: warning: Member getNbnxmSubGroupSize(const DeviceInformation &deviceInfo) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:1455: warning: Member launchNbnxmKernelHelper(NbnxmGpu *nb, const gmx::StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:106: warning: Member elecEwald (variable) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:109: warning: Member elecEwaldTab (variable) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:112: warning: Member ljEwald (variable) of namespace Nbnxm is not documented. cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen/doxygen-lib-timestamp.txt make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [100%] Built target doxygen-lib /build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi/gmxapi_staging/gmxapi/commandline.py:docstring of gmxapi.commandline.commandline_operation:60: WARNING: 'any' reference target not found: os.getenv /build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi/gmxapi_staging/gmxapi/_logging.py:docstring of gmxapi._logging:6: WARNING: 'any' reference target not found: sys.stderr /build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi/gmxapi_staging/gmxapi/_logging.py:docstring of gmxapi._logging:6: WARNING: 'any' reference target not found: logging /build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi/gmxapi_staging/gmxapi/_logging.py:docstring of gmxapi._logging:6: WARNING: 'any' reference target not found: logging.basicConfig /build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi/gmxapi_staging/gmxapi/_logging.py:docstring of gmxapi._logging:13: WARNING: 'any' reference target not found: logging.StreamHandler /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/gmxapi/userguide/usage.rst:131: WARNING: 'any' reference target not found: os.environ /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/release-notes/2022/2022.1.rst:181: WARNING: 'any' reference target not found: subprocess.run make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [100%] Built target webpage-sphinx The following warnings were produced by Doxygen: /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/energyhistory.cpp:44: warning: Conditional section with label 'INTERNAL' does not have a corresponding \endcond command within this file. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/arrayref.h:314: warning: @copybrief or @copydoc target 'arrayRefFromArray' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:81: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:117: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/options/abstractoptionstorage.h:144: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:92: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:97: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/electricfield.cpp:174: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:118: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:123: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:58: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:403: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:169: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:98: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:142: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:300: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd_memory.h:154: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd_memory.h:163: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:62: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_insolidangle.cpp:99: warning: unable to resolve reference to 'sm_insolidangle' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:345: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/filestream.h:158: warning: @copybrief or @copydoc target 'TextInputFile::TextInputFile(const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/selection/selectionenums.h:82: warning: explicit link request to 'SelectionFlag' could not be resolved warning: Included by graph for 'functions.h' not generated, too many nodes (56), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'basicoptions.h' not generated, too many nodes (51), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/selectioncollection.cpp:964: warning: Member swap(SelectionCollection &lhs, SelectionCollection &rhs) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/selection/selectionenums.h:82: warning: explicit link request to 'SelectionFlag' could not be resolved warning: Included by graph for 'arrayref.h' not generated, too many nodes (193), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'basedefinitions.h' not generated, too many nodes (124), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'classhelpers.h' not generated, too many nodes (60), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'enumerationhelpers.h' not generated, too many nodes (56), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'exceptions.h' not generated, too many nodes (230), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'gmxassert.h' not generated, too many nodes (228), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'real.h' not generated, too many nodes (132), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'smalloc.h' not generated, too many nodes (98), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'stringutil.h' not generated, too many nodes (208), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:81: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:98: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:117: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:142: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/colvarproxy_gromacs_version.h:42: warning: Member COLVARPROXY_VERSION (macro definition) of file colvarproxy_gromacs_version.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/tests/colvarsoptions.cpp:80: warning: Member colvarsConfig (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:87: warning: Member Ensures(cond) (macro definition) of file pointers.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:194: warning: Member operator!=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() !=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:200: warning: Member operator<(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()< rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:206: warning: Member operator<=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()<=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:212: warning: Member operator>(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() > rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:218: warning: Member operator>=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() >=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/iframeconverter.h:116: warning: invalid argument for command '\iline' /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:58: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:62: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/computemultibodycutoffs.cpp:267: warning: Member dd_bonded_cg_distance(const gmx::MDLogger &mdlog, const gmx_mtop_t &mtop, const t_inputrec &inputrec, ArrayRef< const RVec > x, const matrix box, const DDBondedChecking ddBondedChecking, real *r_2b, real *r_mb) (function) of file computemultibodycutoffs.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/domdec_network.cpp:140: warning: Member dd_sendrecv2_rvec(const struct gmx_domdec_t gmx_unused *dd, int gmx_unused ddimind, rvec gmx_unused *buf_s_fw, int gmx_unused n_s_fw, rvec gmx_unused *buf_r_fw, int gmx_unused n_r_fw, rvec gmx_unused *buf_s_bw, int gmx_unused n_s_bw, rvec gmx_unused *buf_r_bw, int gmx_unused n_r_bw) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/domdec_network.cpp:226: warning: Member dd_bcast(const gmx_domdec_t gmx_unused *dd, int gmx_unused nbytes, void gmx_unused *data) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/domdec_network.cpp:236: warning: Member dd_scatter(const gmx_domdec_t gmx_unused *dd, int gmx_unused nbytes, const void gmx_unused *src, void *dest) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/domdec_network.cpp:255: warning: Member dd_gather(const gmx_domdec_t gmx_unused *dd, int gmx_unused nbytes, const void gmx_unused *src, void gmx_unused *dest) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/domdec_network.cpp:274: warning: Member dd_scatterv(const gmx_domdec_t gmx_unused *dd, gmx::ArrayRef< const int > gmx_unused scounts, gmx::ArrayRef< const int > gmx_unused disps, const T *sbuf, int rcount, T *rbuf) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/domdec_network.cpp:317: warning: Member dd_scatterv(const gmx_domdec_t *dd, gmx::ArrayRef< const int > scounts, gmx::ArrayRef< const int > disps, const int *sbuf, int rcount, int *rbuf) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/domdec_network.cpp:324: warning: Member dd_scatterv(const gmx_domdec_t *dd, gmx::ArrayRef< const int > scounts, gmx::ArrayRef< const int > disps, const gmx::RVec *sbuf, int rcount, gmx::RVec *rbuf) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/domdec_network.cpp:332: warning: Member dd_gatherv(const gmx_domdec_t gmx_unused *dd, int gmx_unused scount, const T gmx_unused *sbuf, gmx::ArrayRef< const int > gmx_unused rcounts, gmx::ArrayRef< const int > gmx_unused disps, T gmx_unused *rbuf) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/domdec_network.cpp:371: warning: Member dd_gatherv(const gmx_domdec_t *dd, int scount, const int *sbuf, gmx::ArrayRef< const int > rcounts, gmx::ArrayRef< const int > disps, int *rbuf) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/domdec_network.cpp:378: warning: Member dd_gatherv(const gmx_domdec_t *dd, int scount, const gmx::RVec *sbuf, gmx::ArrayRef< const int > rcounts, gmx::ArrayRef< const int > disps, gmx::RVec *rbuf) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/domdec_struct.h:113: warning: Member gmx_domdec_zone_size_t (typedef) of file domdec_struct.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/gpuhaloexchange_impl_gpu.cpp:63: warning: Member supportedLibMpiBuild (variable) of file gpuhaloexchange_impl_gpu.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/gpuhaloexchange_impl_gpu.cpp:66: warning: Member supportedThreadMpiBuild (variable) of file gpuhaloexchange_impl_gpu.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:63: warning: Member packSendBufKernel(Float3 *__restrict__ gm_dataPacked, const Float3 *__restrict__ gm_data, const int *__restrict__ gm_map, int mapSize, Float3 coordinateShift) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:117: warning: Member launchPackSendBufKernel(const DeviceStream &deviceStream, int xSendSize, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:131: warning: Member launchUnpackRecvBufKernel(const DeviceStream &deviceStream, int fRecvSize, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/localtopology.cpp:946: warning: Member dd_make_local_top(const gmx_domdec_t &dd, const gmx_domdec_zones_t &zones, int npbcdim, matrix box, rvec cellsize_min, const ivec npulse, t_forcerec *fr, ArrayRef< const RVec > coordinates, const gmx_mtop_t &mtop, gmx::ArrayRef< const int64_t > atomInfo, gmx_localtop_t *ltop) (function) of file localtopology.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/reversetopology.cpp:401: warning: Member dd_make_reverse_top(FILE *fplog, gmx_domdec_t *dd, const gmx_mtop_t &mtop, const gmx::VirtualSitesHandler *vsite, const t_inputrec &inputrec, const DDBondedChecking ddBondedChecking) (function) of file reversetopology.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/ewald.cpp:71: warning: Member cvec (typedef) of file ewald.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_force_sender_gpu_impl.h:57: warning: Member hardware_destructive_interference_size (variable) of file pme_force_sender_gpu_impl.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gather_sycl.cpp:699: warning: Member INSTANTIATE_2(order, numGrids, threadsPerAtom, subGroupSize) (macro definition) of file pme_gather_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gather_sycl.cpp:703: warning: Member INSTANTIATE(order, subGroupSize) (macro definition) of file pme_gather_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu.cpp:281: warning: Member pme_gpu_launch_gather(const gmx_pme_t *pme, gmx_wallcycle gmx_unused *wcycle, const real lambdaQ, const bool computeVirial) (function) of file pme_gpu.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_calculate_splines_sycl.h:90: warning: Member mode (typedef) of file pme_gpu_calculate_splines_sycl.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_calculate_splines_sycl.h:74: warning: Member assertIsFinite(Float3 gmx_unused arg) (function) of namespace anonymous_namespace{pme_gpu_calculate_splines_sycl.h} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_calculate_splines_sycl.h:82: warning: Member assertIsFinite(T gmx_unused arg) (function) of namespace anonymous_namespace{pme_gpu_calculate_splines_sycl.h} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_grid.h:49: warning: Member gmx_parallel_3dfft_t (typedef) of file pme_gpu_grid.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_grid.h:105: warning: Member convertPmeGridToFftGrid< true >(const PmeGpu *, float *, gmx_parallel_3dfft_t *, int) (function) of file pme_gpu_grid.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_grid.h:110: warning: Member convertPmeGridToFftGrid< false >(const PmeGpu *, float *, gmx_parallel_3dfft_t *, int) (function) of file pme_gpu_grid.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_grid.h:115: warning: Member convertPmeGridToFftGrid< true >(const PmeGpu *, DeviceBuffer< float > *, int) (function) of file pme_gpu_grid.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_grid.h:119: warning: Member convertPmeGridToFftGrid< false >(const PmeGpu *, DeviceBuffer< float > *, int) (function) of file pme_gpu_grid.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_grid_sycl.cpp:61: warning: Member mode (typedef) of file pme_gpu_grid_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_grid_sycl.cpp:1403: warning: Member convertPmeGridToFftGrid< true >(const PmeGpu *pmeGpu, float *h_fftRealGrid, gmx_parallel_3dfft_t *fftSetup, const int gridIndex) (function) of file pme_gpu_grid_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_grid_sycl.cpp:1408: warning: Member convertPmeGridToFftGrid< false >(const PmeGpu *pmeGpu, float *h_fftRealGrid, gmx_parallel_3dfft_t *fftSetup, const int gridIndex) (function) of file pme_gpu_grid_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_grid_sycl.cpp:1413: warning: Member convertPmeGridToFftGrid< true >(const PmeGpu *pmeGpu, DeviceBuffer< float > *d_fftRealGrid, const int gridIndex) (function) of file pme_gpu_grid_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_grid_sycl.cpp:1417: warning: Member convertPmeGridToFftGrid< false >(const PmeGpu *pmeGpu, DeviceBuffer< float > *d_fftRealGrid, const int gridIndex) (function) of file pme_gpu_grid_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_internal.cpp:1120: warning: Member pme_gpu_update_input_box(PmeGpu gmx_unused *pmeGpu, const matrix gmx_unused box) (function) of file pme_gpu_internal.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_internal.cpp:2525: warning: Member pme_gpu_set_kernelparam_useNvshmem(const PmeGpu *pmeGpu, bool useNvshmem) (function) of file pme_gpu_internal.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_internal.h:69: warning: Member gmx_parallel_3dfft_t (typedef) of file pme_gpu_internal.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_internal.h:450: warning: Member pme_gpu_set_kernelparam_useNvshmem(const PmeGpu *pmeGpu, bool useNvshmem) (function) of file pme_gpu_internal.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_ocl_stubs.cpp:82: warning: Member convertPmeGridToFftGrid< true >(const PmeGpu *, float *, gmx_parallel_3dfft_t *, const int) (function) of file pme_gpu_ocl_stubs.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_ocl_stubs.cpp:87: warning: Member convertPmeGridToFftGrid< false >(const PmeGpu *, float *, gmx_parallel_3dfft_t *, const int) (function) of file pme_gpu_ocl_stubs.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_ocl_stubs.cpp:92: warning: Member convertPmeGridToFftGrid< true >(const PmeGpu *, DeviceBuffer< float > *, const int) (function) of file pme_gpu_ocl_stubs.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_ocl_stubs.cpp:96: warning: Member convertPmeGridToFftGrid< false >(const PmeGpu *, DeviceBuffer< float > *, const int) (function) of file pme_gpu_ocl_stubs.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:91: warning: Member INSTANTIATE_SPREAD_2( order, computeSplines, spreadCharges, numGrids, writeGlobal, threadsPerAtom, subGroupSize) (macro definition) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:94: warning: Member INSTANTIATE_SPREAD(order, numGrids, threadsPerAtom, subGroupSize) (macro definition) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:100: warning: Member INSTANTIATE_GATHER_2(order, numGrids, readGlobal, threadsPerAtom, subGroupSize) (macro definition) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:103: warning: Member INSTANTIATE_GATHER(order, numGrids, threadsPerAtom, subGroupSize) (macro definition) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:107: warning: Member INSTANTIATE_X(x, order, subGroupSize) (macro definition) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:113: warning: Member INSTANTIATE_SOLVE(subGroupSize) (macro definition) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:123: warning: Member INSTANTIATE(order, subGroupSize) (macro definition) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:67: warning: Member chooseSubGroupSizeForDevice(const DeviceInformation &deviceInfo) (function) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:59: warning: Member c_pmeOrder (variable) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:61: warning: Member c_wrapX (variable) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:62: warning: Member c_wrapY (variable) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:64: warning: Member c_stateA (variable) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:65: warning: Member c_stateB (variable) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_types_host.h:72: warning: Member PmeGpuHaloExchange (typedef) of file pme_gpu_types_host.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_internal.h:79: warning: Member PME_GRID_C6A (macro definition) of file pme_internal.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_internal.h:85: warning: Member DO_Q_AND_LJ (macro definition) of file pme_internal.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_internal.h:86: warning: Member DO_Q_AND_LJ_LB (macro definition) of file pme_internal.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp.cpp:477: warning: Member gmx_pme_send_resetcounters(const t_commrec gmx_unused *cr, int64_t gmx_unused step) (function) of file pme_pp.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_communication.h:76: warning: Member PP_PME_CHARGEB (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_communication.h:77: warning: Member PP_PME_SQRTC6 (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_communication.h:78: warning: Member PP_PME_SQRTC6B (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_communication.h:79: warning: Member PP_PME_SIGMA (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_communication.h:80: warning: Member PP_PME_SIGMAB (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_communication.h:81: warning: Member PP_PME_COORD (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_communication.h:82: warning: Member PP_PME_ENER_VIR (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_communication.h:83: warning: Member PP_PME_FINISH (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_communication.h:84: warning: Member PP_PME_SWITCHGRID (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_communication.h:85: warning: Member PP_PME_RESETCOUNTERS (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_communication.h:86: warning: Member PP_PME_GPUCOMMS (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_communication.h:88: warning: Member PP_PME_RECVFTOGPU (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_communication.h:90: warning: Member PP_PME_MDGPUGRAPH (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_solve_sycl.cpp:53: warning: Member mode (typedef) of file pme_solve_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_spread_sycl.cpp:436: warning: Member INSTANTIATE_2(order, numGrids, threadsPerAtom, subGroupSize) (macro definition) of file pme_spread_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_spread_sycl.cpp:442: warning: Member INSTANTIATE(order, subGroupSize) (macro definition) of file pme_spread_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmegathertest.cpp:429: warning: Member registerDynamicalPmeGatherTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmesolvetest.cpp:108: warning: Member enumValueToString(PmeSolveAlgorithm enumValue) (function) of namespace gmx::test::anonymous_namespace{pmesolvetest.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmesolvetest.cpp:115: warning: Member enumValueToString(GridOrdering enumValue) (function) of namespace gmx::test::anonymous_namespace{pmesolvetest.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmesolvetest.cpp:414: warning: Member registerDynamicalPmeSolveTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:173: warning: Member enumValueToString(SplineAndSpreadOptions enumValue) (function) of namespace gmx::test::anonymous_namespace{pmesplinespreadtest.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:85: warning: Member c_testSystems (variable) of namespace gmx::test::anonymous_namespace{pmesplinespreadtest.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmesolvetest.cpp:414: warning: Member registerDynamicalPmeSolveTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmegathertest.cpp:429: warning: Member registerDynamicalPmeGatherTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests/fft.cpp:293: warning: Member FFTTest3DParameters (typedef) of namespace gmx::test::anonymous_namespace{fft.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_cufftmp.cpp:102: warning: Member handleCufftError(cufftResult_t status, const char *msg) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:251: warning: Member launchVkFft(const DeviceBuffer< float > &realGrid, const DeviceBuffer< float > &complexGrid, NativeQueue queue, gmx_fft_direction fftDirection, VkFFTApplication *application, VkFFTLaunchParams *launchParams) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests/fft_mpi.cpp:72: warning: Member GpuFftTestParams (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests/fft_mpi.cpp:77: warning: Member GpuFftTestGridParams (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests/fft_mpi.cpp:79: warning: Member getGpuAwareMpiStatusForFftBackend(const FftBackend fftBackend) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests/fft_mpi.cpp:263: warning: Member inputGrids (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests/fft_mpi.cpp:267: warning: Member inputBackends (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/filetypes.cpp:62: warning: Member TypeAndName (typedef) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/filetypes.cpp:64: warning: Member FileTypeTestParams (typedef) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/filetypes.cpp:115: warning: Member testParams (variable) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/filetypes.cpp:124: warning: Member prefixes (variable) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/fileioxdrserializer.cpp:73: warning: Member c_int32Value (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/fileioxdrserializer.cpp:74: warning: Member c_int64Value (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/fileioxdrserializer.cpp:76: warning: Member c_intAndFloat32 (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/fileioxdrserializer.cpp:77: warning: Member c_intAndFloat64 (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/xvgio.cpp:63: warning: Member compareValues(basic_mdspan< const double, dynamicExtents2D > ref, basic_mdspan< const double, dynamicExtents2D > test) (function) of namespace gmx::test::anonymous_namespace{xvgio.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:97: warning: Member c_numAtomTypes (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:511: warning: Member c_softcoreBeutlerAlphaOrGapsysLinpointScaling (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:512: warning: Member c_softcoreCoulomb (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:513: warning: Member c_softcoreType (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/device_stream_sycl.cpp:52: warning: Member makeQueuePropertyList(bool enableProfiling, DeviceStreamPriority priority) (function) of file device_stream_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/devicebuffer_ocl.h:386: warning: Member asMpiPointer(DeviceBuffer< ValueType > &) (function) of file devicebuffer_ocl.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/devicebuffer_sycl.h:437: warning: Member asMpiPointer(DeviceBuffer< ValueType > &buffer) (function) of file devicebuffer_sycl.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gmxopencl.h:56: warning: Member CL_USE_DEPRECATED_OPENCL_2_0_APIS (macro definition) of file gmxopencl.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:61: warning: unable to resolve reference to 'GpuEventSynchronizer::markEvent' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:62: warning: unable to resolve reference to 'GpuEventSynchronizer::waitForEvent' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:63: warning: unable to resolve reference to 'GpuEventSynchronizer::enqueueWaitEvent' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:77: warning: unable to resolve reference to 'GpuEventSynchronizer::reset' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:79: warning: unable to resolve reference to 'GpuEventSynchronizer::consume' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:81: warning: unable to resolve reference to 'GpuEventSynchronizer::markEvent' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:84: warning: unable to resolve reference to 'GpuEventSynchronizer::waitForEvent' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:86: warning: unable to resolve reference to 'GpuEventSynchronizer::enqueueWaitEvent' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:91: warning: unable to resolve reference to 'GpuEventSynchronizer::markEvent' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:92: warning: unable to resolve reference to 'GpuEventSynchronizer::enqueueWaitEvent' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:92: warning: unable to resolve reference to 'GpuEventSynchronizer::enqueueWaitEvent' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gputraits.h:63: warning: Member DeviceTexture (typedef) of file gputraits.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gputraits_ocl.h:50: warning: Member DeviceTexture (typedef) of file gputraits_ocl.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/oclraii.h:131: warning: Member ClCommandQueue (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/oclraii.h:132: warning: Member ClProgram (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/oclraii.h:133: warning: Member ClKernel (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/pmalloc.cpp:83: warning: Member pmallocSetDefaultDeviceContext(const DeviceContext *) (function) of file pmalloc.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/pmalloc.cpp:88: warning: Member pmallocClearDefaultDeviceContext() (function) of file pmalloc.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/pmalloc_sycl.cpp:128: warning: Member pmallocSetDefaultDeviceContext(const DeviceContext *deviceContext) (function) of file pmalloc_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/pmalloc_sycl.cpp:137: warning: Member pmallocClearDefaultDeviceContext() (function) of file pmalloc_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:57: warning: Member SYCL_ASSERT(condition) (macro definition) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:78: warning: Member compilingForHost() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:94: warning: Member compilingForSubGroupSize() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:108: warning: Member skipKernelCompilation() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:130: warning: Member atomicAddDefault(T &val, const T delta) (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:167: warning: Member atomicFetchAddLocal(T &val, const T delta) (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:321: warning: Member __attribute__((always_inline)) static AmdPackedFloat3 operator*(const AmdPackedFloat3 &v (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:321: warning: Member s (variable) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:325: warning: Member v (variable) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/tests/device_availability.cpp:66: warning: Member getRequiredNumberOfDevices() (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/device_management_sycl.cpp:68: warning: Member parseHardwareVersionNvidia(const std::string &archName) (function) of file device_management_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/device_management_sycl.cpp:105: warning: Member getHardwareVersionNvidia(const sycl::device &device) (function) of file device_management_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/device_management_sycl.cpp:140: warning: Member parseHardwareVersionAmd(const std::string &archName) (function) of file device_management_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/device_management_sycl.cpp:180: warning: Member getHardwareVersionAmd(const sycl::device &device) (function) of file device_management_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/device_management_sycl.cpp:214: warning: Member getHardwareVersionIntel(const sycl::device &device) (function) of file device_management_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/device_management_sycl.cpp:250: warning: Member getDeviceGpuAwareMpiStatus(const sycl::backend backend) (function) of file device_management_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/device_management_sycl.cpp:543: warning: Member partitionDevices(const std::vector< sycl::device > &&devices) (function) of file device_management_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/device_management_sycl_intel_device_ids.cpp:51: warning: Member IntelProductConfig (enumeration) of file device_management_sycl_intel_device_ids.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/device_management_sycl_intel_device_ids.cpp:506: warning: Member getHardwareVersionFromIntelProductConfig(const IntelProductConfig productConfig) (function) of file device_management_sycl_intel_device_ids.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/device_management_sycl_intel_device_ids.cpp:517: warning: Member getProductConfigFromPciExpressID(unsigned int pciExpressID) (function) of file device_management_sycl_intel_device_ids.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/device_management_sycl_intel_device_ids.cpp:129: warning: Member c_pciExpressIdsForProduct (variable) of file device_management_sycl_intel_device_ids.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/hardwaretopology.cpp:1099: warning: Member detectCpuLimit(const std::string &root="") (function) of namespace gmx::anonymous_namespace{hardwaretopology.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/hardwaretopology.cpp:1180: warning: Member setMaxThreads(float cpuLimit, int topologyCpus, int systemCpus) (function) of namespace gmx::anonymous_namespace{hardwaretopology.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/simd_support.cpp:70: warning: Member simdString(SimdType s) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/simd_support.cpp:199: warning: Member simdCompiled() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/tests/mockhardwaretopology.cpp:162: warning: Member checkHardwareTopology(TestReferenceChecker *checker, const HardwareTopology &hwTop) (function) of namespace gmx::test::anonymous_namespace{mockhardwaretopology.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/bonded.cpp:3080: warning: Member CmapForceStructure (typedef) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/bonded.cpp:3082: warning: Member processCmapForceComponent(const gmx::RVec a, const gmx::RVec b, const real df, const real gaa, const real fga, const real gbb, const real hgb, const int dim) (function) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/bonded.cpp:3098: warning: Member applyCmapForceComponent(const gmx::RVec forceComponent) (function) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/bonded.cpp:3109: warning: Member accumulateCmapForces(const rvec x[], rvec4 f[], rvec fshift[], const t_pbc *pbc, const gmx::RVec r_ij, const gmx::RVec r_kj, const gmx::RVec r_kl, const gmx::RVec a, const gmx::RVec b, gmx::RVec h, const real ra2r, const real rb2r, const real rgr, const real rg, const int ai, const int aj, const int ak, const int al, const real df, const int t1, const int t2) (function) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_impl_gpu.cpp:67: warning: Member chooseSubGroupSizeForDevice(const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_impl_gpu.cpp:61: warning: Member c_threadsPerBlock (variable) of file listed_forces_gpu_impl_gpu.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:875: warning: Member mode (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:113: warning: Member staggeredAtomicAddForce(sycl::global_ptr< Float3 > gm_f, Float3 f, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:134: warning: Member harmonic_gpu(const float kA, const float xA, const float x, sycl::private_ptr< float > V, sycl::private_ptr< float > F) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:152: warning: Member bonds_gpu(const int i, sycl::private_ptr< float > vtot_loc, const sycl::global_ptr< const t_iatom > gm_forceatoms, const sycl::global_ptr< const t_iparams > gm_forceparams, const sycl::global_ptr< const sycl::float4 > gm_xq, sycl::global_ptr< Float3 > gm_f, sycl::local_ptr< Float3 > sm_fShiftLoc, const PbcAiuc &pbcAiuc, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:260: warning: Member bond_angle_gpu(const sycl::float4 xi, const sycl::float4 xj, const sycl::float4 xk, const PbcAiuc &pbcAiuc, sycl::private_ptr< Float3 > r_ij, sycl::private_ptr< Float3 > r_kj, sycl::private_ptr< float > costh, sycl::private_ptr< int > t1, sycl::private_ptr< int > t2) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:279: warning: Member angles_gpu(const int i, sycl::private_ptr< float > vtot_loc, const sycl::global_ptr< const t_iatom > gm_forceatoms, const sycl::global_ptr< const t_iparams > gm_forceparams, const sycl::global_ptr< const sycl::float4 > gm_xq, sycl::global_ptr< Float3 > gm_f, sycl::local_ptr< Float3 > sm_fShiftLoc, const PbcAiuc &pbcAiuc, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:347: warning: Member urey_bradley_gpu(const int i, sycl::private_ptr< float > vtot_loc, const sycl::global_ptr< const t_iatom > gm_forceatoms, const sycl::global_ptr< const t_iparams > gm_forceparams, const sycl::global_ptr< const sycl::float4 > gm_xq, sycl::global_ptr< Float3 > gm_f, sycl::local_ptr< Float3 > sm_fShiftLoc, const PbcAiuc &pbcAiuc, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:460: warning: Member dih_angle_gpu(const T xi, const T xj, const T xk, const T xl, const PbcAiuc &pbcAiuc, sycl::private_ptr< Float3 > r_ij, sycl::private_ptr< Float3 > r_kj, sycl::private_ptr< Float3 > r_kl, sycl::private_ptr< Float3 > m, sycl::private_ptr< Float3 > n, sycl::private_ptr< int > t1, sycl::private_ptr< int > t2, sycl::private_ptr< int > t3) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:489: warning: Member dih_angle_gpu_sincos(const T xi, const T xj, const T xk, const T xl, const PbcAiuc &pbcAiuc, sycl::private_ptr< Float3 > r_ij, sycl::private_ptr< Float3 > r_kj, sycl::private_ptr< Float3 > r_kl, sycl::private_ptr< Float3 > m, sycl::private_ptr< Float3 > n, sycl::private_ptr< int > t1, sycl::private_ptr< int > t2, sycl::private_ptr< float > cosval) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:529: warning: Member dopdihs_gpu(const float cpA, const float phiA, const int mult, const float phi, sycl::private_ptr< float > v, sycl::private_ptr< float > f) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:543: warning: Member do_dih_fup_gpu(const int i, const int j, const int k, const int l, const float ddphi, const Float3 r_ij, const Float3 r_kj, const Float3 r_kl, const Float3 m, const Float3 n, sycl::global_ptr< Float3 > gm_f, sycl::local_ptr< Float3 > sm_fShiftLoc, const PbcAiuc &pbcAiuc, const sycl::global_ptr< const Float4 > gm_xq, const int t1, const int t2, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:603: warning: Member pdihs_gpu(const int i, sycl::private_ptr< float > vtot_loc, const sycl::global_ptr< const t_iatom > gm_forceatoms, const sycl::global_ptr< const t_iparams > gm_forceparams, const sycl::global_ptr< const sycl::float4 > gm_xq, sycl::global_ptr< Float3 > gm_f, sycl::local_ptr< Float3 > sm_fShiftLoc, const PbcAiuc &pbcAiuc, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:649: warning: Member rbdihs_gpu(const int i, sycl::private_ptr< float > vtot_loc, const sycl::global_ptr< const t_iatom > gm_forceatoms, const sycl::global_ptr< const t_iparams > gm_forceparams, const sycl::global_ptr< const sycl::float4 > gm_xq, sycl::global_ptr< Float3 > gm_f, sycl::local_ptr< Float3 > sm_fShiftLoc, const PbcAiuc &pbcAiuc, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:761: warning: Member idihs_gpu(const int i, sycl::private_ptr< float > vtot_loc, const sycl::global_ptr< const t_iatom > gm_forceatoms, const sycl::global_ptr< const t_iparams > gm_forceparams, const sycl::global_ptr< const sycl::float4 > gm_xq, sycl::global_ptr< Float3 > gm_f, sycl::local_ptr< Float3 > sm_fShiftLoc, const PbcAiuc &pbcAiuc, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:814: warning: Member pairs_gpu(const int i, const sycl::global_ptr< const t_iatom > gm_forceatoms, const sycl::global_ptr< const t_iparams > gm_iparams, const sycl::global_ptr< const sycl::float4 > gm_xq, sycl::global_ptr< Float3 > gm_f, sycl::local_ptr< Float3 > sm_fShiftLoc, const PbcAiuc &pbcAiuc, const float scale_factor, sycl::private_ptr< float > vtotVdw_loc, sycl::private_ptr< float > vtotElec_loc, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:878: warning: Member bondedKernel(sycl::handler &cgh, const BondedGpuKernelParameters &kernelParams, const DeviceBuffer< t_iatom > gm_iatoms_[numFTypesOnGpu], float *__restrict__ gm_vTot, const t_iparams *__restrict__ gm_forceParams_, const sycl::float4 *__restrict__ gm_xq_, Float3 *__restrict__ gm_f_, Float3 *__restrict__ gm_fShift_) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:64: warning: Member c_deg2RadF (variable) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:65: warning: Member c_Pi (variable) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/pairs.cpp:164: warning: Member sixthRoot(const real r) (function) of file pairs.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/tests/pairs.cpp:200: warning: Member frHelper (variable) of namespace gmx::test::anonymous_namespace{pairs.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/tests/position_restraints.cpp:148: warning: Member c_emptyLambdas (variable) of namespace gmx::test::anonymous_namespace{position_restraints.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/functions.cpp:388: warning: Member IntegerTypes (typedef) of namespace anonymous_namespace{functions.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/nrjac.h:55: warning: Member jacobi(double **a, int numDimensions, double *eigenvalues, double **eigenvectors, int *numRotations) (function) of file nrjac.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/nrjac.h:65: warning: Member jacobi(gmx::ArrayRef< gmx::DVec > a, gmx::ArrayRef< double > eigenvalues, gmx::ArrayRef< gmx::DVec > eigenvectors) (function) of file nrjac.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/nrjac.h:67: warning: Member m_inv_gen(const real *m, int n, real *minv) (function) of file nrjac.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/neldermead.cpp:97: warning: Member defaultNelderMeadParameters (variable) of namespace gmx::anonymous_namespace{neldermead.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/nrjac.cpp:52: warning: Member do_rotate(MatrixType a, int i, int j, int k, int l, double tau, double s) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/nrjac.cpp:62: warning: Member jacobi(MatrixType a, const int n, double d[], MatrixType v) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/nrjac.cpp:175: warning: Member jacobi(double **a, const int numDimensions, double *eigenvalues, double **eigenvectors, int *numRotations) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/nrjac.cpp:185: warning: Member jacobi(gmx::ArrayRef< gmx::DVec > a, gmx::ArrayRef< double > eigenvalues, gmx::ArrayRef< gmx::DVec > eigenvectors) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/nrjac.cpp:194: warning: Member m_inv_gen(const real *m, int n, real *minv) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/optimization.cpp:60: warning: Member mcCormick(ArrayRef< const real > x) (function) of namespace gmx::test::anonymous_namespace{optimization.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/constr.cpp:85: warning: Member c_pbcs (variable) of namespace gmx::test::anonymous_namespace{constr.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/constr.cpp:156: warning: Member c_constraintsTestSystemList (variable) of namespace gmx::test::anonymous_namespace{constr.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/energyoutput.cpp:93: warning: Member boxs_nm (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/energyoutput.cpp:95: warning: Member tricl_boxs_nm (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/energyoutput.cpp:98: warning: Member vol_nm[] (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/energyoutput.cpp:100: warning: Member dens_nm[] (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/energyoutput.cpp:102: warning: Member pvEnergyFieldName (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/energyoutput.cpp:104: warning: Member enthalpyEnergyFieldName (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/energyoutput.cpp:106: warning: Member virialEnergyFieldNames (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/energyoutput.cpp:110: warning: Member boxvel_nm (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/energyoutput.cpp:123: warning: Member haveFepLambdaMoves(const t_inputrec &inputrec) (function) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/energyoutput.h:84: warning: Member pvEnergyFieldName (variable) of file energyoutput.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/energyoutput.h:86: warning: Member enthalpyEnergyFieldName (variable) of file energyoutput.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/energyoutput.h:88: warning: Member virialEnergyFieldNames (variable) of file energyoutput.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/freeenergyparameters.cpp:58: warning: Member lambdasAtState(const int stateIndex, gmx::ArrayRef< const std::vector< double > > lambdaArray, const int lambdaArrayExtent) (function) of namespace gmx::anonymous_namespace{freeenergyparameters.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/gpuforcereduction.h:62: warning: Member HAVE_GPU_FORCE_REDUCTION (macro definition) of file gpuforcereduction.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:169: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/lincs_gpu_internal_sycl.cpp:451: warning: Member launchLincsKernel(const DeviceStream &deviceStream, const int numConstraintsThreads, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/constrtestrunners.h:58: warning: Member GPU_CONSTRAINTS_SUPPORTED (macro definition) of file constrtestrunners.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/leapfrogtestrunners.h:59: warning: Member GPU_LEAPFROG_SUPPORTED (macro definition) of file leapfrogtestrunners.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/settletestrunners.h:57: warning: Member GPU_SETTLE_SUPPORTED (macro definition) of file settletestrunners.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update_constrain_gpu_impl.cpp:69: warning: Member sc_haveGpuConstraintSupport (variable) of file update_constrain_gpu_impl.cpp is not documented. warning: Include graph for 'md.cpp' not generated, too many nodes (71), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Include graph for 'runner.cpp' not generated, too many nodes (96), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinput.h:120: warning: Member globalSimulationState(const SimulationInput &) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinput.h:121: warning: Member applyGlobalInputRecord(const SimulationInput &, t_inputrec *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinput.h:122: warning: Member applyGlobalTopology(const SimulationInput &, gmx_mtop_t *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:64: warning: Member sc_atomInfo_HasPerturbedCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:65: warning: Member sc_atomInfo_Exclusion (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:66: warning: Member sc_atomInfo_Constraint (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:67: warning: Member sc_atomInfo_Settle (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:68: warning: Member sc_atomInfo_BondCommunication (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:69: warning: Member sc_atomInfo_HasVdw (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:70: warning: Member sc_atomInfo_HasCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/awh_history.cpp:69: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, AwhPointStateHistory *awhPointStateHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/awh_history.cpp:86: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, AwhBiasStateHistory *awhBiasStateHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/awh_history.cpp:100: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, CorrelationBlockDataHistory *correlationBlockDataHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/awh_history.cpp:121: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, CorrelationGridHistory *correlationGridHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/awh_history.cpp:142: warning: Member doCheckpointData(CheckpointData< operation > checkpointData, AwhBiasHistory *awhBiasHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/awh_history.cpp:66: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/forcebuffers.cpp:55: warning: Member c_forces (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/multipletimestepping.cpp:139: warning: Member simpleMtsOpts() (function) of namespace gmx::test::anonymous_namespace{multipletimestepping.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/enerdata.cpp:69: warning: Member makeFepvals(const std::vector< double > &lambdaVdw, const std::vector< double > &lambdaCoul) (function) of namespace gmx::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/enerdata.cpp:60: warning: Member c_numLambdas (variable) of namespace gmx::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/enerdata.cpp:62: warning: Member dhdlVdw (variable) of namespace gmx::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/enerdata.cpp:63: warning: Member dhdlCoul (variable) of namespace gmx::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/enerdata.cpp:65: warning: Member dhdlLinearZero (variable) of namespace gmx::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/energydata.cpp:402: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{energydata.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/expandedensembleelement.cpp:129: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{expandedensembleelement.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/firstorderpressurecoupling.cpp:179: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{firstorderpressurecoupling.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/freeenergyperturbationdata.cpp:165: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{freeenergyperturbationdata.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/mttk.cpp:282: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{mttk.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/nosehooverchains.cpp:67: warning: Member nhcUsageNames (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp:294: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{parrinellorahmanbarostat.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:733: warning: Member hasStartVelocityScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:742: warning: Member hasEndVelocityScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:749: warning: Member hasPositionScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:755: warning: Member hasParrinelloRahmanScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:881: warning: Member getConnection(Propagator< integrationStage > gmx_unused *propagator, const PropagatorTag &propagatorTag) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:63: warning: Member integrationStepNames (variable) of namespace gmx::anonymous_namespace{propagator.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/pullelement.cpp:125: warning: Member doCheckpointData(CheckpointData< operation > *checkpointData, ArrayRef< double > previousStepCom) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/pullelement.cpp:121: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{pullelement.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/grid.cpp:122: warning: Member getMaxNumCells(const Grid::Geometry &geometry, const int numAtoms, const int numColumns) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/gridset.cpp:135: warning: Member getGridOffset(gmx::ArrayRef< const Grid > grids, int gridIndex) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernel_common.h:90: warning: Member EnergyOutput (enumeration) of file kernel_common.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:50: warning: Member nbnxn_kernel_ElecRF_VdwLJFsw_F_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:51: warning: Member nbnxn_kernel_ElecRF_VdwLJPsw_F_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:52: warning: Member nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:53: warning: Member nbnxn_kernel_ElecRF_VdwLJEwCombLB_F_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:54: warning: Member nbnxn_kernel_ElecQSTab_VdwLJ_F_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:55: warning: Member nbnxn_kernel_ElecQSTab_VdwLJFsw_F_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:56: warning: Member nbnxn_kernel_ElecQSTab_VdwLJPsw_F_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:57: warning: Member nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:58: warning: Member nbnxn_kernel_ElecQSTab_VdwLJEwCombLB_F_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:59: warning: Member nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:60: warning: Member nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_F_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:61: warning: Member nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_F_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:62: warning: Member nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:63: warning: Member nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombLB_F_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:65: warning: Member nbnxn_kernel_ElecRF_VdwLJ_VF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:66: warning: Member nbnxn_kernel_ElecRF_VdwLJFsw_VF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:67: warning: Member nbnxn_kernel_ElecRF_VdwLJPsw_VF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:68: warning: Member nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:69: warning: Member nbnxn_kernel_ElecRF_VdwLJEwCombLB_VF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:70: warning: Member nbnxn_kernel_ElecQSTab_VdwLJ_VF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:71: warning: Member nbnxn_kernel_ElecQSTab_VdwLJFsw_VF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:72: warning: Member nbnxn_kernel_ElecQSTab_VdwLJPsw_VF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:73: warning: Member nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:74: warning: Member nbnxn_kernel_ElecQSTab_VdwLJEwCombLB_VF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:75: warning: Member nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:76: warning: Member nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_VF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:77: warning: Member nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_VF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:78: warning: Member nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:79: warning: Member nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombLB_VF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:81: warning: Member nbnxn_kernel_ElecRF_VdwLJ_VgrpF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:82: warning: Member nbnxn_kernel_ElecRF_VdwLJFsw_VgrpF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:83: warning: Member nbnxn_kernel_ElecRF_VdwLJPsw_VgrpF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:84: warning: Member nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:85: warning: Member nbnxn_kernel_ElecRF_VdwLJEwCombLB_VgrpF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:86: warning: Member nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:87: warning: Member nbnxn_kernel_ElecQSTab_VdwLJFsw_VgrpF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:88: warning: Member nbnxn_kernel_ElecQSTab_VdwLJPsw_VgrpF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:89: warning: Member nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:90: warning: Member nbnxn_kernel_ElecQSTab_VdwLJEwCombLB_VgrpF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:91: warning: Member nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:92: warning: Member nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:93: warning: Member nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:94: warning: Member nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:95: warning: Member nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombLB_VgrpF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_buffer_ops.cpp:63: warning: Member nbnxn_gpu_x_to_nbat_x(const Nbnxm::Grid &grid, NbnxmGpu *nb, DeviceBuffer< gmx::RVec > d_x, GpuEventSynchronizer *xReadyOnDevice, const gmx::AtomLocality locality, int gridId, int numColumnsMax, bool mustInsertNonLocalDependency) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:83: warning: Member init_ewald_coulomb_force_table(const EwaldCorrectionTables &tables, NBParamGpu *nbp, const DeviceContext &deviceContext) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:97: warning: Member useTabulatedEwaldByDefault(const DeviceInformation &deviceInfo) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:128: warning: Member nbnxn_gpu_pick_ewald_kernel_type(const interaction_const_t &ic, const DeviceInformation &deviceInfo) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:178: warning: Member set_cutoff_parameters(NBParamGpu *nbp, const interaction_const_t &ic, const PairlistParams &listParams) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:202: warning: Member initPlistSorting(gpuPlistSorting *sorting) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:225: warning: Member init_plist(gpu_plist *pl) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:253: warning: Member init_timings(gmx_wallclock_gpu_nbnxn_t *t) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:302: warning: Member nbnxmGpuPickVdwKernelType(const interaction_const_t &ic, LJCombinationRule ljCombinationRule) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:356: warning: Member nbnxmGpuPickElectrostaticsKernelType(const interaction_const_t &ic, const DeviceInformation &deviceInfo) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:442: warning: Member gpu_init(const gmx::DeviceStreamManager &deviceStreamManager, const interaction_const_t *ic, const PairlistParams &listParams, const nbnxn_atomdata_t *nbat, const bool bLocalAndNonlocal) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:511: warning: Member gpu_pme_loadbal_update_param(nonbonded_verlet_t *nbv, const interaction_const_t &ic) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:528: warning: Member gpu_upload_shiftvec(NbnxmGpu *nb, const nbnxn_atomdata_t *nbatom) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:689: warning: Member gpu_init_atomdata(NbnxmGpu *nb, const nbnxn_atomdata_t *nbat) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:792: warning: Member gpu_clear_outputs(NbnxmGpu *nb, bool computeVirial) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:823: warning: Member gpu_is_kernel_ewald_analytical(const NbnxmGpu *nb) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:829: warning: Member setupGpuShortRangeWork(NbnxmGpu *nb, const gmx::ListedForcesGpu *listedForcesGpu, const gmx::InteractionLocality iLocality) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:842: warning: Member haveGpuShortRangeWork(const NbnxmGpu *nb, const gmx::InteractionLocality interactionLocality) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:981: warning: Member nbnxnInsertNonlocalGpuDependency(NbnxmGpu *nb, const InteractionLocality interactionLocality) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1076: warning: Member nbnxn_gpu_init_x_to_nbat_x(const Nbnxm::GridSet &gridSet, NbnxmGpu *gpu_nbv) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1286: warning: Member gpuGetNBAtomData(NbnxmGpu *nb) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1292: warning: Member gpu_get_f(NbnxmGpu *nb) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_setup.cpp:355: warning: Member getENbnxnInitCombRule(const t_forcerec &forcerec) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_simd.h:115: warning: Member GMX_HAVE_NBNXM_SIMD_4XM (macro definition) of file nbnxm_simd.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlistparams.h:73: warning: Member c_gpuNumClusterPerCellY (variable) of file pairlistparams.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlistparams.h:74: warning: Member c_gpuNumClusterPerCellX (variable) of file pairlistparams.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_gpu_buffer_ops_internal_sycl.cpp:50: warning: Member mode (typedef) of file nbnxm_gpu_buffer_ops_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.cpp:53: warning: Member getNbnxmSubGroupSize(const DeviceInformation &deviceInfo) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:1455: warning: Member launchNbnxmKernelHelper(NbnxmGpu *nb, const gmx::StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.h:52: warning: Member SYCL_NBNXM_SUPPORTS_SUBGROUP_SIZE_8 (macro definition) of file nbnxm_sycl_kernel.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.h:53: warning: Member SYCL_NBNXM_SUPPORTS_SUBGROUP_SIZE_32 (macro definition) of file nbnxm_sycl_kernel.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.h:54: warning: Member SYCL_NBNXM_SUPPORTS_SUBGROUP_SIZE_64 (macro definition) of file nbnxm_sycl_kernel.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:72: warning: Member FCiFloat3 (typedef) of file nbnxm_sycl_kernel_body.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:125: warning: Member mode (typedef) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:1455: warning: Member launchNbnxmKernelHelper(NbnxmGpu *nb, const gmx::StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:106: warning: Member elecEwald (variable) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:109: warning: Member elecEwaldTab (variable) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:112: warning: Member ljEwald (variable) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_pruneonly.cpp:53: warning: Member mode (typedef) of file nbnxm_sycl_kernel_pruneonly.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/exclusions.cpp:200: warning: Member testKernelTypes (variable) of namespace gmx::test::anonymous_namespace{exclusions.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:98: warning: Member GENERATE_REFERENCE_DATA (macro definition) of file kernel_test.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:505: warning: Member isTabulated(const CoulombKernelType coulombKernelType) (function) of namespace gmx::test::anonymous_namespace{kernel_test.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:530: warning: Member makeRefDataFileName() (function) of namespace gmx::test::anonymous_namespace{kernel_test.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:203: warning: Member c_numEnergyGroups (variable) of namespace gmx::test::anonymous_namespace{kernel_test.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:461: warning: Member coulombKernelTypeName (variable) of namespace gmx::test::anonymous_namespace{kernel_test.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:467: warning: Member vdwKernelTypeName (variable) of namespace gmx::test::anonymous_namespace{kernel_test.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:783: warning: Member testKernelTypes (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/tests/com.cpp:118: warning: Member COMInPlaceTestParams (typedef) of namespace gmx::test::anonymous_namespace{com.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include/gromacs/pbcutil/pbc_aiuc_sycl.h:50: warning: Member xyzToShiftIndex(int x, int y, int z) (function) of file pbc_aiuc_sycl.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/pbc.cpp:1421: warning: Member putAtomsInBoxTemplated(PbcType pbcType, const matrix box, const matrix boxDeformation, gmx::ArrayRef< gmx::RVec > x, gmx::ArrayRef< gmx::RVec > v) (function) of file pbc.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/pbc_simd.cpp:52: warning: Member set_pbc_simd(const t_pbc gmx_unused *pbc, real gmx_unused *pbc_simd) (function) of file pbc_simd.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/compiler.cpp:2017: warning: found documented return type for analyze_static that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/compiler.cpp:1832: warning: found documented return type for evaluate_boolean_static_part that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/compiler.cpp:1754: warning: found documented return type for init_method that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/compiler.cpp:1701: warning: found documented return type for process_const that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:1025: warning: found documented return type for _gmx_sel_evaluate_and that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:1140: warning: found documented return type for _gmx_sel_evaluate_arithmetic that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:482: warning: found documented return type for _gmx_sel_evaluate_children that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:915: warning: found documented return type for _gmx_sel_evaluate_method that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:880: warning: found documented return type for _gmx_sel_evaluate_method_params that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:965: warning: found documented return type for _gmx_sel_evaluate_modifier that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:1003: warning: found documented return type for _gmx_sel_evaluate_not that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:1076: warning: found documented return type for _gmx_sel_evaluate_or that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.h:102: warning: found documented return type for _gmx_sel_evaluate_root that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.h:122: warning: found documented return type for _gmx_sel_evaluate_static that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:599: warning: found documented return type for _gmx_sel_evaluate_subexpr that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:539: warning: found documented return type for _gmx_sel_evaluate_subexpr_simple that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:564: warning: found documented return type for _gmx_sel_evaluate_subexpr_staticeval that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:752: warning: found documented return type for _gmx_sel_evaluate_subexprref that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:717: warning: found documented return type for _gmx_sel_evaluate_subexprref_simple that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:1025: warning: found documented return type for _gmx_sel_evaluate_and that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:1140: warning: found documented return type for _gmx_sel_evaluate_arithmetic that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:482: warning: found documented return type for _gmx_sel_evaluate_children that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:915: warning: found documented return type for _gmx_sel_evaluate_method that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:880: warning: found documented return type for _gmx_sel_evaluate_method_params that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:965: warning: found documented return type for _gmx_sel_evaluate_modifier that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:1003: warning: found documented return type for _gmx_sel_evaluate_not that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:1076: warning: found documented return type for _gmx_sel_evaluate_or that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.h:102: warning: found documented return type for _gmx_sel_evaluate_root that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.h:122: warning: found documented return type for _gmx_sel_evaluate_static that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:599: warning: found documented return type for _gmx_sel_evaluate_subexpr that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:539: warning: found documented return type for _gmx_sel_evaluate_subexpr_simple that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:564: warning: found documented return type for _gmx_sel_evaluate_subexpr_staticeval that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:752: warning: found documented return type for _gmx_sel_evaluate_subexprref that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:717: warning: found documented return type for _gmx_sel_evaluate_subexprref_simple that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/params.cpp:895: warning: found documented return type for parse_values_enum that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/selectioncollection.cpp:964: warning: Member swap(SelectionCollection &lhs, SelectionCollection &rhs) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_compare.cpp:357: warning: found documented return type for convert_real_int that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_compare.cpp:119: warning: found documented return type for init_compare that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_distance.cpp:96: warning: found documented return type for init_common that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_distance.cpp:114: warning: found documented return type for init_frame_common that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_insolidangle.cpp:99: warning: unable to resolve reference to 'sm_insolidangle' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_insolidangle.cpp:248: warning: found documented return type for init_insolidangle that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_keywords.cpp:345: warning: found documented return type for init_kweval that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_keywords.cpp:105: warning: found documented return type for init_kwreal that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_keywords.cpp:357: warning: found documented return type for init_output_kweval that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_merge.cpp:71: warning: found documented return type for init_merge that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_permute.cpp:82: warning: found documented return type for init_permute that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_position.cpp:94: warning: found documented return type for init_cog that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_position.cpp:104: warning: found documented return type for init_com that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_position.cpp:81: warning: found documented return type for init_kwpos that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_position.cpp:114: warning: found documented return type for init_output_pos that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_same.cpp:113: warning: found documented return type for init_same that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_simple.cpp:83: warning: found documented return type for check_molecules that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_simple.cpp:153: warning: found documented return type for check_pdbinfo that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:647: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_FLOAT (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:658: warning: Member GMX_SIMD4N_FLOAT_WIDTH (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:693: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_DOUBLE (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:704: warning: Member GMX_SIMD4N_DOUBLE_WIDTH (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:738: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_REAL (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:747: warning: Member GMX_SIMD4N_REAL_WIDTH (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:657: warning: Member Simd4NFloat (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:703: warning: Member Simd4NDouble (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:746: warning: Member Simd4NReal (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:517: warning: Member load(const std::enable_if_t< std::is_arithmetic_v< T >, T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:523: warning: Member load(const AlignedArray< internal::SimdTraitsT< T >, N > &m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:541: warning: Member loadU(const std::enable_if_t< std::is_arithmetic_v< T >, T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:547: warning: Member loadU(const AlignedArray< internal::SimdTraitsT< T >, N > &m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:628: warning: Member load(const internal::Simd4TraitsT< T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:633: warning: Member loadU(const internal::Simd4TraitsT< T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:662: warning: Member loadUNDuplicate4(const float *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:666: warning: Member load4DuplicateN(const float *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:670: warning: Member loadU4NOffset(const float *f, int) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:708: warning: Member loadUNDuplicate4(const double *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:712: warning: Member load4DuplicateN(const double *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:716: warning: Member loadU4NOffset(const double *f, int) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:300: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:345: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:403: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:379: warning: Member c_simdBestPairAlignment (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:484: warning: Member SimdTraitsT (typedef) of namespace gmx::internal is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:623: warning: Member Simd4TraitsT (typedef) of namespace gmx::internal is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/tables/forcetable.h:79: warning: Member TableFormat (enumeration) of file forcetable.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/decidegpuusage.cpp:165: warning: Member decideWhetherToUseGpusForPmeFft(const TaskTarget pmeFftTarget) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/decidegpuusage.cpp:172: warning: Member canUseGpusForPme(const bool useGpuForNonbonded, const TaskTarget pmeTarget, const TaskTarget pmeFftTarget, const t_inputrec &inputrec, std::string *errorMessage) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/decidegpuusage.cpp:118: warning: Member c_gpuBuildSyclWithoutGpuFft (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/resourcedivision.cpp:116: warning: Member nthreads_omp_faster_Nehalem (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/resourcedivision.cpp:117: warning: Member nthreads_omp_faster_Intel_AVX (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/resourcedivision.cpp:118: warning: Member nthreads_omp_faster_AMD_Ryzen (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/resourcedivision.cpp:125: warning: Member nthreads_omp_faster_gpu_fac (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/resourcedivision.cpp:135: warning: Member nthreads_omp_mpi_ok_max (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/resourcedivision.cpp:136: warning: Member nthreads_omp_mpi_ok_min_cpu (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/resourcedivision.cpp:137: warning: Member nthreads_omp_mpi_ok_min_gpu (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/resourcedivision.cpp:138: warning: Member nthreads_omp_mpi_target_max (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/resourcedivision.cpp:142: warning: Member c_maxAutoTmpiRanksPerGpu (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include/gromacs/timing/instrumentation.h:216: warning: Member traceRangeStart(gmx_unused const char *rangeName, gmx_unused int rangeId) (function) of file instrumentation.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include/gromacs/timing/instrumentation.h:217: warning: Member traceSubRangeStart(gmx_unused const char *rangeName, gmx_unused int rangeId) (function) of file instrumentation.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/tools/tests/trjconv.cpp:155: warning: Member DumpTestParameters (typedef) of namespace gmx::test::anonymous_namespace{trjconv.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/atoms.cpp:192: warning: Member SimulationParticleTestParameters (typedef) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/atoms.cpp:124: warning: Member checkParticleValue(TestReferenceChecker *checker, bool haveBState, const T &valueA, const T &valueB, const std::string &fieldName) (function) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/atoms.cpp:137: warning: Member checkParticleMiscInfo(TestReferenceChecker *checker, ParticleType type, gmx::Index resind, int atomnumber, const std::string &elem) (function) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/atoms.cpp:150: warning: Member checkParticle(TestReferenceChecker *checker, const SimulationParticle &particle) (function) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/atoms.cpp:195: warning: Member testParticleMassOneState (variable) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/atoms.cpp:196: warning: Member testParticleMassTwoState (variable) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/atoms.cpp:197: warning: Member testParticleChargeOneState (variable) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/atoms.cpp:198: warning: Member testParticleChargeTwoState (variable) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/atoms.cpp:199: warning: Member testParticleTypeValueOneState (variable) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/atoms.cpp:200: warning: Member testParticleTypeValueTwoState (variable) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include/gromacs/topology/mtop_atomloops.h:212: warning: Member gmx_mtop_atomloop_block_t (typedef) of file mtop_atomloops.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include/gromacs/topology/mtop_atomloops.h:216: warning: Member gmx_mtop_atomloop_block_init(const gmx_mtop_t &mtop) (function) of file mtop_atomloops.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include/gromacs/topology/mtop_atomloops.h:231: warning: Member gmx_mtop_atomloop_block_next(gmx_mtop_atomloop_block_t aloop, const t_atom **atom, int *nmol) (function) of file mtop_atomloops.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/index.cpp:67: warning: Member checkIndexGroup(TestReferenceChecker *checker, const IndexGroup &group) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/index.cpp:74: warning: Member checkBlocks(TestReferenceChecker *checker, ArrayRef< const IndexGroup > blocks) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/index.cpp:81: warning: Member compareBlocks(ArrayRef< const IndexGroup > one, ArrayRef< const IndexGroup > two) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/index.cpp:95: warning: Member checkFileMatch(TestReferenceChecker *checker, const std::string &fileName, const std::string &fullPath) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/symtab.cpp:326: warning: Member close_symtab(t_symtab gmx_unused *symtab) (function) of file symtab.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/dssp.cpp:73: warning: Member DsspTestParamsDsspNB (typedef) of namespace gmx::test::anonymous_namespace{dssp.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/dssp.cpp:74: warning: Member DsspTestParamsGromacsNB (typedef) of namespace gmx::test::anonymous_namespace{dssp.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/dssp.cpp:75: warning: Member DsspTestParamsDsspNoNB (typedef) of namespace gmx::test::anonymous_namespace{dssp.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/dssp.cpp:76: warning: Member DsspTestParamsGromacsNoNB (typedef) of namespace gmx::test::anonymous_namespace{dssp.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/gyrate.cpp:70: warning: Member GyrateTestParamsMerge (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/modules/hbond.cpp:169: warning: Member DonorType (enumeration) of namespace gmx::analysismodules::anonymous_namespace{hbond.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/modules/hbond.cpp:163: warning: Member c_maxHydrogensWithOxygen (variable) of namespace gmx::analysismodules::anonymous_namespace{hbond.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/modules/hbond.cpp:165: warning: Member c_maxHydrogensWithNitrogen (variable) of namespace gmx::analysismodules::anonymous_namespace{hbond.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/modules/hbond.cpp:167: warning: Member c_maxHydrogenBonds (variable) of namespace gmx::analysismodules::anonymous_namespace{hbond.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/hbond.cpp:70: warning: Member HbondTestParamsMerge (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/scattering.cpp:68: warning: Member ScatteringTestDirectModeParams (typedef) of namespace gmx::test::anonymous_namespace{scattering.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/cstringutil.cpp:100: warning: Member testInplace(F f, const char *input, const char *expectedOutput) (function) of namespace gmx::test::anonymous_namespace{cstringutil.cpp} is not documented. warning: Included by graph for 'fatalerror.h' not generated, too many nodes (104), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:217: warning: Member gmx_call(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:218: warning: Member gmx_comm(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:219: warning: Member gmx_file(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:220: warning: Member gmx_impl(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:221: warning: Member gmx_incons(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:222: warning: Member gmx_input(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:223: warning: Member gmx_mem(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:224: warning: Member gmx_open(fn) (macro definition) of file fatalerror.h is not documented. warning: Included by graph for 'gmxmpi.h' not generated, too many nodes (54), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:64: warning: Member ivec[3] (typedef) of file iserializer.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:200: warning: Member toString(bool t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:204: warning: Member toString(int t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:208: warning: Member toString(int64_t t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:212: warning: Member toString(float t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:216: warning: Member toString(double t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:220: warning: Member toString(unsigned char t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:224: warning: Member toString(std::string t) (function) of namespace gmx is not documented. warning: Included by graph for 'textwriter.h' not generated, too many nodes (53), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/inmemoryserializer.cpp:70: warning: Member c_int16ValueSwapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/inmemoryserializer.cpp:71: warning: Member c_int32Value (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/inmemoryserializer.cpp:72: warning: Member c_int32ValueSwapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/inmemoryserializer.cpp:73: warning: Member c_int64Value (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/inmemoryserializer.cpp:74: warning: Member c_int64ValueSwapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/inmemoryserializer.cpp:76: warning: Member c_intAndFloat32 (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/inmemoryserializer.cpp:77: warning: Member c_intAndFloat64 (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/inmemoryserializer.cpp:79: warning: Member c_intAndFloat32Swapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/inmemoryserializer.cpp:80: warning: Member c_intAndFloat64Swapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/stringutil.cpp:132: warning: Member formatString(gmx_fmtstr const char *fmt,...) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:85: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(p) &this->mask(a)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:86: warning: Member deallocate(p, 1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:93: warning: Member v(10) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:94: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(v.data()) &this->mask(v.get_allocator())) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:99: warning: Member for(std::size_t i=1000;i<=10000;i+=1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:125: warning: Member v1(1) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:127: warning: Member EXPECT_NE(data, nullptr) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:128: warning: Member v2(std::move(v1)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:129: warning: Member EXPECT_EQ(data, v2.data()) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:82: warning: Member a (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:83: warning: Member p (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:126: warning: Member data (variable) of namespace gmx::test is not documented. warning: Included by graph for 'gmxpre.h' not generated, too many nodes (739), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:112: warning: Member NonbondedFlavor (typedef) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:113: warning: Member UpdateFlavor (typedef) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:114: warning: Member PmeFlavor (typedef) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:68: warning: Member ElectrostaticsFlavor (enumeration) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:82: warning: Member CouplingFlavor (enumeration) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:97: warning: Member OffloadFlavor (enumeration) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:116: warning: Member SeparatePmeRankFlavor (enumeration) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:75: warning: Member enumValueToString(const ElectrostaticsFlavor enumValue) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:89: warning: Member enumValueToString(const CouplingFlavor enumValue) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:104: warning: Member enumValueToString(const OffloadFlavor enumValue) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:288: warning: Member sc_mdpFlavors (variable) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:384: warning: Member sc_offloadFlavors (variable) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/freeenergy.cpp:72: warning: Member ListOfInteractionsToTest (typedef) of namespace gmx::test::anonymous_namespace{freeenergy.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/freeenergy.cpp:73: warning: Member FreeEnergyReferenceTestParams (typedef) of namespace gmx::test::anonymous_namespace{freeenergy.cpp} is not documented. warning: Include graph for 'mimic.cpp' not generated, too many nodes (54), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/minimize.cpp:170: warning: Member minimizersToTest_g (variable) of namespace gmx::test::anonymous_namespace{minimize.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/minimize.cpp:172: warning: Member constrainedSystemsToTest_g (variable) of namespace gmx::test::anonymous_namespace{minimize.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/minimize.cpp:175: warning: Member minimizersToTestWithConstraints_g (variable) of namespace gmx::test::anonymous_namespace{minimize.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/multisim.cpp:182: warning: Member gmx_sumd_sim(int gmx_unused nr, double gmx_unused r[], const gmx_multisim_t gmx_unused *ms) (function) of file multisim.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/multisim.cpp:191: warning: Member gmx_sumf_sim(int gmx_unused nr, float gmx_unused r[], const gmx_multisim_t gmx_unused *ms) (function) of file multisim.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/multisim.cpp:200: warning: Member gmx_sumi_sim(int gmx_unused nr, int gmx_unused r[], const gmx_multisim_t gmx_unused *ms) (function) of file multisim.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/multisim.cpp:209: warning: Member gmx_sumli_sim(int gmx_unused nr, int64_t gmx_unused r[], const gmx_multisim_t gmx_unused *ms) (function) of file multisim.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/multisim.cpp:387: warning: Member multisim_int_all_are_equal(const gmx_multisim_t *ms, int64_t value) (function) of file multisim.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/normalmodes.cpp:168: warning: Member GTEST_ALLOW_UNINSTANTIATED_PARAMETERIZED_TEST(NormalModesTest) (function) of namespace gmx::test::anonymous_namespace{normalmodes.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/pmetest.cpp:96: warning: Member PmeTestParameters (typedef) of namespace gmx::test::anonymous_namespace{pmetest.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/pmetest.cpp:404: warning: Member c_reproducesEnergies (variable) of namespace gmx::test::anonymous_namespace{pmetest.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/pull.cpp:173: warning: Member isTransformationPullSetup(const std::string &pullSetupName) (function) of namespace gmx::test::anonymous_namespace{pull.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/pull.cpp:79: warning: Member c_mdpPullParams (variable) of namespace gmx::test::anonymous_namespace{pull.cpp} is not documented. warning: Include graph for 'rerun.cpp' not generated, too many nodes (57), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/rerun.cpp:111: warning: Member executeRerunTest(TestFileManager *fileManager, SimulationRunner *runner, const std::string &simulationName, int numWarningsToTolerate, const MdpFieldValues &mdpFieldValues, const EnergyTermsToCompare &energyTermsToCompare, const TrajectoryComparison &trajectoryComparison) (function) of namespace gmx::test::anonymous_namespace{rerun.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simple_mdrun.cpp:191: warning: Member GTEST_ALLOW_UNINSTANTIATED_PARAMETERIZED_TEST(SimpleMdrunTest) (function) of namespace gmx::test::anonymous_namespace{simple_mdrun.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulatorcomparison.cpp:61: warning: Member runGrompp(SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulatorcomparison.cpp:74: warning: Member runMdrun(SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulatorcomparison.cpp:87: warning: Member compareEnergies(const std::string &edr1Name, const std::string &edr2Name, const EnergyTermsToCompare &energyTermsToCompare, const MaxNumFrames maxNumFrames) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulatorcomparison.cpp:108: warning: Member compareTrajectories(const std::string &trajectory1Name, const std::string &trajectory2Name, const TrajectoryComparison &trajectoryComparison) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulatorcomparison.h:60: warning: Member SimulationOptionTuple (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulatorcomparison.cpp:61: warning: Member runGrompp(SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulatorcomparison.cpp:74: warning: Member runMdrun(SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulatorcomparison.cpp:87: warning: Member compareEnergies(const std::string &edr1Name, const std::string &edr2Name, const EnergyTermsToCompare &energyTermsToCompare, const MaxNumFrames maxNumFrames) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulatorcomparison.cpp:108: warning: Member compareTrajectories(const std::string &trajectory1Name, const std::string &trajectory2Name, const TrajectoryComparison &trajectoryComparison) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/trajectorycomparison.cpp:416: warning: Member checkTrajectoryAgainstReferenceData(const std::string &trajectoryFilename, const TrajectoryComparison &trajectoryComparison, TestReferenceChecker *checker, MaxNumFrames maxNumFrames) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/trajectorycomparison.cpp:416: warning: Member checkTrajectoryAgainstReferenceData(const std::string &trajectoryFilename, const TrajectoryComparison &trajectoryComparison, TestReferenceChecker *checker, MaxNumFrames maxNumFrames) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/virtualsites.cpp:86: warning: Member VirtualSiteTestParams (typedef) of namespace gmx::test::anonymous_namespace{virtualsites.cpp} is not documented. warning: Included by graph for 'cmdlinetest.h' not generated, too many nodes (65), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'refdata.h' not generated, too many nodes (106), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'testasserts.h' not generated, too many nodes (164), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'testfilemanager.h' not generated, too many nodes (62), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2024.4/src/testutils/refdata_xml.cpp:95: warning: Member getCDataChildNode(XMLNodePtr node) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/refdata_xml.cpp:105: warning: Member hasCDataContent(XMLNodePtr node) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/refdata_xml.cpp:333: warning: Member createElementAndContents(XMLElementPtr parentElement, const ReferenceDataEntry &entry) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/refdata_xml.cpp:246: warning: Member setIdAttribute(XMLElementPtr element, const std::string &id) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/refdata_xml.cpp:254: warning: Member createElement(XMLElementPtr parentElement, const ReferenceDataEntry &entry) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/refdata_xml.cpp:262: warning: Member createChildElements(XMLElementPtr parentElement, const ReferenceDataEntry &entry) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/refdata_xml.cpp:304: warning: Member createElementContents(XMLElementPtr element, const ReferenceDataEntry &entry) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/refdata_xml.cpp:339: warning: Member createRootElement(XMLDocumentPtr document) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initOptions()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::optionsFinished()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initAnalysis()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initAfterFirstFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishAnalysis()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::writeOutput()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::startFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::startFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishFrames()' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_float.h:151: warning: unable to resolve reference to 'c_simdBestPairAlignmentFloat' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_float.h:152: warning: unable to resolve reference to 'c_simdBestPairAlignmentDouble' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_double.h:171: warning: @copydetails or @copydoc target 'c_simdBestPairAlignmentFloat' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:200: warning: Member toString(bool t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:204: warning: Member toString(int t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:208: warning: Member toString(int64_t t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:212: warning: Member toString(float t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:216: warning: Member toString(double t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:220: warning: Member toString(unsigned char t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:224: warning: Member toString(std::string t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:81: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:98: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:117: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:142: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:117: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copydetails or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:184: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:98: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copydetails or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:142: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copydetails or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:119: warning: @copydetails or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:113: warning: @copydetails or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/errorcodes.h:111: warning: explicit link request to 'eeUnknownError' could not be resolved /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:179: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copydetails or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copydetails or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:81: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copydetails or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:189: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/selection/selection.h:36: warning: unable to resolve reference to 'sm_insolidangle' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:214: warning: Member __attribute__((ext_vector_type(2))) Native_float2_ (typedef) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:214: warning: Member __attribute__((packed)) (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:240: warning: Member __attribute__((always_inline)) float operator[](Index i) const (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:250: warning: Member __attribute__((always_inline)) float &operator[](Index i) (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:260: warning: Member __attribute__((always_inline)) float x() const (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:261: warning: Member __attribute__((always_inline)) float y() const (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:262: warning: Member __attribute__((always_inline)) Native_float2_ xy() const (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:263: warning: Member __attribute__((always_inline)) float z() const (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:267: warning: Member AmdPackedFloat3(float x, float y, float z) (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:269: warning: Member AmdPackedFloat3(Native_float2_ xy, float z) (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:271: warning: Member AmdPackedFloat3(Float3 r) (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:273: warning: Member operator Float3() const (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/constraint_gpu_helpers.h:51: warning: Member AtomsAdjacencyListElement(int indexOfSecondConstrainedAtom, int indexOfConstraint, int signFactor) (function) of struct AtomsAdjacencyListElement is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/dlbtiming.h:215: warning: Member impl_ (variable) of class BalanceRegion is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_internal.h:112: warning: Member GMX_DISALLOW_COPY_MOVE_AND_ASSIGN(bonded_threading_t) (function) of struct bonded_threading_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlist_tuning.cpp:436: warning: Member mtop (variable) of struct CalcVerletBufferParameters is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlist_tuning.cpp:437: warning: Member effectiveAtomDensity (variable) of struct CalcVerletBufferParameters is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlist_tuning.cpp:438: warning: Member inputrec (variable) of struct CalcVerletBufferParameters is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlist_tuning.cpp:439: warning: Member pressureTolerance (variable) of struct CalcVerletBufferParameters is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlist_tuning.cpp:440: warning: Member listSetup (variable) of struct CalcVerletBufferParameters is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlist_tuning.cpp:441: warning: Member useGpuList (variable) of struct CalcVerletBufferParameters is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlist_tuning.cpp:442: warning: Member mtsFactor (variable) of struct CalcVerletBufferParameters is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/device_information.h:176: warning: Member supportedSubGroupSizes() const (function) of struct DeviceInformation is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/device_information.h:175: warning: Member supportedSubGroupSizesSize (variable) of struct DeviceInformation is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/device_information.h:181: warning: Member gpuAwareMpiStatus (variable) of struct DeviceInformation is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/commrec.h:66: warning: Member bUse (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/commrec.h:67: warning: Member comm_intra (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/commrec.h:68: warning: Member rank_intra (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/commrec.h:69: warning: Member comm_inter (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_communication.h:121: warning: Member ewaldcoeff_q (variable) of struct gmx_pme_comm_n_box_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_communication.h:122: warning: Member ewaldcoeff_lj (variable) of struct gmx_pme_comm_n_box_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_communication.h:137: warning: Member vir_lj (variable) of struct gmx_pme_comm_vir_ene_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_communication.h:138: warning: Member energy_q (variable) of struct gmx_pme_comm_vir_ene_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_communication.h:139: warning: Member energy_lj (variable) of struct gmx_pme_comm_vir_ene_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_communication.h:140: warning: Member dvdlambda_q (variable) of struct gmx_pme_comm_vir_ene_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_communication.h:141: warning: Member dvdlambda_lj (variable) of struct gmx_pme_comm_vir_ene_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_only.cpp:107: warning: Member gmx_pme_pp(MPI_Comm simulationCommunicator, std::vector< PpRanks > &&ppRanks) (function) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_only.cpp:114: warning: Member chargeB (variable) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_only.cpp:115: warning: Member sqrt_c6A (variable) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_only.cpp:116: warning: Member sqrt_c6B (variable) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_only.cpp:117: warning: Member sigmaA (variable) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_only.cpp:118: warning: Member sigmaB (variable) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_only.cpp:125: warning: Member stat (variable) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/replicaexchange.cpp:146: warning: Member cyclic (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/replicaexchange.cpp:147: warning: Member order (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/replicaexchange.cpp:148: warning: Member tmpswap (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/replicaexchange.cpp:149: warning: Member incycle (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/replicaexchange.cpp:150: warning: Member bEx (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/replicaexchange.cpp:156: warning: Member Epot (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/replicaexchange.cpp:157: warning: Member beta (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/replicaexchange.cpp:158: warning: Member Vol (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/replicaexchange.cpp:159: warning: Member de (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/grompp_impl.h:68: warning: Member aj() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/grompp_impl.h:69: warning: Member ak() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/grompp_impl.h:70: warning: Member al() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/grompp_impl.h:71: warning: Member am() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/grompp_impl.h:73: warning: Member c0() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/grompp_impl.h:74: warning: Member c1() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/grompp_impl.h:75: warning: Member c2() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/grompp_impl.h:77: warning: Member interactionTypeName() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:144: warning: Member kernel_noener_noprune_ptr[Nbnxm::c_numElecTypes][Nbnxm::c_numVdwTypes] (variable) of struct NbnxmGpu is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:145: warning: Member kernel_ener_noprune_ptr[Nbnxm::c_numElecTypes][Nbnxm::c_numVdwTypes] (variable) of struct NbnxmGpu is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:146: warning: Member kernel_noener_prune_ptr[Nbnxm::c_numElecTypes][Nbnxm::c_numVdwTypes] (variable) of struct NbnxmGpu is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:147: warning: Member kernel_ener_prune_ptr[Nbnxm::c_numElecTypes][Nbnxm::c_numVdwTypes] (variable) of struct NbnxmGpu is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:157: warning: Member kernel_memset_f (variable) of struct NbnxmGpu is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:158: warning: Member kernel_memset_f2 (variable) of struct NbnxmGpu is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:159: warning: Member kernel_memset_f3 (variable) of struct NbnxmGpu is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm.h:482: warning: Member setupFepThreadedForceBuffer(int numAtomsForce) (function) of struct nonbonded_verlet_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlist.h:241: warning: Member PackedJClusterList(const gmx::PinningPolicy pinningPolicy) (function) of class PackedJClusterList is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_types_host.h:263: warning: Member useNvshmem (variable) of struct PmeGpu is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_types_host.h:265: warning: Member nvshmemParams (variable) of struct PmeGpu is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:176: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(PmeGpuProgramImpl) (function) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:115: warning: Member splineKernelSingle (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:116: warning: Member splineKernelThPerAtom4Single (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:117: warning: Member spreadKernelSingle (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:118: warning: Member spreadKernelThPerAtom4Single (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:119: warning: Member splineAndSpreadKernelSingle (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:120: warning: Member splineAndSpreadKernelThPerAtom4Single (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:121: warning: Member splineAndSpreadKernelWriteSplinesSingle (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:122: warning: Member splineAndSpreadKernelWriteSplinesThPerAtom4Single (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:123: warning: Member splineKernelDual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:124: warning: Member splineKernelThPerAtom4Dual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:125: warning: Member spreadKernelDual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:126: warning: Member spreadKernelThPerAtom4Dual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:127: warning: Member splineAndSpreadKernelDual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:128: warning: Member splineAndSpreadKernelThPerAtom4Dual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:129: warning: Member splineAndSpreadKernelWriteSplinesDual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:130: warning: Member splineAndSpreadKernelWriteSplinesThPerAtom4Dual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:143: warning: Member gatherKernelSingle (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:144: warning: Member gatherKernelThPerAtom4Single (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:145: warning: Member gatherKernelReadSplinesSingle (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:146: warning: Member gatherKernelReadSplinesThPerAtom4Single (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:147: warning: Member gatherKernelDual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:148: warning: Member gatherKernelThPerAtom4Dual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:149: warning: Member gatherKernelReadSplinesDual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:150: warning: Member gatherKernelReadSplinesThPerAtom4Dual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:160: warning: Member solveYZXKernelA (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:161: warning: Member solveXYZKernelA (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:162: warning: Member solveYZXEnergyKernelA (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:163: warning: Member solveXYZEnergyKernelA (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:164: warning: Member solveYZXKernelB (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:165: warning: Member solveXYZKernelB (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:166: warning: Member solveYZXEnergyKernelB (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:167: warning: Member solveXYZEnergyKernelB (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:169: warning: Member nvshmemSignalKern (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/tables/forcetable.h:88: warning: Member t_forcetable(TableInteraction interaction, TableFormat format) (function) of struct t_forcetable is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/fcdata.h:216: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(t_oriresdata) (function) of struct t_oriresdata is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:213: warning: Member fnTpr (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:213: warning: Member fnPullf (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:213: warning: Member fnCoordSel (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:215: warning: Member bPullf (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:216: warning: Member tmin (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:216: warning: Member tmax (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:228: warning: Member min (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:228: warning: Member max (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:228: warning: Member dz (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:229: warning: Member Temperature (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:245: warning: Member bBoundsOnly (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:256: warning: Member bTauIntGiven (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:267: warning: Member bHistEq (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:293: warning: Member bsMethod (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:296: warning: Member tauBootStrap (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:300: warning: Member histBootStrapBlockLength (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:306: warning: Member bs_verbose (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:312: warning: Member bTab (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:313: warning: Member tabX (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:313: warning: Member tabY (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:313: warning: Member tabMin (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:313: warning: Member tabMax (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:313: warning: Member tabDz (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:314: warning: Member tabNbins (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/vsite_parm.cpp:89: warning: Member aj() const (function) of class VsiteBondedInteraction is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/vsite_parm.cpp:90: warning: Member ak() const (function) of class VsiteBondedInteraction is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/vsite_parm.cpp:91: warning: Member al() const (function) of class VsiteBondedInteraction is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/vsite_parm.cpp:93: warning: Member parameterValue() const (function) of class VsiteBondedInteraction is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/warninp.h:71: warning: Member WarningHandler(bool allowWarnings, int maxNumberWarnings) (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/warninp.h:89: warning: Member errorCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/warninp.h:91: warning: Member warningCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/warninp.h:93: warning: Member noteCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/warninp.h:95: warning: Member maxWarningCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/options/abstractoptionstorage.h:144: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/options/abstractoptionstorage.h:144: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/options/abstractoptionstorage.h:145: warning: @copydetails or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/bonded.cpp:3080: warning: Member CmapForceStructure (typedef) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/bonded.cpp:3082: warning: Member processCmapForceComponent(const gmx::RVec a, const gmx::RVec b, const real df, const real gaa, const real fga, const real gbb, const real hgb, const int dim) (function) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/bonded.cpp:3098: warning: Member applyCmapForceComponent(const gmx::RVec forceComponent) (function) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/bonded.cpp:3109: warning: Member accumulateCmapForces(const rvec x[], rvec4 f[], rvec fshift[], const t_pbc *pbc, const gmx::RVec r_ij, const gmx::RVec r_kj, const gmx::RVec r_kl, const gmx::RVec a, const gmx::RVec b, gmx::RVec h, const real ra2r, const real rb2r, const real rgr, const real rg, const int ai, const int aj, const int ak, const int al, const real df, const int t1, const int t2) (function) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:112: warning: Member NonbondedFlavor (typedef) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:113: warning: Member UpdateFlavor (typedef) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:114: warning: Member PmeFlavor (typedef) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:68: warning: Member ElectrostaticsFlavor (enumeration) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:82: warning: Member CouplingFlavor (enumeration) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:97: warning: Member OffloadFlavor (enumeration) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:116: warning: Member SeparatePmeRankFlavor (enumeration) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:75: warning: Member enumValueToString(const ElectrostaticsFlavor enumValue) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:89: warning: Member enumValueToString(const CouplingFlavor enumValue) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:104: warning: Member enumValueToString(const OffloadFlavor enumValue) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:288: warning: Member sc_mdpFlavors (variable) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:384: warning: Member sc_offloadFlavors (variable) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/freeenergydispatch.cpp:146: warning: Member dispatchFreeEnergyKernel(gmx::ArrayRef< const std::unique_ptr< t_nblist > > nbl_fep, const gmx::ArrayRefWithPadding< const gmx::RVec > &coords, bool useSimd, int ntype, const interaction_const_t &ic, gmx::ArrayRef< const gmx::RVec > shiftvec, gmx::ArrayRef< const real > nbfp, gmx::ArrayRef< const real > nbfp_grid, gmx::ArrayRef< const real > chargeA, gmx::ArrayRef< const real > chargeB, gmx::ArrayRef< const int > typeA, gmx::ArrayRef< const int > typeB, gmx::ArrayRef< const real > lambda, const bool clearForcesAndEnergies, gmx::ThreadedForceBuffer< gmx::RVec > *threadedForceBuffer, gmx::ThreadedForceBuffer< gmx::RVec > *threadedForeignEnergyBuffer, gmx_grppairener_t *foreignGroupPairEnergies, gmx_enerdata_t *enerd, const gmx::StepWorkload &stepWork, t_nrnb *nrnb) (function) of namespace anonymous_namespace{freeenergydispatch.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/functions.cpp:388: warning: Member IntegerTypes (typedef) of namespace anonymous_namespace{functions.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/indexutil.cpp:91: warning: Member setGroup(const int(&atoms)[count]) (function) of class anonymous_namespace{indexutil.cpp}::IndexBlockTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/minimize.cpp:915: warning: Member mdModulesNotifiers (variable) of class anonymous_namespace{minimize.cpp}::EnergyEvaluator is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:124: warning: Member AspartateStates (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:146: warning: Member GlutamateStates (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:168: warning: Member GlutamineStates (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:190: warning: Member LysineStates (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:211: warning: Member ArginineStates (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1274: warning: Member ChainSeparationType (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1533: warning: Member VSitesType (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1544: warning: Member WaterType (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1560: warning: Member MergeType (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:105: warning: Member res2bb_notermini(const std::string &name, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:116: warning: Member enumValueToLongString(HistidineStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:131: warning: Member enumValueToString(AspartateStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:138: warning: Member enumValueToLongString(AspartateStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:153: warning: Member enumValueToString(GlutamateStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:160: warning: Member enumValueToLongString(GlutamateStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:175: warning: Member enumValueToString(GlutamineStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:182: warning: Member enumValueToLongString(GlutamineStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:197: warning: Member enumValueToString(LysineStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:203: warning: Member enumValueToLongString(LysineStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:218: warning: Member enumValueToString(ArginineStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:225: warning: Member enumValueToLongString(ArginineStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:234: warning: Member select_res(int resnr, const char *title, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:256: warning: Member get_asptp(int resnr, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:261: warning: Member get_glutp(int resnr, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:266: warning: Member get_glntp(int resnr, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:271: warning: Member get_lystp(int resnr, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:276: warning: Member get_argtp(int resnr, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:281: warning: Member get_histp(int resnr, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:286: warning: Member read_rtprename(const char *fname, FILE *fp, std::vector< RtpRename > *rtprename) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:344: warning: Member search_resrename(gmx::ArrayRef< const RtpRename > rr, const char *name, bool bStart, bool bEnd, bool bCompareFFRTPname) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:387: warning: Member rename_resrtp(t_atoms *pdba, int nterpairs, gmx::ArrayRef< const int > r_start, gmx::ArrayRef< const int > r_end, gmx::ArrayRef< const RtpRename > rr, t_symtab *symtab, bool bVerbose, const gmx::MDLogger &logger) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:445: warning: Member pdbres_to_gmxrtp(t_atoms *pdba) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:458: warning: Member rename_pdbres(t_atoms *pdba, const char *oldnm, const char *newnm, bool bFullCompare, t_symtab *symtab) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:553: warning: Member check_occupancy(t_atoms *atoms, const char *filename, bool bVerbose, const gmx::MDLogger &logger) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:616: warning: Member write_posres(const char *fn, t_atoms *pdba, real fc) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:645: warning: Member read_pdball(const char *inf, bool bOutput, const char *outf, char **title, t_atoms *atoms, rvec **x, PbcType *pbcType, matrix box, bool bRemoveH, t_symtab *symtab, const ResidueTypeMap &residueTypeMap, const char *watres, AtomProperties *aps, bool bVerbose) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:719: warning: Member process_chain(const gmx::MDLogger &logger, t_atoms *pdba, gmx::ArrayRef< gmx::RVec > x, bool bTrpU, bool bPheU, bool bTyrU, bool bLysMan, bool bAspMan, bool bGluMan, bool bHisMan, bool bArgMan, bool bGlnMan, real angle, real distance, t_symtab *symtab, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:809: warning: Member pdbicomp(const t_pdbindex &a, const t_pdbindex &b) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:827: warning: Member sort_pdbatoms(gmx::ArrayRef< const PreprocessResidue > restp_chain, int natoms, t_atoms **pdbaptr, t_atoms **newPdbAtoms, std::vector< gmx::RVec > *x) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:913: warning: Member remove_duplicate_atoms(t_atoms *pdba, gmx::ArrayRef< gmx::RVec > x, bool bVerbose, const gmx::MDLogger &logger) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:985: warning: Member checkResidueTypeSanity(t_atoms *pdba, int r0, int r1, const ResidueTypeMap &residueTypeMap) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1059: warning: Member find_nc_ter(t_atoms *pdba, int r0, int r1, int *r_start, int *r_end, const ResidueTypeMap &residueTypeMap, const gmx::MDLogger &logger) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1294: warning: Member modify_chain_numbers(t_atoms *pdba, ChainSeparationType chainSeparation, const gmx::MDLogger &logger) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1418: warning: Member checkChainCyclicity(t_atoms *pdba, rvec *pdbx, int start_ter, int end_ter, gmx::ArrayRef< const PreprocessResidue > rtpFFDB, gmx::ArrayRef< const RtpRename > rr, real long_bond_dist_, real short_bond_dist_) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1283: warning: Member c_chainSeparationTypeNames (variable) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1286: warning: Member c_chainSeparationTypeNotificationMessages (variable) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1540: warning: Member c_vsitesTypeNames (variable) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1556: warning: Member c_waterTypeNames (variable) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1567: warning: Member c_mergeTypeNames (variable) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_calculate_splines_sycl.h:74: warning: Member assertIsFinite(Float3 gmx_unused arg) (function) of namespace anonymous_namespace{pme_gpu_calculate_splines_sycl.h} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_calculate_splines_sycl.h:82: warning: Member assertIsFinite(T gmx_unused arg) (function) of namespace anonymous_namespace{pme_gpu_calculate_splines_sycl.h} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/state.cpp:94: warning: Member c_currentVersion (variable) of namespace anonymous_namespace{state.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/state.cpp:199: warning: Member c_dfHistoryCurrentVersion (variable) of namespace anonymous_namespace{state.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:875: warning: Member mode (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/selection/selectionenums.h:82: warning: explicit link request to 'SelectionFlag' could not be resolved /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/oclraii.h:131: warning: Member ClCommandQueue (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/oclraii.h:132: warning: Member ClProgram (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/oclraii.h:133: warning: Member ClKernel (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:63: warning: Member packSendBufKernel(Float3 *__restrict__ gm_dataPacked, const Float3 *__restrict__ gm_data, const int *__restrict__ gm_map, int mapSize, Float3 coordinateShift) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:117: warning: Member launchPackSendBufKernel(const DeviceStream &deviceStream, int xSendSize, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:131: warning: Member launchUnpackRecvBufKernel(const DeviceStream &deviceStream, int fRecvSize, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_cufftmp.cpp:102: warning: Member handleCufftError(cufftResult_t status, const char *msg) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:251: warning: Member launchVkFft(const DeviceBuffer< float > &realGrid, const DeviceBuffer< float > &complexGrid, NativeQueue queue, gmx_fft_direction fftDirection, VkFFTApplication *application, VkFFTLaunchParams *launchParams) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:92: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:97: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:118: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:123: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/massrepartitioning.cpp:44: warning: Member smallestAtomMass(const gmx_mtop_t &mtop) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/simd_support.cpp:70: warning: Member simdString(SimdType s) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/simd_support.cpp:199: warning: Member simdCompiled() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_impl_gpu.cpp:67: warning: Member chooseSubGroupSizeForDevice(const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:878: warning: Member bondedKernel(sycl::handler &cgh, const BondedGpuKernelParameters &kernelParams, const DeviceBuffer< t_iatom > gm_iatoms_[numFTypesOnGpu], float *__restrict__ gm_vTot, const t_iparams *__restrict__ gm_forceParams_, const sycl::float4 *__restrict__ gm_xq_, Float3 *__restrict__ gm_f_, Float3 *__restrict__ gm_fShift_) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:169: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/lincs_gpu_internal_sycl.cpp:451: warning: Member launchLincsKernel(const DeviceStream &deviceStream, const int numConstraintsThreads, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:733: warning: Member hasStartVelocityScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:742: warning: Member hasEndVelocityScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:749: warning: Member hasPositionScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:755: warning: Member hasParrinelloRahmanScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:881: warning: Member getConnection(Propagator< integrationStage > gmx_unused *propagator, const PropagatorTag &propagatorTag) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/pullelement.cpp:125: warning: Member doCheckpointData(CheckpointData< operation > *checkpointData, ArrayRef< double > previousStepCom) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:62: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:74: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:86: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:98: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:110: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:122: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:134: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:146: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:158: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:170: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:182: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:194: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:206: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:218: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:230: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:242: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:254: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:266: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:278: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:290: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:302: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:314: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:326: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:338: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:350: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:362: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:374: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:386: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:398: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:410: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:423: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:435: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:447: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:459: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:471: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:483: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:495: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:507: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:519: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:531: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:543: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:555: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:567: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:579: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:591: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:603: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:615: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:627: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:639: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:651: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:663: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:675: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:687: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:699: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:711: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:723: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:735: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:747: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:759: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:771: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:784: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:796: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:808: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:820: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:832: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:844: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:856: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:868: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:880: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:892: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:904: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:916: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:928: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:940: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:952: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:964: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:976: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:988: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1000: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1012: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1024: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1036: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1048: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1060: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1072: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1084: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1096: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1108: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1120: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1132: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:62: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:74: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:86: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:98: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:110: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:122: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:134: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:146: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:158: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:170: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:182: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:194: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:206: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:218: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:230: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:242: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:254: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:266: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:278: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:290: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:302: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:314: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:326: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:338: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:350: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:362: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:374: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:386: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:398: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:410: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:423: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:435: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:447: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:459: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:471: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:483: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:495: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:507: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:519: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:531: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:543: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:555: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:567: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:579: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:591: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:603: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:615: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:627: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:639: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:651: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:663: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:675: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:687: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:699: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:711: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:723: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:735: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:747: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:759: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:771: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:784: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:796: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:808: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:820: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:832: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:844: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:856: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:868: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:880: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:892: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:904: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:916: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:928: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:940: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:952: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:964: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:976: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:988: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1000: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1012: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1024: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1036: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1048: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1060: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1072: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1084: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1096: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1108: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1120: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1132: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/selectioncollection.cpp:964: warning: Member swap(SelectionCollection &lhs, SelectionCollection &rhs) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/decidegpuusage.cpp:165: warning: Member decideWhetherToUseGpusForPmeFft(const TaskTarget pmeFftTarget) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/decidegpuusage.cpp:172: warning: Member canUseGpusForPme(const bool useGpuForNonbonded, const TaskTarget pmeTarget, const TaskTarget pmeFftTarget, const t_inputrec &inputrec, std::string *errorMessage) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/stringutil.cpp:132: warning: Member formatString(gmx_fmtstr const char *fmt,...) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:81: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:98: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:117: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:142: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinput.h:120: warning: Member globalSimulationState(const SimulationInput &) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinput.h:121: warning: Member applyGlobalInputRecord(const SimulationInput &, t_inputrec *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinput.h:122: warning: Member applyGlobalTopology(const SimulationInput &, gmx_mtop_t *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:200: warning: Member toString(bool t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:204: warning: Member toString(int t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:208: warning: Member toString(int64_t t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:212: warning: Member toString(float t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:216: warning: Member toString(double t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:220: warning: Member toString(unsigned char t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:224: warning: Member toString(std::string t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/vec.h:625: warning: Member norm2(T *v) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/tests/colvarsoptions.cpp:80: warning: Member colvarsConfig (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:58: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:62: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/forcebuffers.cpp:55: warning: Member c_forces (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/nosehooverchains.cpp:67: warning: Member nhcUsageNames (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:55: warning: Member c_centralShiftIndex (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:56: warning: Member c_numShiftVectors (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/decidegpuusage.cpp:118: warning: Member c_gpuBuildSyclWithoutGpuFft (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:83: warning: Member c_angstrom (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:84: warning: Member c_kilo (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:85: warning: Member c_nano (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:86: warning: Member c_pico (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:87: warning: Member c_nm2A (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:88: warning: Member c_cal2Joule (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:89: warning: Member c_electronCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:91: warning: Member c_amu (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:92: warning: Member c_boltzmann (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:93: warning: Member c_avogadro (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:94: warning: Member c_universalGasConstant (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:95: warning: Member c_boltz (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:96: warning: Member c_faraday (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:97: warning: Member c_planck1 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:98: warning: Member c_planck (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:100: warning: Member c_epsilon0Si (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:102: warning: Member c_epsilon0 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:105: warning: Member c_speedOfLight (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:108: warning: Member c_rydberg (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:110: warning: Member c_one4PiEps0 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:115: warning: Member c_barMdunits (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:116: warning: Member c_presfac (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:121: warning: Member c_debye2Enm (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:122: warning: Member c_enm2Debye (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:126: warning: Member c_fieldfac (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:129: warning: Member c_hartree2Kj (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:130: warning: Member c_bohr2Nm (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:131: warning: Member c_hartreeBohr2Md (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:133: warning: Member c_rad2Deg (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:134: warning: Member c_deg2Rad (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:64: warning: Member sc_atomInfo_HasPerturbedCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:65: warning: Member sc_atomInfo_Exclusion (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:66: warning: Member sc_atomInfo_Constraint (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:67: warning: Member sc_atomInfo_Settle (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:68: warning: Member sc_atomInfo_BondCommunication (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:69: warning: Member sc_atomInfo_HasVdw (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:70: warning: Member sc_atomInfo_HasCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:44: warning: Member c_dBoxY (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:45: warning: Member c_dBoxX (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:300: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:345: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:403: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:379: warning: Member c_simdBestPairAlignment (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:657: warning: Member Simd4NFloat (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:703: warning: Member Simd4NDouble (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:746: warning: Member Simd4NReal (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:517: warning: Member load(const std::enable_if_t< std::is_arithmetic_v< T >, T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:523: warning: Member load(const AlignedArray< internal::SimdTraitsT< T >, N > &m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:541: warning: Member loadU(const std::enable_if_t< std::is_arithmetic_v< T >, T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:547: warning: Member loadU(const AlignedArray< internal::SimdTraitsT< T >, N > &m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:628: warning: Member load(const internal::Simd4TraitsT< T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:633: warning: Member loadU(const internal::Simd4TraitsT< T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:662: warning: Member loadUNDuplicate4(const float *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:666: warning: Member load4DuplicateN(const float *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:670: warning: Member loadU4NOffset(const float *f, int) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:708: warning: Member loadUNDuplicate4(const double *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:712: warning: Member load4DuplicateN(const double *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:716: warning: Member loadU4NOffset(const double *f, int) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:403: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:300: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:310: warning: unable to resolve reference to 'SimdIBool' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:345: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:357: warning: unable to resolve reference to 'SimdBool' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:358: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:358: warning: unable to resolve reference to 'SimdIBool' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:359: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:361: warning: unable to resolve reference to 'cvtB2IB' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:361: warning: unable to resolve reference to 'cvtIB2B' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/correlationhistory.h:61: warning: unable to resolve reference to 'updateCorrelationGridHistory' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:97: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:98: warning: @copydetails or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:92: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:93: warning: @copydetails or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:123: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:124: warning: @copydetails or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:118: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:119: warning: @copydetails or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:62: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:58: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/options/basicoptionstorage.h:73: warning: Member formatSingleValue(const bool &value) const override (function) of class gmx::BooleanOptionStorage is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionstoragetemplate.h:321: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< bool > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/booltype.h:72: warning: Member value_ (variable) of struct gmx::BoolType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_force_sender_gpu_impl.h:69: warning: Member flag (variable) of struct gmx::CacheLineAlignedFlag is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/clfftinitializer.h:96: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(ClfftInitializer) (function) of class gmx::ClfftInitializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:78: warning: Member gmxPbc_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:81: warning: Member logger_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:88: warning: Member rng_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:89: warning: Member normalDistribution_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:78: warning: Member gmxPbc_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:81: warning: Member logger_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:88: warning: Member rng_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:89: warning: Member normalDistribution_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:78: warning: Member gmxPbc_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:81: warning: Member logger_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:88: warning: Member rng_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:89: warning: Member normalDistribution_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/modules/scattering-debye.h:101: warning: Member getIntensity(size_t qi) (function) of class gmx::ComputeDebyeScattering is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/computeglobalselement.cpp:377: warning: Member getElementPointerImpl(LegacySimulatorData *legacySimulatorData, ModularSimulatorAlgorithmBuilderHelper *builderHelper, StatePropagatorData *statePropagatorData, EnergyData *energyData, FreeEnergyPerturbationData *freeEnergyPerturbationData, GlobalCommunicationHelper *globalCommunicationHelper, ObservablesReducer *observablesReducer) (function) of class gmx::ComputeGlobalsElement is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/computeglobalselement.cpp:411: warning: Member getElementPointerImpl(LegacySimulatorData *simulator, ModularSimulatorAlgorithmBuilderHelper *builderHelper, StatePropagatorData *statePropagatorData, EnergyData *energyData, FreeEnergyPerturbationData *freeEnergyPerturbationData, GlobalCommunicationHelper *globalCommunicationHelper, ObservablesReducer *observablesReducer) (function) of class gmx::ComputeGlobalsElement is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/mdmodulesnotifiers.h:157: warning: Member coordinates_ (variable) of struct gmx::CoordinatesAndBoxPreprocessed is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/mdmodulesnotifiers.h:158: warning: Member box_ (variable) of struct gmx::CoordinatesAndBoxPreprocessed is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/mdmodulesnotifiers.h:159: warning: Member pbc_ (variable) of struct gmx::CoordinatesAndBoxPreprocessed is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/coordstate.h:84: warning: found documented return type for gmx::CoordState::sampleUmbrellaGridpoint that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_coulomb_functions.h:134: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldAnalytical > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_coulomb_functions.h:145: warning: Member force(const std::array< SimdReal, nR > &rSquaredV, const std::array< SimdReal, nR > gmx_unused &dummyRInvV, const std::array< SimdReal, nR > &rInvExclV, const std::array< SimdBool, nR > &withinCutoffV) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldAnalytical > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_coulomb_functions.h:194: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldTabulated > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_coulomb_functions.h:83: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::RF > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_diagonal_masker.h:108: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeEqualsISize > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_diagonal_masker.h:132: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsDoubleISize > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_diagonal_masker.h:163: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsHalfISize > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/options/basicoptionstorage.h:134: warning: Member formatSingleValue(const double &value) const override (function) of class gmx::DoubleOptionStorage is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionstoragetemplate.h:321: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< double > is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:251: warning: Member const_iterator (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:252: warning: Member reverse_iterator (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:253: warning: Member const_reverse_iterator (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:275: warning: Member const_pointer (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:230: warning: Member operator[](const std::size_t arrayIndex) const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:236: warning: Member operator[](const EnumType enumIndex) (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:241: warning: Member operator[](const EnumType enumIndex) const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:259: warning: Member end() (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:260: warning: Member begin() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:261: warning: Member end() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:267: warning: Member rend() (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:268: warning: Member rbegin() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:269: warning: Member rend() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:182: warning: Member end() const (function) of class gmx::EnumerationWrapper is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/options/basicoptionstorage.h:236: warning: Member formatSingleValue(const int &value) const override (function) of class gmx::EnumOptionStorage is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionstoragetemplate.h:321: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< int > is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:440: warning: Member operator()(const std::string &lhs, const std::string &rhs) const (function) of class gmx::EqualCaseInsensitive is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:87: warning: Member IExceptionInfo(const IExceptionInfo &)=default (function) of class gmx::internal::IExceptionInfo is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:88: warning: Member IExceptionInfo(IExceptionInfo &&) noexcept=default (function) of class gmx::internal::IExceptionInfo is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:89: warning: Member operator=(const IExceptionInfo &)=default (function) of class gmx::internal::IExceptionInfo is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:90: warning: Member operator=(IExceptionInfo &&) noexcept=default (function) of class gmx::internal::IExceptionInfo is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:126: warning: Member doUShortArray(unsigned short *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:133: warning: Member doIntArray(int *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:140: warning: Member doInt32Array(int32_t *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:147: warning: Member doInt64Array(int64_t *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:154: warning: Member doFloatArray(float *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:161: warning: Member doDoubleArray(double *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:168: warning: Member doRealArray(real *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:175: warning: Member doIvecArray(ivec *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/options/filenameoptionstorage.h:74: warning: Member formatSingleValue(const std::string &value) const override (function) of class gmx::FileNameOptionStorage is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionstoragetemplate.h:321: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< std::string > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/options/basicoptionstorage.h:162: warning: Member formatSingleValue(const float &value) const override (function) of class gmx::FloatOptionStorage is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionstoragetemplate.h:321: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< float > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/iforceprovider.h:106: warning: Member homenr_ (variable) of class gmx::ForceProviderInput is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/iforceprovider.h:107: warning: Member chargeA_ (variable) of class gmx::ForceProviderInput is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/iforceprovider.h:108: warning: Member massT_ (variable) of class gmx::ForceProviderInput is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:106: warning: Member configuration_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:107: warning: Member application_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:108: warning: Member launchParams_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:109: warning: Member bufferSize_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:110: warning: Member inputBufferSize_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:111: warning: Member context_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:112: warning: Member device_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:113: warning: Member commandQueue_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:115: warning: Member realGrid_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_sycl_rocfft.cpp:360: warning: Member complexGrid_ (variable) of class gmx::Gpu3dFft::ImplSyclRocfft::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:124: warning: Member configuration_ (variable) of class gmx::Gpu3dFft::ImplSyclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:125: warning: Member application_ (variable) of class gmx::Gpu3dFft::ImplSyclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:126: warning: Member launchParams_ (variable) of class gmx::Gpu3dFft::ImplSyclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:127: warning: Member bufferSize_ (variable) of class gmx::Gpu3dFft::ImplSyclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:128: warning: Member inputBufferSize_ (variable) of class gmx::Gpu3dFft::ImplSyclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:129: warning: Member queue_device_ (variable) of class gmx::Gpu3dFft::ImplSyclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:131: warning: Member realGrid_ (variable) of class gmx::Gpu3dFft::ImplSyclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/gpuforcereduction.h:125: warning: Member registerForcesReadyNvshmemFlags(DeviceBuffer< uint64_t > syncObj) (function) of class gmx::GpuForceReduction is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/gpuhaloexchange.h:100: warning: Member GpuHaloExchange(GpuHaloExchange &&source) noexcept (function) of class gmx::GpuHaloExchange is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/gpuhaloexchange.h:101: warning: Member operator=(GpuHaloExchange &&source) noexcept (function) of class gmx::GpuHaloExchange is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/options/basicoptionstorage.h:115: warning: Member formatSingleValue(const int64_t &value) const override (function) of class gmx::Int64OptionStorage is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionstoragetemplate.h:321: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< int64_t > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/options/basicoptionstorage.h:95: warning: Member formatSingleValue(const int &value) const override (function) of class gmx::IntegerOptionStorage is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionstoragetemplate.h:321: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< int > is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:86: warning: Member doUChar(unsigned char *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:87: warning: Member doChar(char *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:88: warning: Member doUShort(unsigned short *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:89: warning: Member doInt(int *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:90: warning: Member doInt32(int32_t *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:91: warning: Member doInt64(int64_t *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:92: warning: Member doFloat(float *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:93: warning: Member doDouble(double *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:94: warning: Member doReal(real *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:95: warning: Member doIvec(ivec *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:96: warning: Member doRvec(rvec *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:97: warning: Member doString(std::string *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:98: warning: Member doOpaque(char *data, std::size_t size)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:112: warning: Member doCharArray(char *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:119: warning: Member doUCharArray(unsigned char *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:126: warning: Member doUShortArray(unsigned short *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:133: warning: Member doIntArray(int *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:140: warning: Member doInt32Array(int32_t *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:147: warning: Member doInt64Array(int64_t *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:154: warning: Member doFloatArray(float *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:161: warning: Member doDoubleArray(double *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:168: warning: Member doRealArray(real *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:175: warning: Member doIvecArray(ivec *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:182: warning: Member doRvecArray(rvec *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:137: warning: Member value (variable) of struct gmx::IsSerializableEnum is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:124: warning: Member value (variable) of struct gmx::IsSerializableType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:143: warning: Member ddrank_opt_choices[static_cast< int >(DdRankOrder::Count)+1] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:148: warning: Member dddlb_opt_choices[static_cast< int >(DlbOption::Count)+1] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:153: warning: Member thread_aff_opt_choices[static_cast< int >(ThreadAffinity::Count)+1] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:158: warning: Member nbpu_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:159: warning: Member pme_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:160: warning: Member pme_fft_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:161: warning: Member bonded_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:162: warning: Member update_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:163: warning: Member devicesSelectedByUser (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:164: warning: Member userGpuTaskAssignment (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:167: warning: Member imdOptions (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:169: warning: Member pa[48] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_lennardjones_functions.h:332: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< calculateEnergies, InteractionModifiers::ForceSwitch > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_lennardjones_functions.h:483: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< calculateEnergies, InteractionModifiers::PotSwitch > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_lennardjones_functions.h:179: warning: Member LennardJonesCalculator(const interaction_const_t gmx_unused &ic) (function) of class gmx::LennardJonesCalculator< false, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_lennardjones_functions.h:209: warning: Member forceSigmaEpsilon(const std::array< SimdReal, inputSize > &rInvV, const std::array< SimdBool, interactSize > &interactV, SimdBool *withinCutoffV, const std::array< SimdReal, nR > &sigmaV, const std::array< SimdReal, nR > &epsilonV, SimdReal sixth, SimdReal twelfth, std::array< SimdReal, nR > &frLJV, std::array< SimdReal, vljvSize > &vLJV) (function) of class gmx::LennardJonesCalculator< false, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_lennardjones_functions.h:231: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< true, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_lennardjones_functions.h:270: warning: Member forceSigmaEpsilon(const std::array< SimdReal, inputSize > &rInvV, const std::array< SimdBool, interactSize > &interactV, SimdBool *withinCutoffV, const std::array< SimdReal, nR > &sigmaV, const std::array< SimdReal, nR > &epsilonV, SimdReal sixth, SimdReal twelfth, std::array< SimdReal, nR > &frLJV, std::array< SimdReal, vljvSize > &vLJV) (function) of class gmx::LennardJonesCalculator< true, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/lincs.cpp:212: warning: Member tmpncc (variable) of class gmx::Lincs is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/lincs.cpp:213: warning: Member tmp1 (variable) of class gmx::Lincs is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/lincs.cpp:214: warning: Member tmp2 (variable) of class gmx::Lincs is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/lincs.cpp:215: warning: Member tmp3 (variable) of class gmx::Lincs is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/lincs.cpp:216: warning: Member tmp4 (variable) of class gmx::Lincs is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/mdgraph_gpu_impl.h:139: warning: Member Graph (typedef) of class gmx::MdGpuGraph::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/mdgraph_gpu_impl.h:140: warning: Member GraphInstance (typedef) of class gmx::MdGpuGraph::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/mdmodulesnotifiers.h:85: warning: Member MDModulesAtomsRedistributedSignal(const matrix box, gmx::ArrayRef< const RVec > x) (function) of struct gmx::MDModulesAtomsRedistributedSignal is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/runner.h:145: warning: Member operator=(Mdrunner &&handle) noexcept (function) of class gmx::Mdrunner is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/runner.h:391: warning: Member operator=(MdrunnerBuilder &&builder) noexcept (function) of class gmx::MdrunnerBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/message_string_collector.h:67: warning: Member MessageStringCollector(MessageStringCollector &&) noexcept (function) of class gmx::MessageStringCollector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/message_string_collector.h:68: warning: Member operator=(MessageStringCollector &&) noexcept (function) of class gmx::MessageStringCollector is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:218: warning: Member allocator_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:219: warning: Member size_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:220: warning: Member reference (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:221: warning: Member const_reference (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:222: warning: Member storage_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:223: warning: Member pointer (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:224: warning: Member const_pointer (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:225: warning: Member iterator (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:226: warning: Member const_iterator (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:227: warning: Member difference_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:351: warning: Member data() const noexcept (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:353: warning: Member begin() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:354: warning: Member end() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:356: warning: Member cbegin() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:357: warning: Member cend() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:359: warning: Member begin() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:360: warning: Member end() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:362: warning: Member cbegin() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:363: warning: Member cend() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_force_sender_gpu.h:112: warning: Member waitForEvents() (function) of class gmx::PmeForceSenderGpu is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_force_sender_gpu_impl.h:132: warning: Member waitForEvents() (function) of class gmx::PmeForceSenderGpu::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/qmmm/qmmmforceprovider.h:71: warning: Member QMMMForceProvider(const QMMMParameters ¶meters, const LocalAtomSet &localQMAtomSet, const LocalAtomSet &localMMAtomSet, PbcType pbcType, const MDLogger &logger) (function) of class gmx::QMMMForceProvider is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/qmmm/qmmmtypes.h:142: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(QMMMParameters) (function) of struct gmx::QMMMParameters is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/manager.h:89: warning: Member operator=(const RestraintManager &)=default (function) of class gmx::RestraintManager is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/manager.h:90: warning: Member RestraintManager(RestraintManager &&) noexcept=default (function) of class gmx::RestraintManager is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/manager.h:91: warning: Member operator=(RestraintManager &&) noexcept=default (function) of class gmx::RestraintManager is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/restraintmdmodule_impl.h:287: warning: Member operator=(RestraintMDModuleImpl &&) noexcept=default (function) of class gmx::RestraintMDModuleImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/modules/scattering-debye.h:101: warning: Member getIntensity(size_t qi) (function) of class gmx::ComputeDebyeScattering is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/modules/scattering-debye.h:101: warning: Member getIntensity(size_t qi) (function) of class gmx::ComputeDebyeScattering is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update_constrain_gpu_internal.h:63: warning: Member ScalingMatrix(const Matrix3x3 &m) (function) of struct gmx::ScalingMatrix is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update_constrain_gpu_internal.h:67: warning: Member xx (variable) of struct gmx::ScalingMatrix is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update_constrain_gpu_internal.h:67: warning: Member zz (variable) of struct gmx::ScalingMatrix is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update_constrain_gpu_internal.h:67: warning: Member yx (variable) of struct gmx::ScalingMatrix is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update_constrain_gpu_internal.h:67: warning: Member zx (variable) of struct gmx::ScalingMatrix is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update_constrain_gpu_internal.h:67: warning: Member zy (variable) of struct gmx::ScalingMatrix is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/selection/selectioncollection.h:144: warning: Member SelectionCollection(const SelectionCollection &rhs) (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/selection/selectioncollection.h:145: warning: Member operator=(SelectionCollection rhs) (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/selection/selectioncollection.h:146: warning: Member swap(SelectionCollection &rhs) (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:406: warning: found documented return type for gmx::SelectionEvaluator::evaluate that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinputhandle.h:139: warning: Member SimulationInputHandle(const SimulationInputHandle &source) (function) of class gmx::SimulationInputHandle is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinputhandle.h:140: warning: Member SimulationInputHandle(SimulationInputHandle &&) noexcept=default (function) of class gmx::SimulationInputHandle is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinputhandle.h:142: warning: Member operator=(const SimulationInputHandle &rhs) (function) of class gmx::SimulationInputHandle is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinputhandle.h:143: warning: Member operator=(SimulationInputHandle &&) noexcept=default (function) of class gmx::SimulationInputHandle is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:341: warning: Member add(MembedHolder &&membedHolder) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:343: warning: Member add(std::unique_ptr< StopHandlerBuilder > stopHandlerBuilder) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:348: warning: Member add(SimulatorStateData &&simulatorStateData) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:353: warning: Member add(SimulatorConfig &&simulatorConfig) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:360: warning: Member add(SimulatorEnv &&simulatorEnv) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:365: warning: Member add(Profiling &&profiling) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:367: warning: Member add(ConstraintsParam &&constraintsParam) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:372: warning: Member add(LegacyInput &&legacyInput) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:377: warning: Member add(ReplicaExchangeParameters &&replicaExchangeParameters) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:379: warning: Member add(InteractiveMD &&interactiveMd) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:384: warning: Member add(SimulatorModules &&simulatorModules) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:389: warning: Member add(CenterOfMassPulling &¢erOfMassPulling) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:394: warning: Member add(IonSwapping &&ionSwapping) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:399: warning: Member add(TopologyData &&topologyData) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:404: warning: Member add(BoxDeformationHandle &&boxDeformation) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/options/basicoptionstorage.h:191: warning: Member formatSingleValue(const std::string &value) const override (function) of class gmx::StringOptionStorage is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionstoragetemplate.h:321: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< std::string > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/filestream.h:158: warning: @copybrief or @copydoc target 'TextInputFile::TextInputFile(const std::string &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/filestream.h:158: warning: @copybrief or @copydoc target 'TextInputFile::TextInputFile(const std::string &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/filestream.h:159: warning: @copydetails or @copydoc target 'TextInputFile::TextInputFile(const std::string &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/threaded_force_buffer.h:113: warning: Member processMask() (function) of class gmx::ThreadForceBuffer is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update.cpp:123: warning: Member update_coords(const t_inputrec &inputRecord, int64_t step, int homenr, bool havePartiallyFrozenAtoms, gmx::ArrayRef< const ParticleType > ptype, gmx::ArrayRef< const real > invMass, gmx::ArrayRef< const gmx::RVec > invMassPerDim, t_state *state, const gmx::ArrayRefWithPadding< const gmx::RVec > &f, t_fcdata *fcdata, const gmx_ekindata_t *ekind, const Matrix3x3 &parrinelloRahmanM, int UpdatePart, const t_commrec *cr, bool haveConstraints) (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update.cpp:139: warning: Member finish_update(const t_inputrec &inputRecord, bool havePartiallyFrozenAtoms, int homenr, gmx::ArrayRef< const unsigned short > cFREEZE, t_state *state, gmx_wallcycle *wcycle, bool haveConstraints) (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update.cpp:147: warning: Member update_sd_second_half(const t_inputrec &inputRecord, int64_t step, real *dvdlambda, int homenr, gmx::ArrayRef< const ParticleType > ptype, gmx::ArrayRef< const real > invMass, t_state *state, const t_commrec *cr, t_nrnb *nrnb, gmx_wallcycle *wcycle, gmx::Constraints *constr, bool do_log, bool do_ene) (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update.cpp:161: warning: Member update_for_constraint_virial(const t_inputrec &inputRecord, int homenr, bool havePartiallyFrozenAtoms, gmx::ArrayRef< const real > invmass, gmx::ArrayRef< const gmx::RVec > invMassPerDim, const t_state &state, const gmx::ArrayRefWithPadding< const gmx::RVec > &f, const gmx_ekindata_t &ekind) (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update.cpp:170: warning: Member update_temperature_constants(const t_inputrec &inputRecord, const gmx_ekindata_t &ekind) (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update.cpp:172: warning: Member getAndersenRandomizeGroup() const (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update.cpp:174: warning: Member getBoltzmanFactor() const (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update.cpp:176: warning: Member xp() (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update.cpp:178: warning: Member deform() const (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/updategroups.h:112: warning: Member useUpdateGroups() const (function) of class gmx::UpdateGroups is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/updategroups.h:113: warning: Member maxUpdateGroupRadius() const (function) of class gmx::UpdateGroups is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/updategroups.h:114: warning: Member updateGroupingPerMoleculeType() const (function) of class gmx::UpdateGroups is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:412: warning: Member empty() const (function) of class gmx::WriteCheckpointDataHolder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/modules/hbond.cpp:169: warning: Member DonorType (enumeration) of namespace gmx::analysismodules::anonymous_namespace{hbond.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/modules/hbond.cpp:163: warning: Member c_maxHydrogensWithOxygen (variable) of namespace gmx::analysismodules::anonymous_namespace{hbond.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/modules/hbond.cpp:165: warning: Member c_maxHydrogensWithNitrogen (variable) of namespace gmx::analysismodules::anonymous_namespace{hbond.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/modules/hbond.cpp:167: warning: Member c_maxHydrogenBonds (variable) of namespace gmx::analysismodules::anonymous_namespace{hbond.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/modules/hbond.cpp:113: warning: Member HbondStorageFrame(int frnr, std::vector< HBond > data) (function) of struct gmx::analysismodules::anonymous_namespace{hbond.cpp}::HbondStorageFrame is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/modules/msd.cpp:283: warning: Member MsdCoordinateManager(const int numAtoms, ArrayRef< const MoleculeData > molecules, ArrayRef< const int > moleculeIndexMapping) (function) of class gmx::analysismodules::anonymous_namespace{msd.cpp}::MsdCoordinateManager is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/modules/msd.cpp:107: warning: Member MsdColumnProxy(std::vector< double > *column) (function) of class gmx::analysismodules::anonymous_namespace{msd.cpp}::MsdData::MsdColumnProxy is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/modules/msd.cpp:109: warning: Member push_back(double value) (function) of class gmx::analysismodules::anonymous_namespace{msd.cpp}::MsdData::MsdColumnProxy is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/modules/msd.cpp:363: warning: Member MsdGroupData(const Selection &inputSel, ArrayRef< const MoleculeData > molecules, ArrayRef< const int > moleculeAtomMapping) (function) of struct gmx::analysismodules::anonymous_namespace{msd.cpp}::MsdGroupData is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/awh_history.cpp:69: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, AwhPointStateHistory *awhPointStateHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/awh_history.cpp:86: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, AwhBiasStateHistory *awhBiasStateHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/awh_history.cpp:100: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, CorrelationBlockDataHistory *correlationBlockDataHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/awh_history.cpp:121: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, CorrelationGridHistory *correlationGridHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/awh_history.cpp:142: warning: Member doCheckpointData(CheckpointData< operation > checkpointData, AwhBiasHistory *awhBiasHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/awh_history.cpp:66: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/electricfield.cpp:174: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/electricfield.cpp:174: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/electricfield.cpp:175: warning: @copydetails or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/enerdata.cpp:69: warning: Member makeFepvals(const std::vector< double > &lambdaVdw, const std::vector< double > &lambdaCoul) (function) of namespace gmx::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/enerdata.cpp:60: warning: Member c_numLambdas (variable) of namespace gmx::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/enerdata.cpp:62: warning: Member dhdlVdw (variable) of namespace gmx::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/enerdata.cpp:63: warning: Member dhdlCoul (variable) of namespace gmx::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/enerdata.cpp:65: warning: Member dhdlLinearZero (variable) of namespace gmx::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/energydata.cpp:402: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{energydata.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/expandedensembleelement.cpp:129: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{expandedensembleelement.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/firstorderpressurecoupling.cpp:179: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{firstorderpressurecoupling.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/freeenergyparameters.cpp:58: warning: Member lambdasAtState(const int stateIndex, gmx::ArrayRef< const std::vector< double > > lambdaArray, const int lambdaArrayExtent) (function) of namespace gmx::anonymous_namespace{freeenergyparameters.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/freeenergyperturbationdata.cpp:165: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{freeenergyperturbationdata.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/hardwaretopology.cpp:1099: warning: Member detectCpuLimit(const std::string &root="") (function) of namespace gmx::anonymous_namespace{hardwaretopology.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/hardwaretopology.cpp:1180: warning: Member setMaxThreads(float cpuLimit, int topologyCpus, int systemCpus) (function) of namespace gmx::anonymous_namespace{hardwaretopology.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/massrepartitioning.cpp:53: warning: Member setupMTop(gmx_mtop_t *mtop, ArrayRef< const real > masses, ArrayRef< const int > bonds) (function) of namespace gmx::anonymous_namespace{massrepartitioning.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/mttk.cpp:282: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{mttk.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/neldermead.cpp:97: warning: Member defaultNelderMeadParameters (variable) of namespace gmx::anonymous_namespace{neldermead.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp:294: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{parrinellorahmanbarostat.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:63: warning: Member integrationStepNames (variable) of namespace gmx::anonymous_namespace{propagator.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/pullelement.cpp:121: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{pullelement.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/template_mp.cpp:45: warning: Member Options (enumeration) of namespace gmx::anonymous_namespace{template_mp.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/template_mp.cpp:54: warning: Member testEnumTwoIPlusJPlusK(int k) (function) of namespace gmx::anonymous_namespace{template_mp.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/template_mp.cpp:60: warning: Member testBoolEnumTwoIPlusJPlusK(int k) (function) of namespace gmx::anonymous_namespace{template_mp.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/template_mp.cpp:66: warning: Member testBoolDoubleOrNot(int k) (function) of namespace gmx::anonymous_namespace{template_mp.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:194: warning: Member operator!=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() !=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:200: warning: Member operator<(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()< rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:206: warning: Member operator<=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()<=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:212: warning: Member operator>(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() > rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:218: warning: Member operator>=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() >=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:134: warning: Member not_null(const not_null &other)=default (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:135: warning: Member operator=(const not_null &other)=default (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:146: warning: Member operator T() const (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:147: warning: Member operator->() const (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:49: warning: Member c_nBoxZ (variable) of namespace gmx::detail is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:50: warning: Member c_nBoxY (variable) of namespace gmx::detail is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:51: warning: Member c_nBoxX (variable) of namespace gmx::detail is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:52: warning: Member c_numIvecs (variable) of namespace gmx::detail is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:484: warning: Member SimdTraitsT (typedef) of namespace gmx::internal is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:623: warning: Member Simd4TraitsT (typedef) of namespace gmx::internal is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:87: warning: Member IExceptionInfo(const IExceptionInfo &)=default (function) of class gmx::internal::IExceptionInfo is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:88: warning: Member IExceptionInfo(IExceptionInfo &&) noexcept=default (function) of class gmx::internal::IExceptionInfo is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:89: warning: Member operator=(const IExceptionInfo &)=default (function) of class gmx::internal::IExceptionInfo is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:90: warning: Member operator=(IExceptionInfo &&) noexcept=default (function) of class gmx::internal::IExceptionInfo is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/options/options_impl.h:200: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(OptionSectionImpl) (function) of class gmx::internal::OptionSectionImpl is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd_memory.h:154: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd_memory.h:163: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd_memory.h:154: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd_memory.h:155: warning: @copydetails or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd_memory.h:163: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd_memory.h:164: warning: @copydetails or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests/fft_mpi.cpp:72: warning: Member GpuFftTestParams (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests/fft_mpi.cpp:77: warning: Member GpuFftTestGridParams (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/gyrate.cpp:70: warning: Member GyrateTestParamsMerge (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/hbond.cpp:70: warning: Member HbondTestParamsMerge (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulatorcomparison.h:60: warning: Member SimulationOptionTuple (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests/fft_mpi.cpp:79: warning: Member getGpuAwareMpiStatusForFftBackend(const FftBackend fftBackend) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/tests/device_availability.cpp:66: warning: Member getRequiredNumberOfDevices() (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:85: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(p) &this->mask(a)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:86: warning: Member deallocate(p, 1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:93: warning: Member v(10) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:94: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(v.data()) &this->mask(v.get_allocator())) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:99: warning: Member for(std::size_t i=1000;i<=10000;i+=1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:125: warning: Member v1(1) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:127: warning: Member EXPECT_NE(data, nullptr) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:128: warning: Member v2(std::move(v1)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:129: warning: Member EXPECT_EQ(data, v2.data()) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulatorcomparison.cpp:61: warning: Member runGrompp(SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulatorcomparison.cpp:74: warning: Member runMdrun(SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulatorcomparison.cpp:87: warning: Member compareEnergies(const std::string &edr1Name, const std::string &edr2Name, const EnergyTermsToCompare &energyTermsToCompare, const MaxNumFrames maxNumFrames) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulatorcomparison.cpp:108: warning: Member compareTrajectories(const std::string &trajectory1Name, const std::string &trajectory2Name, const TrajectoryComparison &trajectoryComparison) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmegathertest.cpp:429: warning: Member registerDynamicalPmeGatherTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmesolvetest.cpp:414: warning: Member registerDynamicalPmeSolveTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/trajectorycomparison.cpp:416: warning: Member checkTrajectoryAgainstReferenceData(const std::string &trajectoryFilename, const TrajectoryComparison &trajectoryComparison, TestReferenceChecker *checker, MaxNumFrames maxNumFrames) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/friction_metric.cpp:68: warning: Member g_sampleWeightCentral (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/friction_metric.cpp:69: warning: Member g_sampleWeightNeighbor (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/friction_metric.cpp:70: warning: Member g_sampleTimeStep (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/friction_metric.cpp:71: warning: Member g_numPointsPerDim (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests/fft_mpi.cpp:263: warning: Member inputGrids (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests/fft_mpi.cpp:267: warning: Member inputBackends (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:783: warning: Member testKernelTypes (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:82: warning: Member a (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:83: warning: Member p (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:126: warning: Member data (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/awh_setup.h:71: warning: Member AwhTestParameters(ISerializer *serializer) (function) of struct gmx::test::AwhTestParameters is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/moduletest.h:200: warning: Member createModule() override (function) of class TrajectoryAnalysisModuleTestFixture< gmx::analysismodules::GyrateInfo > is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/moduletest.h:200: warning: Member createModule() override (function) of class TrajectoryAnalysisModuleTestFixture< gmx::analysismodules::HbondInfo > is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/replicaexchange_equivalence.cpp:267: warning: Member operator()(const testing::TestParamInfo< ParamType > ¶meter) const (function) of struct gmx::test::PrintReplicaExchangeParametersToString is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/moduletest.h:161: warning: Member topFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/moduletest.h:162: warning: Member groFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/moduletest.h:163: warning: Member mdpFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/moduletest.h:164: warning: Member fullPrecisionTrajectoryFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/moduletest.h:165: warning: Member reducedPrecisionTrajectoryFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/moduletest.h:166: warning: Member groOutputFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/moduletest.h:167: warning: Member cptOutputFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/moduletest.h:168: warning: Member ndxFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/moduletest.h:169: warning: Member mdpOutputFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/moduletest.h:170: warning: Member tprFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/moduletest.h:171: warning: Member logFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/moduletest.h:172: warning: Member edrFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/moduletest.h:173: warning: Member mtxFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/moduletest.h:174: warning: Member swapFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/moduletest.h:175: warning: Member dhdlFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/moduletest.h:176: warning: Member nsteps_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/moduletest.h:177: warning: Member maxwarn_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/toputils.h:73: warning: Member requestVelocities() (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/toputils.h:74: warning: Member requestForces() (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/toputils.h:75: warning: Member initFrameIndices(const ArrayRef< const int > &index) (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/toputils.h:86: warning: Member initAtomTypes(const ArrayRef< const char *const > &types) (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/toputils.h:87: warning: Member initUniformResidues(int residueSize) (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/toputils.h:88: warning: Member initUniformMolecules(int moleculeSize) (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/toputils.h:104: warning: Member setMoleculeType(int moleculeTypeIndex, ArrayRef< const int > residueSizes) (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/toputils.h:105: warning: Member setMoleculeBlock(int moleculeBlockIndex, int moleculeTypeIndex, int numMoleculesToAdd) (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/toputils.h:106: warning: Member finalizeTopology() (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/toputils.h:112: warning: Member atoms() (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/toputils.h:113: warning: Member frame() (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/trajectorycomparison.h:66: warning: Member coordinates (variable) of struct gmx::test::TrajectoryTolerances is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/trajectorycomparison.h:66: warning: Member velocities (variable) of struct gmx::test::TrajectoryTolerances is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/trajectorycomparison.h:66: warning: Member forces (variable) of struct gmx::test::TrajectoryTolerances is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/biasstate.cpp:140: warning: Member grid_ (variable) of class gmx::test::UserInputTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/biasstate.cpp:141: warning: Member gridIndexToDataIndex_ (variable) of class gmx::test::UserInputTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/biasstate.cpp:142: warning: Member data_ (variable) of class gmx::test::UserInputTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/biasstate.cpp:143: warning: Member numColumns_ (variable) of class gmx::test::UserInputTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/biasstate.cpp:144: warning: Member numRows_ (variable) of class gmx::test::UserInputTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/biasstate.cpp:145: warning: Member filename_ (variable) of class gmx::test::UserInputTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:350: warning: Member WriteFunction (typedef) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:351: warning: Member TestFunction (typedef) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:360: warning: Member addTestValues() (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:380: warning: Member test() (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:354: warning: Member writeFunctions_ (variable) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:356: warning: Member testFunctions_ (variable) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:428: warning: Member addTestValueFunctions_ (variable) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:444: warning: Member testingTypes_ (variable) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:458: warning: Member fileManager_ (variable) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:459: warning: Member filename_ (variable) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:64: warning: Member value (variable) of struct gmx::test::anonymous_namespace{checkpointdata.cpp}::IsVectorOfSerializableType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:173: warning: Member getTestVector() (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:179: warning: Member getTestVector() (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:185: warning: Member getTestVector() (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:191: warning: Member getTestVector() (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:197: warning: Member getTestVector() (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:105: warning: Member begin() const (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues::TestValueGenerator is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:106: warning: Member end() const (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues::TestValueGenerator is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:96: warning: Member Iterator(const T *ptr) (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues::TestValueGenerator::Iterator is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:97: warning: Member operator++() (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues::TestValueGenerator::Iterator is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:98: warning: Member operator!=(const Iterator &other) const (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues::TestValueGenerator::Iterator is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:99: warning: Member operator*() const (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues::TestValueGenerator::Iterator is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/cmdlinetest.cpp:254: warning: Member ViewMatchesCString(const std::string_view view) (function) of struct gmx::test::anonymous_namespace{cmdlinetest.cpp}::ViewMatchesCString is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/cmdlinetest.cpp:253: warning: Member view_ (variable) of struct gmx::test::anonymous_namespace{cmdlinetest.cpp}::ViewMatchesCString is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/tests/com.cpp:118: warning: Member COMInPlaceTestParams (typedef) of namespace gmx::test::anonymous_namespace{com.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/constr.cpp:85: warning: Member c_pbcs (variable) of namespace gmx::test::anonymous_namespace{constr.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/constr.cpp:156: warning: Member c_constraintsTestSystemList (variable) of namespace gmx::test::anonymous_namespace{constr.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/cstringutil.cpp:100: warning: Member testInplace(F f, const char *input, const char *expectedOutput) (function) of namespace gmx::test::anonymous_namespace{cstringutil.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/dssp.cpp:73: warning: Member DsspTestParamsDsspNB (typedef) of namespace gmx::test::anonymous_namespace{dssp.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/dssp.cpp:74: warning: Member DsspTestParamsGromacsNB (typedef) of namespace gmx::test::anonymous_namespace{dssp.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/dssp.cpp:75: warning: Member DsspTestParamsDsspNoNB (typedef) of namespace gmx::test::anonymous_namespace{dssp.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/dssp.cpp:76: warning: Member DsspTestParamsGromacsNoNB (typedef) of namespace gmx::test::anonymous_namespace{dssp.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/moduletest.h:200: warning: Member createModule() override (function) of class TrajectoryAnalysisModuleTestFixture< gmx::analysismodules::DsspInfo > is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/moduletest.h:200: warning: Member createModule() override (function) of class TrajectoryAnalysisModuleTestFixture< gmx::analysismodules::DsspInfo > is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/moduletest.h:200: warning: Member createModule() override (function) of class TrajectoryAnalysisModuleTestFixture< gmx::analysismodules::DsspInfo > is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/moduletest.h:200: warning: Member createModule() override (function) of class TrajectoryAnalysisModuleTestFixture< gmx::analysismodules::DsspInfo > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/exclusions.cpp:200: warning: Member testKernelTypes (variable) of namespace gmx::test::anonymous_namespace{exclusions.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests/fft.cpp:293: warning: Member FFTTest3DParameters (typedef) of namespace gmx::test::anonymous_namespace{fft.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/fileioxdrserializer.cpp:73: warning: Member c_int32Value (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/fileioxdrserializer.cpp:74: warning: Member c_int64Value (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/fileioxdrserializer.cpp:76: warning: Member c_intAndFloat32 (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/fileioxdrserializer.cpp:77: warning: Member c_intAndFloat64 (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/filetypes.cpp:62: warning: Member TypeAndName (typedef) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/filetypes.cpp:64: warning: Member FileTypeTestParams (typedef) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/filetypes.cpp:115: warning: Member testParams (variable) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/filetypes.cpp:124: warning: Member prefixes (variable) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/freeenergy.cpp:72: warning: Member ListOfInteractionsToTest (typedef) of namespace gmx::test::anonymous_namespace{freeenergy.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/freeenergy.cpp:73: warning: Member FreeEnergyReferenceTestParams (typedef) of namespace gmx::test::anonymous_namespace{freeenergy.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/index.cpp:67: warning: Member checkIndexGroup(TestReferenceChecker *checker, const IndexGroup &group) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/index.cpp:74: warning: Member checkBlocks(TestReferenceChecker *checker, ArrayRef< const IndexGroup > blocks) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/index.cpp:81: warning: Member compareBlocks(ArrayRef< const IndexGroup > one, ArrayRef< const IndexGroup > two) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/index.cpp:95: warning: Member checkFileMatch(TestReferenceChecker *checker, const std::string &fileName, const std::string &fullPath) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/inmemoryserializer.cpp:70: warning: Member c_int16ValueSwapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/inmemoryserializer.cpp:71: warning: Member c_int32Value (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/inmemoryserializer.cpp:72: warning: Member c_int32ValueSwapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/inmemoryserializer.cpp:73: warning: Member c_int64Value (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/inmemoryserializer.cpp:74: warning: Member c_int64ValueSwapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/inmemoryserializer.cpp:76: warning: Member c_intAndFloat32 (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/inmemoryserializer.cpp:77: warning: Member c_intAndFloat64 (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/inmemoryserializer.cpp:79: warning: Member c_intAndFloat32Swapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/inmemoryserializer.cpp:80: warning: Member c_intAndFloat64Swapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:505: warning: Member isTabulated(const CoulombKernelType coulombKernelType) (function) of namespace gmx::test::anonymous_namespace{kernel_test.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:530: warning: Member makeRefDataFileName() (function) of namespace gmx::test::anonymous_namespace{kernel_test.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:203: warning: Member c_numEnergyGroups (variable) of namespace gmx::test::anonymous_namespace{kernel_test.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:461: warning: Member coulombKernelTypeName (variable) of namespace gmx::test::anonymous_namespace{kernel_test.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:467: warning: Member vdwKernelTypeName (variable) of namespace gmx::test::anonymous_namespace{kernel_test.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:374: warning: Member TupleT (typedef) of struct gmx::test::anonymous_namespace{kernel_test.cpp}::KernelInputParameters is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:381: warning: Member KernelInputParameters(TupleT t) (function) of struct gmx::test::anonymous_namespace{kernel_test.cpp}::KernelInputParameters is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:391: warning: Member NbnxmKernelTest(LJCombinationRule ljCombinationRule) (function) of class gmx::test::anonymous_namespace{kernel_test.cpp}::NbnxmKernelTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:393: warning: Member options_ (variable) of class gmx::test::anonymous_namespace{kernel_test.cpp}::NbnxmKernelTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:394: warning: Member system_ (variable) of class gmx::test::anonymous_namespace{kernel_test.cpp}::NbnxmKernelTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:395: warning: Member nbv_ (variable) of class gmx::test::anonymous_namespace{kernel_test.cpp}::NbnxmKernelTest is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/minimize.cpp:170: warning: Member minimizersToTest_g (variable) of namespace gmx::test::anonymous_namespace{minimize.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/minimize.cpp:172: warning: Member constrainedSystemsToTest_g (variable) of namespace gmx::test::anonymous_namespace{minimize.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/minimize.cpp:175: warning: Member minimizersToTestWithConstraints_g (variable) of namespace gmx::test::anonymous_namespace{minimize.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/tests/mockhardwaretopology.cpp:162: warning: Member checkHardwareTopology(TestReferenceChecker *checker, const HardwareTopology &hwTop) (function) of namespace gmx::test::anonymous_namespace{mockhardwaretopology.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/tests/mockhardwaretopology.cpp:256: warning: Member runTest(const HardwareTopology &hwTop) (function) of class gmx::test::anonymous_namespace{mockhardwaretopology.cpp}::MockHardwareTopologyTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/multipletimestepping.cpp:139: warning: Member simpleMtsOpts() (function) of namespace gmx::test::anonymous_namespace{multipletimestepping.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:97: warning: Member c_numAtomTypes (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:511: warning: Member c_softcoreBeutlerAlphaOrGapsysLinpointScaling (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:512: warning: Member c_softcoreCoulomb (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:513: warning: Member c_softcoreType (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:349: warning: Member getNbList() (function) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:331: warning: Member idef (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:334: warning: Member chargeA (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:335: warning: Member chargeB (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:336: warning: Member typeA (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:337: warning: Member typeB (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:341: warning: Member iAtoms (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:342: warning: Member jAtoms (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:343: warning: Member jIndex (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:344: warning: Member shift (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:345: warning: Member gid (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:346: warning: Member exclFep (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/normalmodes.cpp:168: warning: Member GTEST_ALLOW_UNINSTANTIATED_PARAMETERIZED_TEST(NormalModesTest) (function) of namespace gmx::test::anonymous_namespace{normalmodes.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/optimization.cpp:60: warning: Member mcCormick(ArrayRef< const real > x) (function) of namespace gmx::test::anonymous_namespace{optimization.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/tests/pairs.cpp:200: warning: Member frHelper (variable) of namespace gmx::test::anonymous_namespace{pairs.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/tests/pairs.cpp:102: warning: Member OutputQuantities(int energyGroup) (function) of struct gmx::test::anonymous_namespace{pairs.cpp}::OutputQuantities is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmesolvetest.cpp:108: warning: Member enumValueToString(PmeSolveAlgorithm enumValue) (function) of namespace gmx::test::anonymous_namespace{pmesolvetest.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmesolvetest.cpp:115: warning: Member enumValueToString(GridOrdering enumValue) (function) of namespace gmx::test::anonymous_namespace{pmesolvetest.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:173: warning: Member enumValueToString(SplineAndSpreadOptions enumValue) (function) of namespace gmx::test::anonymous_namespace{pmesplinespreadtest.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:85: warning: Member c_testSystems (variable) of namespace gmx::test::anonymous_namespace{pmesplinespreadtest.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/pmetest.cpp:96: warning: Member PmeTestParameters (typedef) of namespace gmx::test::anonymous_namespace{pmetest.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/pmetest.cpp:404: warning: Member c_reproducesEnergies (variable) of namespace gmx::test::anonymous_namespace{pmetest.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/tests/position_restraints.cpp:148: warning: Member c_emptyLambdas (variable) of namespace gmx::test::anonymous_namespace{position_restraints.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/pull.cpp:173: warning: Member isTransformationPullSetup(const std::string &pullSetupName) (function) of namespace gmx::test::anonymous_namespace{pull.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/pull.cpp:79: warning: Member c_mdpPullParams (variable) of namespace gmx::test::anonymous_namespace{pull.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/refdata_xml.cpp:95: warning: Member getCDataChildNode(XMLNodePtr node) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/refdata_xml.cpp:105: warning: Member hasCDataContent(XMLNodePtr node) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/refdata_xml.cpp:333: warning: Member createElementAndContents(XMLElementPtr parentElement, const ReferenceDataEntry &entry) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/refdata_xml.cpp:246: warning: Member setIdAttribute(XMLElementPtr element, const std::string &id) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/refdata_xml.cpp:254: warning: Member createElement(XMLElementPtr parentElement, const ReferenceDataEntry &entry) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/refdata_xml.cpp:262: warning: Member createChildElements(XMLElementPtr parentElement, const ReferenceDataEntry &entry) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/refdata_xml.cpp:304: warning: Member createElementContents(XMLElementPtr element, const ReferenceDataEntry &entry) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/refdata_xml.cpp:339: warning: Member createRootElement(XMLDocumentPtr document) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/rerun.cpp:111: warning: Member executeRerunTest(TestFileManager *fileManager, SimulationRunner *runner, const std::string &simulationName, int numWarningsToTolerate, const MdpFieldValues &mdpFieldValues, const EnergyTermsToCompare &energyTermsToCompare, const TrajectoryComparison &trajectoryComparison) (function) of namespace gmx::test::anonymous_namespace{rerun.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/scattering.cpp:68: warning: Member ScatteringTestDirectModeParams (typedef) of namespace gmx::test::anonymous_namespace{scattering.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/moduletest.h:200: warning: Member createModule() override (function) of class TrajectoryAnalysisModuleTestFixture< gmx::analysismodules::ScatteringInfo > is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simple_mdrun.cpp:191: warning: Member GTEST_ALLOW_UNINSTANTIATED_PARAMETERIZED_TEST(SimpleMdrunTest) (function) of namespace gmx::test::anonymous_namespace{simple_mdrun.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/timing/tests/timing.cpp:75: warning: Member delayInMilliseconds (variable) of class gmx::test::anonymous_namespace{timing.cpp}::TimingTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/timing/tests/timing.cpp:76: warning: Member wcycle (variable) of class gmx::test::anonymous_namespace{timing.cpp}::TimingTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/tools/tests/trjconv.cpp:155: warning: Member DumpTestParameters (typedef) of namespace gmx::test::anonymous_namespace{trjconv.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/virtualsites.cpp:86: warning: Member VirtualSiteTestParams (typedef) of namespace gmx::test::anonymous_namespace{virtualsites.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/xvgio.cpp:63: warning: Member compareValues(basic_mdspan< const double, dynamicExtents2D > ref, basic_mdspan< const double, dynamicExtents2D > test) (function) of namespace gmx::test::anonymous_namespace{xvgio.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:125: warning: Member mode (typedef) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/grid.cpp:122: warning: Member getMaxNumCells(const Grid::Geometry &geometry, const int numAtoms, const int numColumns) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/gridset.cpp:135: warning: Member getGridOffset(gmx::ArrayRef< const Grid > grids, int gridIndex) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_buffer_ops.cpp:63: warning: Member nbnxn_gpu_x_to_nbat_x(const Nbnxm::Grid &grid, NbnxmGpu *nb, DeviceBuffer< gmx::RVec > d_x, GpuEventSynchronizer *xReadyOnDevice, const gmx::AtomLocality locality, int gridId, int numColumnsMax, bool mustInsertNonLocalDependency) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:83: warning: Member init_ewald_coulomb_force_table(const EwaldCorrectionTables &tables, NBParamGpu *nbp, const DeviceContext &deviceContext) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:97: warning: Member useTabulatedEwaldByDefault(const DeviceInformation &deviceInfo) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:128: warning: Member nbnxn_gpu_pick_ewald_kernel_type(const interaction_const_t &ic, const DeviceInformation &deviceInfo) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:178: warning: Member set_cutoff_parameters(NBParamGpu *nbp, const interaction_const_t &ic, const PairlistParams &listParams) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:202: warning: Member initPlistSorting(gpuPlistSorting *sorting) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:225: warning: Member init_plist(gpu_plist *pl) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:253: warning: Member init_timings(gmx_wallclock_gpu_nbnxn_t *t) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:302: warning: Member nbnxmGpuPickVdwKernelType(const interaction_const_t &ic, LJCombinationRule ljCombinationRule) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:356: warning: Member nbnxmGpuPickElectrostaticsKernelType(const interaction_const_t &ic, const DeviceInformation &deviceInfo) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:442: warning: Member gpu_init(const gmx::DeviceStreamManager &deviceStreamManager, const interaction_const_t *ic, const PairlistParams &listParams, const nbnxn_atomdata_t *nbat, const bool bLocalAndNonlocal) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:511: warning: Member gpu_pme_loadbal_update_param(nonbonded_verlet_t *nbv, const interaction_const_t &ic) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:528: warning: Member gpu_upload_shiftvec(NbnxmGpu *nb, const nbnxn_atomdata_t *nbatom) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:689: warning: Member gpu_init_atomdata(NbnxmGpu *nb, const nbnxn_atomdata_t *nbat) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:792: warning: Member gpu_clear_outputs(NbnxmGpu *nb, bool computeVirial) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:823: warning: Member gpu_is_kernel_ewald_analytical(const NbnxmGpu *nb) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:829: warning: Member setupGpuShortRangeWork(NbnxmGpu *nb, const gmx::ListedForcesGpu *listedForcesGpu, const gmx::InteractionLocality iLocality) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:842: warning: Member haveGpuShortRangeWork(const NbnxmGpu *nb, const gmx::InteractionLocality interactionLocality) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:981: warning: Member nbnxnInsertNonlocalGpuDependency(NbnxmGpu *nb, const InteractionLocality interactionLocality) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1076: warning: Member nbnxn_gpu_init_x_to_nbat_x(const Nbnxm::GridSet &gridSet, NbnxmGpu *gpu_nbv) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1286: warning: Member gpuGetNBAtomData(NbnxmGpu *nb) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1292: warning: Member gpu_get_f(NbnxmGpu *nb) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_setup.cpp:355: warning: Member getENbnxnInitCombRule(const t_forcerec &forcerec) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.cpp:53: warning: Member getNbnxmSubGroupSize(const DeviceInformation &deviceInfo) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:1455: warning: Member launchNbnxmKernelHelper(NbnxmGpu *nb, const gmx::StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:106: warning: Member elecEwald (variable) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:109: warning: Member elecEwaldTab (variable) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:112: warning: Member ljEwald (variable) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/gpu_types_common.h:276: warning: Member scanTemporary (variable) of struct Nbnxm::gpuPlistSorting is not documented. /build/reproducible-path/gromacs-2024.4/docs/doxygen/directories.cpp:96: warning: unable to resolve reference to 'sm_insolidangle' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_insolidangle.cpp:99: warning: unable to resolve reference to 'sm_insolidangle' for \ref command cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen/doxygen-full-timestamp.txt make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [100%] Built target doxygen-full /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-all.dir/build.make docs/doxygen/CMakeFiles/doxygen-all.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/docs/doxygen /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen/CMakeFiles/doxygen-all.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-all.dir/build.make docs/doxygen/CMakeFiles/doxygen-all.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'docs/doxygen/CMakeFiles/doxygen-all.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [100%] Built target doxygen-all /usr/bin/make -f docs/CMakeFiles/webpage.dir/build.make docs/CMakeFiles/webpage.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/docs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/docs /build/reproducible-path/gromacs-2024.4/build/documentation/docs/CMakeFiles/webpage.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f docs/CMakeFiles/webpage.dir/build.make docs/CMakeFiles/webpage.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E remove -f /build/reproducible-path/gromacs-2024.4/build/documentation/docs/html/manual-2024.4-Debian_2024.4_1.pdf cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/build/documentation/docs/manual/gromacs.pdf /build/reproducible-path/gromacs-2024.4/build/documentation/docs/html/manual-2024.4-Debian_2024.4_1.pdf cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E echo "Webpage output: file:///build/reproducible-path/gromacs-2024.4/build/documentation/docs/html/index.html" Webpage output: file:///build/reproducible-path/gromacs-2024.4/build/documentation/docs/html/index.html make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [100%] Built target webpage make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2024.4/build/documentation/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[1]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' touch build-manual dh_testdir dh_testroot dh_prep dh_installdirs /usr/bin/make -j12 -C build/mpi install DESTDIR=/build/reproducible-path/gromacs-2024.4/debian/tmp make[1]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/cmake -P /build/reproducible-path/gromacs-2024.4/build/mpi/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2024.4 -B/build/reproducible-path/gromacs-2024.4/build/mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2024.4/build/mpi/CMakeFiles /build/reproducible-path/gromacs-2024.4/build/mpi//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/selection /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/selection /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra 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src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2024.4-Debian_2024.4_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2024.4 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2024.4/build/mpi/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2024.4/build/mpi/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2024.4-1 -P /build/reproducible-path/gromacs-2024.4/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd 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src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2024.4/build/mpi 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target taskassignment make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 11%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 95%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 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/build/reproducible-path/gromacs-2024.4/api/nblib /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Nothing to be done for 'api/nblib/CMakeFiles/nblib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Nothing to be done for 'api/gmxapi/CMakeFiles/gmxapi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 95%] Built target gmx [ 95%] Built target gmxapi [ 97%] Built target nblib /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/depend /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Nothing to be done for 'python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Nothing to be done for 'python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [100%] Built target gmxapi_extension_resources /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/depend /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/DependInfo.cmake "--color=" [100%] Built target _gmxapi make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Nothing to be done for 'api/nblib/samples/CMakeFiles/methane-water-integration.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Nothing to be done for 'python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build [100%] Built target methane-water-integration make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Nothing to be done for 'api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [100%] Built target gmxapi_extension_test make[3]: Nothing to be done for 'python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [100%] Built target argon-forces-integration [100%] Built target gmxapi_extension_ensemblepotential /usr/bin/make -f python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/build.make python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/src/pythonmodule /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/pythonmodule /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/build.make python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Nothing to be done for 'python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [100%] Built target gmxapi_extension make[2]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2024.4/build/mpi/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/README.tutor -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/README_FreeEnergyModifications.txt -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/nsfactor.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/bonds.dlg -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/residues.dtd -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ps.m2p -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/spc.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/specbond.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ffG43a2.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/phbres.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ha-shift.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.n.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/cmap.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnanonbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.c.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.c.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnabonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.n.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/tips3p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ff_dum.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/xlateat.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ca-shift.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/defselection.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/vdw-msms.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ffG53a5.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ff_dum.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/methanol.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/methanol216.gro -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/spc216.gro -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/scatteringfactors.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ff_dum.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/atomname2type.n2t -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ions.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ff_dum.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/flexspc.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/README -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/residuetypes.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ffoplsaa-n.tst -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/table6-10.xvg -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/1propanol.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ethanol.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/methanol.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomname2type.n2t -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5pe.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/flexspce.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/refi_aa.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/surface.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/watermodels.dat -- Installing: 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/build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-hbond.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-saxs-legacy.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-hydorder.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-dyecoupl.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-spatial.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-trjorder.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-dielectric.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-awh.1 make[1]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -j12 -C build/mpi-dp install DESTDIR=/build/reproducible-path/gromacs-2024.4/debian/tmp make[1]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2024.4 -B/build/reproducible-path/gromacs-2024.4/build/mpi-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2024.4/build/mpi-dp/CMakeFiles /build/reproducible-path/gromacs-2024.4/build/mpi-dp//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/selection /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/selection /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/options /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/options /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/programs /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/programs /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2024.4-Debian_2024.4_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2024.4 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2024.4/build/mpi-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2024.4/build/mpi-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2024.4-1 -P /build/reproducible-path/gromacs-2024.4/cmake/gmxGenerateVersionInfoWithoutGit.cmake /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make 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mdrun_objlib /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend [ 6%] Built target lmfit_objlib make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/pulling /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/options/CMakeFiles/options.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' [ 6%] Built target release-version-info [ 6%] Built target gmx_objlib [ 8%] Built target options make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' [ 12%] Built target colvars_objlib [ 14%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/taskassignment /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' [ 14%] Built target taskassignment make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' [ 16%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs 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Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/gmxapi /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib 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'/build/reproducible-path/gromacs-2024.4/build/mpi-dp' [ 95%] Built target gmx make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Nothing to be done for 'api/gmxapi/CMakeFiles/gmxapi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build [ 97%] Built target gmxapi make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Nothing to be done for 'api/nblib/CMakeFiles/nblib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' [100%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Nothing to be done for 'api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Nothing to be done for 'api/nblib/samples/CMakeFiles/methane-water-integration.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' [100%] Built target argon-forces-integration [100%] Built target methane-water-integration make[2]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2024.4/build/mpi-dp/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/README.tutor -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/README_FreeEnergyModifications.txt -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/nsfactor.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/bonds.dlg -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/residues.dtd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ps.m2p -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/specbond.dat -- Up-to-date: 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Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.vsd -- Up-to-date: 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Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.arn -- Up-to-date: 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Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip3p.itp -- Up-to-date: 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/build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/1propanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ethanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/methanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomname2type.n2t -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5pe.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.rtp -- Up-to-date: 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Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/flexspce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/refi_aa.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/surface.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/electroneg.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/table6-11.xvg -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/flexwat-ferguson.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/atommass.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/cb-shift.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/vdwradii.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/table6-12.xvg -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/elements.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/residues.xml -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/edissoc.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ss.map -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ffG53a6.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/tip5p.gro -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ffoplsaa.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/atom_nom.tbl -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/sfactor.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/sw.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/export.dlg -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/dppc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tmcl.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/popc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/tip4p.gro -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ffG43a1.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ffG45a3.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/table6-8.xvg -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/random.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/dgsolv.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/co-shift.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/table6-9.xvg -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/GMXRC -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/GMXRC.bash -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/GMXRC.zsh -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/GMXRC.csh -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/demux.pl -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/xplor2gmx.pl -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/x86_64-linux-gnu/libgmxapi_mpi_d.so.0.4.0 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/x86_64-linux-gnu/libgmxapi_mpi_d.so.0 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/x86_64-linux-gnu/libgmxapi_mpi_d.so -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gmxapi/gmxapi.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gmxapi/gmxapi-release.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config.cmake -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/session.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/context.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/md -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/md/mdsignals.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/md/mdmodule.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/exceptions.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/gmxapi.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/gromacsfwd.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/system.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/compat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/compat/mdparams.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/compat/tpr.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/status.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/session -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/session/resources.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/mpi -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/mpi/gmxapi_mpi.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/md.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/gmxapicompat.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/version.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/mpi/resourceassignment.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/x86_64-linux-gnu/libnblib_gmx.so.0.1.0 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/x86_64-linux-gnu/libnblib_gmx.so.0 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/x86_64-linux-gnu/libnblib_gmx.so -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/nblib.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/nbnxmsetuphelpers.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/particlesequencer.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/topology.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/interactions.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/util -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/util/util.hpp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/util/traits.hpp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/util/setup.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/molecules.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/tpr.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/gmxcalculatorcpu.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/kerneloptions.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/basicdefinitions.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/integrator.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/vector.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/particletype.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/exception.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/simulationstate.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/box.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/listed_forces -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/listed_forces/calculator.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/listed_forces/bondtypes.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/listed_forces/definitions.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/mdrun/simulationinputhandle.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/x86_64-linux-gnu/libgromacs_mpi_d.so.9.0.0 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/x86_64-linux-gnu/libgromacs_mpi_d.so.9 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/x86_64-linux-gnu/libgromacs_mpi_d.so -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/libgromacs_mpi_d.pc -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gromacs_mpi_d/libgromacs.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gromacs_mpi_d/libgromacs-release.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gromacs_mpi_d/gromacs_mpi_d-config.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gromacs_mpi_d/gromacs_mpi_d-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gromacs_mpi_d/gromacs-hints_mpi_d.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/gmx_mpi_d -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/gmx-completion.bash -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/gmx-completion-gmx_mpi_d.bash -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-mdmat.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-helix.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-order.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-wham.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-genion.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-rms.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-rama.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-filter.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-grompp.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-anaeig.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-nonbonded-benchmark.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-current.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-gyrate-legacy.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-confrms.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-gyrate.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-disre.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-dos.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-polystat.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-angle.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-distance.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-traj.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-trajectory.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-mindist.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-genconf.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-density.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-nmens.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-potential.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-densorder.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-spol.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-xpm2ps.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-dipoles.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-tune_pme.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-principal.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-report-methods.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-mdrun.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-tcaf.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-gangle.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-pdb2gmx.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-dump.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-sigeps.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-rotmat.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-sasa.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-dssp.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-eneconv.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-hbond-legacy.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-make_ndx.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-analyze.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-convert-trj.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-genrestr.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-nmr.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-sorient.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-nmtraj.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-sham.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-solvate.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-pairdist.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-chi.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-clustsize.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-rdf.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-help.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-make_edi.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-rmsdist.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-sans-legacy.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-bar.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-cluster.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-velacc.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-saltbr.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-densmap.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-editconf.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-energy.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-trjconv.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-convert-tpr.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-extract-cluster.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-helixorient.1 -- 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api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E 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Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.hdb -- Up-to-date: 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Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/watermodels.dat -- Up-to-date: 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Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/urea.itp -- Up-to-date: 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/build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/ffnonbonded.itp -- Up-to-date: 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/build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/1propanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ethanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/methanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomname2type.n2t -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5pe.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/flexspce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/refi_aa.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/surface.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/electroneg.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/table6-11.xvg -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/flexwat-ferguson.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/atommass.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/cb-shift.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/vdwradii.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/table6-12.xvg -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/elements.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/residues.xml -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/edissoc.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ss.map -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ffG53a6.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/tip5p.gro -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ffoplsaa.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/atom_nom.tbl -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/sfactor.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/sw.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/export.dlg -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/dppc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tmcl.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/popc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/tip4p.gro -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ffG43a1.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ffG45a3.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/table6-8.xvg -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/random.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/dgsolv.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/co-shift.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/table6-9.xvg -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/GMXRC -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/GMXRC.bash -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/GMXRC.zsh -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/GMXRC.csh -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/demux.pl -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/xplor2gmx.pl -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/math -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/math/units.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/math/utilities.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/math/functions.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/math/vectypes.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/math/vec.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/math/do_fit.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/selection -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/selection/nbsearch.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/selection/indexutil.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/selection/selectionoptionmanager.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/selection/selectioncollection.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/selection/selectionoption.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/selection/selectionenums.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/selection/selection.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/selection/position.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/selection/selectionoptionbehavior.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/restraint -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/restraint/restraintpotential.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/pbcutil -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/pbcutil/pbc.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/trajectory -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/trajectory/trajectoryframe.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/utility -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/utility/listoflists.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/utility/gmxassert.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/utility/real.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/utility/baseversion.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/utility/unique_cptr.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/utility/fileptr.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/utility/enumerationhelpers.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/utility/exceptions.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/utility/smalloc.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/utility/programcontext.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/utility/pleasecite.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/utility/range.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/utility/classhelpers.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/utility/flags.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/utility/futil.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/utility/basedefinitions.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/utility/stringutil.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/utility/current_function.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/utility/arrayref.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/mdtypes -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/mdtypes/md_enums.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/mdtypes/inputrec.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/topology -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/topology/ifunc.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/topology/topology_enums.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/topology/topology.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/topology/block.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/topology/index.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/topology/atomprop.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/topology/symtab.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/topology/forcefieldparameters.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/topology/atoms.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/topology/idef.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/trajectoryanalysis -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/trajectoryanalysis/topologyinformation.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/trajectoryanalysis/analysissettings.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/trajectoryanalysis/cmdlinerunner.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/trajectoryanalysis/analysismodule.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/analysisdata -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/analysisdata/modules -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/analysisdata/modules/average.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/analysisdata/modules/plot.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/analysisdata/modules/lifetime.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/analysisdata/modules/histogram.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/analysisdata/modules/displacement.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/analysisdata/analysisdata.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/analysisdata/arraydata.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/analysisdata/abstractdata.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/analysisdata/dataframe.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/analysisdata/datamodule.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/options -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/options/filenameoption.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/options/ioptionscontainerwithsections.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/options/basicoptions.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/options/options.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/options/ivaluestore.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/options/timeunitmanager.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/options/ioptionscontainer.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/options/abstractoption.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/options/ioptionsbehavior.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/options/filenameoptionmanager.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/options/optionfiletype.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/options/optionflags.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/fileio -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/fileio/trxio.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/fileio/tpxio.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/fileio/oenv.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/fileio/filetypes.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/fileio/pdbio.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/fileio/confio.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/version.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/libgromacs_export.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/x86_64-linux-gnu/libgmxapi.so.0.4.0 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/x86_64-linux-gnu/libgmxapi.so.0 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/x86_64-linux-gnu/libgmxapi.so -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gmxapi/gmxapi.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gmxapi/gmxapi-release.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config.cmake -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/session.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/context.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/md -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/md/mdsignals.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/md/mdmodule.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/exceptions.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/gmxapi.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/gromacsfwd.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/system.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/compat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/compat/mdparams.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/compat/tpr.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/status.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/session -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/session/resources.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/mpi -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/mpi/gmxapi_mpi.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/md.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/gmxapicompat.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/version.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/mpi/resourceassignment.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/x86_64-linux-gnu/libnblib_gmx.so.0.1.0 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/x86_64-linux-gnu/libnblib_gmx.so.0 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/x86_64-linux-gnu/libnblib_gmx.so -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/nblib.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/nbnxmsetuphelpers.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/particlesequencer.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/topology.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/interactions.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/util -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/util/util.hpp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/util/traits.hpp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/util/setup.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/molecules.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/tpr.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/gmxcalculatorcpu.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/kerneloptions.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/basicdefinitions.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/integrator.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/vector.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/particletype.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/exception.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/simulationstate.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/box.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/listed_forces -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/listed_forces/calculator.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/listed_forces/bondtypes.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/listed_forces/definitions.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/external/boost/stl_interfaces/fwd.hpp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/external/boost/stl_interfaces/iterator_interface.hpp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/mdrun/simulationinputhandle.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/x86_64-linux-gnu/libgromacs.so.9.0.0 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/x86_64-linux-gnu/libgromacs.so.9 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/x86_64-linux-gnu/libgromacs.so -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/libgromacs.pc -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gromacs/libgromacs.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gromacs/libgromacs-release.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gromacs/gromacs-config.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gromacs/gromacs-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gromacs/gromacs-hints.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/gmx -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/gmx-completion.bash -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/gmx-completion-gmx.bash -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-mdmat.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-helix.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-order.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-wham.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-genion.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-rms.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-rama.1 -- Up-to-date: 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/CMakeFiles /build/reproducible-path/gromacs-2024.4/build/basic-dp//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/selection /build/reproducible-path/gromacs-2024.4/build/basic-dp 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src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/basic-dp 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'/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 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cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/options /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2024.4-Debian_2024.4_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2024.4 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2024.4/build/basic-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2024.4/build/basic-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2024.4-1 -P /build/reproducible-path/gromacs-2024.4/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Leaving directory 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directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 0%] Built target mdrun_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build [ 1%] Built target tng_io_obj /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build [ 1%] Built target linearalgebra /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Nothing to be done for 'src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pulling /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Nothing to be done for 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src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/taskassignment /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 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src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build [ 13%] Built target taskassignment make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 15%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/basic-dp 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'/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/gmxapi /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi 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directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build [ 94%] Built target gmx make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Nothing to be done for 'api/nblib/CMakeFiles/nblib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Nothing to be done for 'api/gmxapi/CMakeFiles/gmxapi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 98%] Built target gmxapi [ 96%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Nothing to be done for 'api/nblib/samples/CMakeFiles/methane-water-integration.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Nothing to be done for 'api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [100%] Built target methane-water-integration [100%] Built target argon-forces-integration make[2]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2024.4/build/basic-dp/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/README.tutor -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/README_FreeEnergyModifications.txt -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/nsfactor.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/bonds.dlg -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/residues.dtd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ps.m2p -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/specbond.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ffG43a2.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/phbres.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ha-shift.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.n.tdb -- Up-to-date: 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Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.arn -- 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Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/methanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/methanol216.gro -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.rtp -- Up-to-date: 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Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.vsd -- Up-to-date: 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Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.arn -- Up-to-date: 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Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip3p.itp -- Up-to-date: 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/build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/1propanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ethanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/methanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomname2type.n2t -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5pe.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.rtp -- Up-to-date: 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Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/flexspce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/refi_aa.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/surface.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/electroneg.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/table6-11.xvg -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/flexwat-ferguson.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/atommass.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/cb-shift.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/vdwradii.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/table6-12.xvg -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/elements.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/residues.xml -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/edissoc.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ss.map -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ffG53a6.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/tip5p.gro -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ffoplsaa.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/atom_nom.tbl -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/sfactor.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/sw.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/export.dlg -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/dppc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tmcl.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/popc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/tip4p.gro -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ffG43a1.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ffG45a3.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/table6-8.xvg -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/random.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/dgsolv.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/co-shift.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/table6-9.xvg -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/GMXRC -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/GMXRC.bash -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/GMXRC.zsh -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/GMXRC.csh -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/demux.pl -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/xplor2gmx.pl -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/x86_64-linux-gnu/libgmxapi_d.so.0.4.0 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/x86_64-linux-gnu/libgmxapi_d.so.0 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/x86_64-linux-gnu/libgmxapi_d.so -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gmxapi/gmxapi.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gmxapi/gmxapi-release.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config.cmake -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/session.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/context.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/md -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/md/mdsignals.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/md/mdmodule.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/exceptions.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/gmxapi.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/gromacsfwd.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/system.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/compat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/compat/mdparams.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/compat/tpr.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/status.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/session -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/session/resources.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/mpi -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/mpi/gmxapi_mpi.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/md.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/gmxapicompat.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/version.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/mpi/resourceassignment.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/x86_64-linux-gnu/libnblib_gmx.so.0.1.0 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/x86_64-linux-gnu/libnblib_gmx.so.0 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/x86_64-linux-gnu/libnblib_gmx.so -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/nblib.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/nbnxmsetuphelpers.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/particlesequencer.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/topology.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/interactions.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/util -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/util/util.hpp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/util/traits.hpp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/util/setup.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/molecules.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/tpr.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/gmxcalculatorcpu.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/kerneloptions.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/basicdefinitions.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/integrator.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/vector.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/particletype.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/exception.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/simulationstate.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/box.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/listed_forces -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/listed_forces/calculator.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/listed_forces/bondtypes.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/listed_forces/definitions.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/mdrun/simulationinputhandle.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/x86_64-linux-gnu/libgromacs_d.so.9.0.0 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/x86_64-linux-gnu/libgromacs_d.so.9 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/x86_64-linux-gnu/libgromacs_d.so -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/libgromacs_d.pc -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gromacs_d/libgromacs.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gromacs_d/libgromacs-release.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gromacs_d/gromacs_d-config.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gromacs_d/gromacs_d-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gromacs_d/gromacs-hints_d.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/gmx_d -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/gmx-completion.bash -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/gmx-completion-gmx_d.bash -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-mdmat.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-helix.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-order.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-wham.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-genion.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-rms.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-rama.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-filter.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-grompp.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-anaeig.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-nonbonded-benchmark.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-current.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-gyrate-legacy.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-confrms.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-gyrate.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-disre.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-dos.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-polystat.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-angle.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-distance.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-traj.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-trajectory.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-mindist.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-genconf.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-density.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-nmens.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-potential.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-densorder.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-spol.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-xpm2ps.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-dipoles.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-tune_pme.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-principal.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-report-methods.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-mdrun.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-tcaf.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-gangle.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-pdb2gmx.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-dump.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-sigeps.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-rotmat.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-sasa.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-dssp.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-eneconv.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-hbond-legacy.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-make_ndx.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-analyze.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-convert-trj.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-genrestr.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-nmr.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-sorient.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-nmtraj.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-sham.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-solvate.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-pairdist.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-chi.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-clustsize.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-rdf.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-help.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-make_edi.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-rmsdist.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-sans-legacy.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-bar.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-cluster.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-velacc.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-saltbr.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-densmap.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-editconf.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-energy.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-trjconv.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-convert-tpr.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-extract-cluster.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-helixorient.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-trjcat.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-select.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-wheel.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-freevolume.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-mk_angndx.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-lie.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-rmsf.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-check.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-covar.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-msd.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-scattering.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-h2order.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-x2top.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-enemat.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-insert-molecules.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-nmeig.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-bundle.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-rotacf.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-vanhove.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-pme_error.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-hbond.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-saxs-legacy.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-hydorder.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-dyecoupl.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-spatial.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-trjorder.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-dielectric.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-awh.1 make[1]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' chrpath -d /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/gmx_mpi /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/gmx_mpi_d chrpath -d /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/*/libgromacs_mpi*.so.* perl -lne 'print' /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/gmx-completion.bash \ /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/gmx-completion-*.bash > \ /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/gmx-completion-concat mv /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/demux.pl /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/demux mv /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/xplor2gmx.pl /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/xplor2gmx dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_bash-completion -a dh_lintian -a dh_link -a dh_testdir -i dh_testroot -i dh_installdirs -i dh_install -i dh_installdocs -i dh_installchangelogs -i dh_installman -i find /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/ -type f -a \( -name '*.md5' -o -name '*.map' \) -delete rdfind -outputname /dev/null -makesymlinks true /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/ Now scanning "/build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc", found 23450 files. Now have 23450 files in total. Removed 0 files due to nonunique device and inode. Total size is 376889989 bytes or 359 MiB Removed 7953 files due to unique sizes from list. 15497 files left. Now eliminating candidates based on first bytes: removed 3350 files from list. 12147 files left. Now eliminating candidates based on last bytes: removed 1749 files from list. 10398 files left. Now eliminating candidates based on sha1 checksum: removed 3288 files from list. 7110 files left. It seems like you have 7110 files that are not unique Totally, 23 MiB can be reduced. Now making results file /dev/null Now making symbolic links. creating Making 4129 links. symlinks -r -s -c /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/ absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1BoxDeformationHandle-members.xhtml -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1BoxDeformationHandle-members.xhtml changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1BoxDeformationHandle-members.xhtml -> ../html-full/classgmx_1_1BoxDeformationHandle-members.xhtml absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__localtop__t__coll__graph.svg -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__localtop__t__coll__graph.svg changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__localtop__t__coll__graph.svg -> ../html-full/structgmx__localtop__t__coll__graph.svg absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/folderclosedd.svg -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/folderclosedd.svg changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/folderclosedd.svg -> ../html-full/folderclosedd.svg absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_371.svg -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_609.svg changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_371.svg -> ../html-full/inherit_graph_609.svg absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Selection-members.xhtml -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Selection-members.xhtml changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1Selection-members.xhtml -> ../html-full/classgmx_1_1Selection-members.xhtml absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnumerationWrapper-members.xhtml -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnumerationWrapper-members.xhtml changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1EnumerationWrapper-members.xhtml -> ../html-full/classgmx_1_1EnumerationWrapper-members.xhtml absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_20.png -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_20.png changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_20.png -> ../html-full/form_20.png absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/mdmodulesnotifier_8h__incl.svg -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/mdmodulesnotifier_8h__incl.svg changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/mdmodulesnotifier_8h__incl.svg -> ../html-full/mdmodulesnotifier_8h__incl.svg absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/restraintmdmodule_8h__incl.svg -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/restraintmdmodule_8h__incl.svg changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/restraintmdmodule_8h__incl.svg -> ../html-full/restraintmdmodule_8h__incl.svg absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/vector__operations_8h__incl.svg -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/vector__operations_8h__incl.svg changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/vector__operations_8h__incl.svg -> ../html-full/vector__operations_8h__incl.svg absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CoulombCalculator.xhtml -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CoulombCalculator.xhtml changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CoulombCalculator.xhtml -> ../html-full/classgmx_1_1CoulombCalculator.xhtml absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IntegerOption__inherit__graph.svg -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IntegerOption__coll__graph.svg changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1IntegerOption__inherit__graph.svg -> ../html-full/classgmx_1_1IntegerOption__coll__graph.svg absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/textwriter_8h.xhtml -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/textwriter_8h.xhtml changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/textwriter_8h.xhtml -> ../html-full/textwriter_8h.xhtml absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__ga2la__t_1_1Entry.xhtml -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx__ga2la__t_1_1Entry.xhtml changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structgmx__ga2la__t_1_1Entry.xhtml -> ../html-full/structgmx__ga2la__t_1_1Entry.xhtml absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1TextFileMatch__inherit__graph.svg -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TextFileMatch__coll__graph.svg changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1TextFileMatch__inherit__graph.svg -> ../html-full/classgmx_1_1test_1_1TextFileMatch__coll__graph.svg absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ICommandLineOptionsModule-members.xhtml -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ICommandLineOptionsModule-members.xhtml changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ICommandLineOptionsModule-members.xhtml -> ../html-full/classgmx_1_1ICommandLineOptionsModule-members.xhtml absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1EwaldAnalytical_01_4.xhtml -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1EwaldAnalytical_01_4.xhtml changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1EwaldAnalytical_01_4.xhtml -> ../html-full/classgmx_1_1CoulombCalculator_3_01KernelCoulombType_1_1EwaldAnalytical_01_4.xhtml absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_32.png -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/form_34.png changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/form_32.png -> ../html-full/form_34.png absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000092_000014.xhtml -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000092_000014.xhtml changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000092_000014.xhtml -> ../html-full/dir_000092_000014.xhtml absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/tab_sd.png -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/tab_sd.png changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/tab_sd.png -> ../html-full/tab_sd.png absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TabulatedNormalDistribution.xhtml -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TabulatedNormalDistribution.xhtml changed: 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../../html-full/search/groups_5.js absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_4.js -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_4.js changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_4.js -> ../../html-full/search/groups_4.js absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_6.js -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_6.js changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_6.js -> ../../html-full/search/groups_6.js absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/defines_9.js -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/defines_a.js changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/defines_9.js -> ../../html-full/search/defines_a.js absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/search.css -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/search.css changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/search.css -> ../../html-full/search/search.css absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_9.js -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_9.js changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_9.js -> ../../html-full/search/groups_9.js absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_10.js -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_10.js changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_10.js -> ../../html-full/search/groups_10.js absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_11.js -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_12.js changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_11.js -> ../../html-full/search/pages_12.js absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enums_13.js -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/enums_13.js changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enums_13.js -> ../../html-full/search/enums_13.js absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_4.js -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/related_5.js changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_4.js -> ../../html-full/search/related_5.js absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_3.js -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_3.js changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_3.js -> ../../html-full/search/groups_3.js absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_a.js -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_a.js changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_a.js -> ../../html-full/search/groups_a.js absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_d.js -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_d.js changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_d.js -> ../../html-full/search/groups_d.js absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_8.js -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_8.js changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_8.js -> ../../html-full/search/groups_8.js absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/search.js -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/search.js changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/search.js -> ../../html-full/search/search.js absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_5.js -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_5.js changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_5.js -> ../../html-full/search/pages_5.js absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_4.js -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_4.js changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_4.js -> ../../html-full/search/pages_4.js absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/functions_1b.js -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/all_1d.js changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/functions_1b.js -> all_1d.js absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_7.js -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/pages_7.js changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_7.js -> ../../html-full/search/pages_7.js absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_5.js -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/related_7.js changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_5.js -> ../../html-full/search/related_7.js absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_1.js -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_1.js changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_1.js -> ../../html-full/search/groups_1.js absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_1.js -> 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/build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/pages_0.js -> ../../html-full/search/pages_0.js absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_a.js -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/related_c.js changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_a.js -> ../../html-full/search/related_c.js absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enums_15.js -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/enums_15.js changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enums_15.js -> 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/build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/typedefs_11.js -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/typedefs_11.js changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/typedefs_11.js -> ../../html-full/search/typedefs_11.js absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/defines_0.js -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/defines_0.js changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/defines_0.js -> ../../html-full/search/defines_0.js absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_c.js -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_c.js changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_c.js -> ../../html-full/search/groups_c.js absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/mag_d.svg -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/mag_d.svg changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/mag_d.svg -> ../../html-full/search/mag_d.svg absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_7.js -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/related_9.js changed: 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/build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1analysismodules_1_1anonymous__namespace_02sasa_8cpp_03_1_1SasaModuleData__inherit__graph.svg -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1analysismodules_1_1anonymous__namespace_02sasa_8cpp_03_1_1SasaModuleData__coll__graph.svg changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1analysismodules_1_1anonymous__namespace_02sasa_8cpp_03_1_1SasaModuleData__inherit__graph.svg -> classgmx_1_1analysismodules_1_1anonymous__namespace_02sasa_8cpp_03_1_1SasaModuleData__coll__graph.svg dh_bash-completion -i dh_lintian -i dh_link -i dh_strip_nondeterminism -i dh_compress -i -X.pdf dh_fixperms -i dh_missing -i dh_installdeb -i dh_gencontrol -i dh_md5sums -i dh_builddeb -i dpkg-deb: building package 'gromacs-data' in '../gromacs-data_2024.4-1_all.deb'. dh_testdir -a dh_testroot -a dh_installchangelogs -a dh_installdocs -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_strip -A dh_makeshlibs -a dh_shlibdeps -plibgromacs9 -L libgromacs9 -l debian/libgromacs9/usr/lib dh_shlibdeps -plibnblib-gmx0 -L libnblib-gmx0 -l debian/libnblib-gmx0/usr/lib:debian/libgromacs9/usr/lib dh_shlibdeps -pgromacs -L libgromacs9 -l debian/libgromacs9/usr/lib:debian/gromacs/usr/lib dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: Depends field of package libgromacs-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package libnblib-gmx-dev: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'gromacs-dbgsym' in '../gromacs-dbgsym_2024.4-1_amd64.deb'. dpkg-deb: building package 'libgromacs9' in '../libgromacs9_2024.4-1_amd64.deb'. dpkg-deb: building package 'gromacs' in '../gromacs_2024.4-1_amd64.deb'. dpkg-deb: building package 'libgromacs-dev' in '../libgromacs-dev_2024.4-1_amd64.deb'. dpkg-deb: building package 'libgromacs9-dbgsym' in '../libgromacs9-dbgsym_2024.4-1_amd64.deb'. dpkg-deb: building package 'libnblib-gmx0' in '../libnblib-gmx0_2024.4-1_amd64.deb'. dpkg-deb: building package 'libnblib-gmx0-dbgsym' in '../libnblib-gmx0-dbgsym_2024.4-1_amd64.deb'. dpkg-deb: building package 'libnblib-gmx-dev' in '../libnblib-gmx-dev_2024.4-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../gromacs_2024.4-1_amd64.buildinfo dpkg-genchanges --build=binary -O../gromacs_2024.4-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3342599 and its subdirectories I: Current time: Mon Jan 5 06:59:03 -12 2026 I: pbuilder-time-stamp: 1767639543 Tue Dec 3 12:36:15 UTC 2024 I: 1st build successful. Starting 2nd build on remote node infom01-amd64.debian.net. Tue Dec 3 12:36:15 UTC 2024 I: Preparing to do remote build '2' on infom01-amd64.debian.net. Tue Dec 3 13:27:41 UTC 2024 I: Deleting $TMPDIR on infom01-amd64.debian.net. Tue Dec 3 13:27:42 UTC 2024 I: gromacs_2024.4-1_amd64.changes: Format: 1.8 Date: Thu, 31 Oct 2024 20:23:53 -0700 Source: gromacs Binary: gromacs gromacs-data gromacs-dbgsym libgromacs-dev libgromacs9 libgromacs9-dbgsym libnblib-gmx-dev libnblib-gmx0 libnblib-gmx0-dbgsym Architecture: all amd64 Version: 2024.4-1 Distribution: unstable Urgency: medium Maintainer: Debichem Team Changed-By: Nicholas Breen Description: gromacs - Molecular dynamics simulator, with building and analysis tools gromacs-data - GROMACS molecular dynamics sim, data and documentation libgromacs-dev - GROMACS molecular dynamics sim, development kit libgromacs9 - GROMACS molecular dynamics sim, shared libraries libnblib-gmx-dev - GROMACS molecular dynamics sim, NB-LIB development kit libnblib-gmx0 - GROMACS molecular dynamics sim, NB-LIB shared libraries Closes: 1086272 Changes: gromacs (2024.4-1) unstable; urgency=medium . * New upstream version. * Update oversubscription environment variable for OpenMPI 5.0. (Closes: #1086272) * Remove obsolete workaround for #494046. * Add chrpath workaround for OpenMPI 5.x RPATH bug, #1085509. Checksums-Sha1: 3e01bb09305752ab0eb8848e49a50a72e3904e4d 43418212 gromacs-data_2024.4-1_all.deb 497ad9dc976bb46c0b26cc519378d551a7a0b054 1003072 gromacs-dbgsym_2024.4-1_amd64.deb d8b2f5f14ab1fcd71de5deca95387940794d562b 18204 gromacs_2024.4-1_amd64.buildinfo c47b0abc5cee5fb68723b79f83d1bdb855eb1927 63960 gromacs_2024.4-1_amd64.deb 9c95f468657b216183cd6aa94f698caa96b224e1 172720 libgromacs-dev_2024.4-1_amd64.deb 62e319b23f549ac49e2669879eb79f0a0713777f 537728312 libgromacs9-dbgsym_2024.4-1_amd64.deb b8dcc6db8330c1331eb06e404967d34ed517b010 31980384 libgromacs9_2024.4-1_amd64.deb 2c0c3569141e3aa7c6e80654e28f693729e11e2d 33348 libnblib-gmx-dev_2024.4-1_amd64.deb eb1b6f04962d36b0cd7f4384bb6efbfaa2ef6424 7371928 libnblib-gmx0-dbgsym_2024.4-1_amd64.deb 679ae42f1affe864587f64d188ec748a31a69dd8 349076 libnblib-gmx0_2024.4-1_amd64.deb Checksums-Sha256: cc5fc829b8bdd4142bc85584777c87d78643b0fb0de736696c7a38c60d5dafbf 43418212 gromacs-data_2024.4-1_all.deb c9a69541c795635d70b92b3632a5c94b6a39500820479f5cd43400211d484a7a 1003072 gromacs-dbgsym_2024.4-1_amd64.deb 0fcb1cf43d959bdcb655ca85b7544e1cf25a6dc256f52e8dadca0901f214d2b4 18204 gromacs_2024.4-1_amd64.buildinfo 5a244bdf1be3a9a8fa99f52b317c75ac868b20c428060728161f00b17f153312 63960 gromacs_2024.4-1_amd64.deb 4c509e281a57c41cda62739d63cadf576f5a3bac4957051a797b5e95fa5f9b6b 172720 libgromacs-dev_2024.4-1_amd64.deb 18c847054953e2155fa7c39a194bdc24cb7107e4c5b4b843e0a2df3fd3b4b19e 537728312 libgromacs9-dbgsym_2024.4-1_amd64.deb 980c39c18ce563269d9aa5f8f0b5a992a129f0e5aa290799adb6024e5df6712b 31980384 libgromacs9_2024.4-1_amd64.deb 482273f7a65a88a76ec6cc7834cc5e73346967c2257fea82d9a4d476ab758db7 33348 libnblib-gmx-dev_2024.4-1_amd64.deb e8d47fd9088ab5e6d7fcc270acb1f603178581c133da89b87be5d601547d200b 7371928 libnblib-gmx0-dbgsym_2024.4-1_amd64.deb a68e034b96971ba36fda04ed33f82920db4073a527201837386123774f332dae 349076 libnblib-gmx0_2024.4-1_amd64.deb Files: 3445aeb3bafedb3ece7748f22560021b 43418212 science optional gromacs-data_2024.4-1_all.deb 0dc68b50cd7d24bad692a6d95e3abc07 1003072 debug optional gromacs-dbgsym_2024.4-1_amd64.deb 7aae8d6b921f5cba3ac88a0e42d38678 18204 science optional gromacs_2024.4-1_amd64.buildinfo 66ec20c9c42e5e08e3d11a65c7334f0c 63960 science optional gromacs_2024.4-1_amd64.deb cbe7dc70cb505158990deccf67f210b6 172720 libdevel optional libgromacs-dev_2024.4-1_amd64.deb 2ec6b3a437c01b29adc7c804b1965e74 537728312 debug optional libgromacs9-dbgsym_2024.4-1_amd64.deb 44f4ba62653d98af75294dec749d13c3 31980384 libs optional libgromacs9_2024.4-1_amd64.deb 87e7e452247e6ab89d9fb092bc0cd3f6 33348 libdevel optional libnblib-gmx-dev_2024.4-1_amd64.deb ba9c7db022b1d20f9861b13643792ed5 7371928 debug optional libnblib-gmx0-dbgsym_2024.4-1_amd64.deb 054ee857f0291ea63a97597a126a48ae 349076 libs optional libnblib-gmx0_2024.4-1_amd64.deb Tue Dec 3 13:27:49 UTC 2024 I: diffoscope 283 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_34-38244.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.lRBR3Ncd/gromacs_2024.4-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.lRBR3Ncd/gromacs_2024.4-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.lRBR3Ncd/gromacs_2024.4-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.lRBR3Ncd/b1/gromacs_2024.4-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.lRBR3Ncd/b2/gromacs_2024.4-1_amd64.changes ## close_archive (total time: 0.000s) 0.000s 4 calls diffoscope.comparators.gzip.GzipContainer 0.000s 6 calls diffoscope.comparators.xz.XzContainer 0.000s 2 calls diffoscope.comparators.deb.DebContainer 0.000s 2 calls diffoscope.comparators.deb.DebTarContainer 0.000s 4 calls diffoscope.comparators.tar.TarContainer ## command (total time: 15.338s) 7.754s 49 calls diff 1.825s 6 calls xz 1.588s 352 calls js-beautify 1.280s 11 calls pdftotext 0.932s 14 calls cmp 0.931s 14 calls cmp (external) 0.498s 20 calls xxd 0.357s 4179 calls cmp (internal) 0.091s 33 calls html2text 0.081s 4 calls gzip ## compare_files (cumulative) (total time: 699.383s) 154.988s 1 call abc.DotChangesFile 154.046s 1 call abc.DebFile 153.827s 2 calls abc.XzFile 151.444s 1 call abc.DebDataTarFile 48.079s 32 calls abc.JavaScriptFile 28.424s 1 call abc.PdfFile 6.926s 2 calls abc.GzipFile 0.499s 1 call abc.TarFile 0.430s 1 call abc.Md5sumsFile 0.351s 3 calls abc.HtmlFile 0.258s 1 call diffoscope.comparators.utils.libarchive.LibarchiveMember 0.093s 2 calls abc.XMLFile 0.018s 1 call abc.TextFile ## container_extract (total time: 10.898s) 8.801s 39718 calls diffoscope.comparators.deb.DebTarContainer 1.825s 6 calls diffoscope.comparators.xz.XzContainer 0.169s 8 calls diffoscope.comparators.deb.DebContainer 0.082s 4 calls diffoscope.comparators.gzip.GzipContainer 0.021s 6 calls diffoscope.comparators.tar.TarContainer ## diff (total time: 5.506s) 5.506s 347 calls linediff ## has_same_content_as (total time: 1.534s) 0.799s 9 calls abc.DebFile 0.593s 4140 calls diffoscope.comparators.utils.libarchive.LibarchiveSymlink 0.114s 1 call abc.DebDataTarFile 0.008s 32 calls abc.JavaScriptFile 0.008s 2 calls abc.XMLFile 0.007s 2 calls abc.Md5sumsFile 0.003s 1 call abc.PdfFile 0.002s 3 calls abc.HtmlFile 0.000s 2 calls abc.TextFile 0.000s 1 call abc.TarFile 0.000s 1 call abc.DotChangesFile 0.000s 2 calls abc.GzipFile 0.000s 2 calls abc.XzFile 0.000s 1 call diffoscope.comparators.utils.libarchive.LibarchiveMember ## main (total time: 168.531s) 168.406s 2 calls outputs 0.125s 1 call cleanup ## open_archive (total time: 0.000s) 0.000s 6 calls diffoscope.comparators.xz.XzContainer 0.000s 4 calls diffoscope.comparators.tar.TarContainer 0.000s 4 calls diffoscope.comparators.gzip.GzipContainer 0.000s 2 calls diffoscope.comparators.deb.DebContainer 0.000s 2 calls diffoscope.comparators.deb.DebTarContainer ## output (total time: 7.644s) 7.606s 1 call html 0.019s 1 call json 0.019s 1 call text ## recognizes (total time: 12.968s) 6.838s 336 calls diffoscope.comparators.utils.archive.ArchiveMember 5.460s 12 calls diffoscope.comparators.binary.FilesystemFile 0.544s 2372 calls diffoscope.comparators.utils.libarchive.LibarchiveMember 0.127s 486 calls diffoscope.comparators.debian.DebControlMember ## specialize (total time: 7.499s) 7.499s 4199 calls specialize Finished with result: success Main processes terminated with: code=exited/status=1 Service runtime: 2min 48.886s CPU time consumed: 2min 53.445s Tue Dec 3 13:30:38 UTC 2024 W: Diffoscope claims the build is reproducible, but there is a diffoscope file. Please investigate. Tue Dec 3 13:30:38 UTC 2024 E: gromacs failed to build reproducibly in unstable on amd64. Tue Dec 3 13:30:40 UTC 2024 I: Submitting .buildinfo files to external archives: Tue Dec 3 13:30:40 UTC 2024 I: Submitting 20K b1/gromacs_2024.4-1_amd64.buildinfo.asc Tue Dec 3 13:30:41 UTC 2024 I: Submitting 20K b2/gromacs_2024.4-1_amd64.buildinfo.asc Tue Dec 3 13:30:42 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Dec 3 13:30:42 UTC 2024 I: Done submitting .buildinfo files. Tue Dec 3 13:30:42 UTC 2024 I: Removing signed gromacs_2024.4-1_amd64.buildinfo.asc files: removed './b1/gromacs_2024.4-1_amd64.buildinfo.asc' removed './b2/gromacs_2024.4-1_amd64.buildinfo.asc'